py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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@comment $NetBSD$
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2012-09-04 00:59:11 +02:00
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${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
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${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
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${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
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${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
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${PYSITELIB}/${EGG_INFODIR}/requires.txt
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${PYSITELIB}/${EGG_INFODIR}/top_level.txt
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/analysis/helanal.py
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2012-09-04 00:59:11 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/analysis/lineardensity.pyo
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${PYSITELIB}/MDAnalysis/analysis/nuclinfo.py
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${PYSITELIB}/MDAnalysis/analysis/nuclinfo.pyc
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${PYSITELIB}/MDAnalysis/analysis/nuclinfo.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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------------------------------------------------------------------------------
??/??/13 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin
* 0.8.0
Enhancements
* Merge AtomGroups into a new Universe (Issue 157)
* TPR parser (currently limited to versions 58, 73 and 83 of the
Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
* fast XTC seeking (Issue 127)
* changing resid (set_resid()) or segid (set_segid()) changes the
topology and lists of resids/segids can be assigned to
groups of objects (AtomGroup, ResidueGroup)
* helanal: additional output of local bend and unit twist angles
(Issue 133)
* added support for reading DMS files (DESRES molecular structure)
* bond connectivity information can be guessed from a PDB file if
the bond=True keyword is set in Universe (Issue 23)
* MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
* Plugin to generate nucleic acid helicoidal parameters using X3DNA;
(must install working version 2.1 of X3DNA independently)
* can use advanced slicing (with arbitrary lists or arrays) at all
levels of the hierarchy (Issue 148)
* coordinate readers and writers can be used as context managers
with the 'with' statement
* Can load multiple trajectories as Universe(topology, traj2, traj2,
...) in addition to providing all trajectories as a list,
i.e. Universe(topology, [traj1, traj2, ...])
* added support for YASP and IBIsCO formats (.trz) (Issue 152)
* new methods for AtomGroup: packintobox() (only orthorhombic boxes)
* added non-standard "extended" PDB format (XPDB) that reads
five-digit residue numbers
* util.convert_aa_code() recognizes non-standard residue names such
as HSE, GLUH, GLH, ...
* added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
* added TopologyDict and TopologyGroup classes for bond analysis
Changes
* dropped support for Python 2.5; minimum requirement is Python 2.6
(Issue 130)
* almost all methods of AtomGroup return NumPy arrays
* slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
SegmentGroup will now always return an appropriate object and
never a simple list
* removed Timeseries.principleAxis (probably was never working)
* dependent on Biopython >= 1.59 (Issue 147)
* Hydrogen bond analysis defaults to updating selection 1 and 2 for
every timestep in order to avoid unexpected behavior (Issue 138)
Fixes
* fixed incorrect computation of distances in serial and parallel
distance_array() with PBC (Issue 151)
* fixed Issue 129 (hole.py module pipe/file closure)
* fixed array comparison bug in MDAnalysis.analysis.helanal
and various enhancements to the helanal module
* fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
if ref_frame != 0
* alignto() now checks that the two selections describe the same
atoms (fixes Issue 143)
* slicing of ResidueGroup will now produce a ResidueGroup, and
slicing of a SegmentGroup will produce a SegmentGroup, not a list
as before (fixes Issue 135)
* detect OpenMP-capable compiler during setup (Issue 145), which should allow
users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
C-compiler (clang) (Issue 142) although they will not get a parallel
version of distance_array.
* PDB with blank lines gave IndexError (Issue 158)
12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi, sebastien.buchoux
* 0.7.7
Enhancements
* multithreaded distance_array() (Issue 80, experimental); see the
new core.parallel.distance module
* MDAnalysis.analysis.rms for simple RMSD analysis
* format of input coordinates can be set as (filename, format)
tuples (Issue 76)
* new AtomGroup.asphericity() and AtomGroup.shapeParameter()
methods to compute shape descriptors.
* access to forces (AtomGroup.forces with get_forces() and set_forces();
the default unit for force is kJ/(mol*A) and it is automatically
converted from/to native). Currently, only the TRR Reader/Writer
support forces.
* all element masses
* logger reports current version when starting
Fixes
* fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
* fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
* fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
* fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
* fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
* Issue 122 (made installation of netCDF4 library optional, which
means that users of the AMBER netcdf Reader/Writer will have to
manually install the library and its dependencies netcdf and HDF5,
see https://code.google.com/p/mdanalysis/wiki/netcdf)
06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0, danny.parton
* 0.7.6
Enhancements
* GRO file velocities may be accessed as AtomGroup.velocities()
or Atom.velocity (Issue 102)
* PrimitivePDBReader can be sliced
* AMBER NetCDF (binary trajectory) reader and writer, supporting
coordinates and velocities; requires netcdf4-python (Issue 109)
* additional attributes and methods for AtomGroup to consolidate
the interface to the Timestep: attribute 'positions' and
'get_positions()' can be used instead of the 'coordinates()'
method. get/set methods for both positions and velocities.
* almost all Readers now support some form of slicing; unsupported
slicing operations will raise a TypeError
* additional analysis for Nucleic Acid order parameters
(MDAnalysis.analysis.nuclinfo)
* AMBER TOPParser now able to do both amber10 and amber12 formats
(Issue 100)
Changes
* selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
*nucleic* includes the two-letter NA code that follows gromacs topolgy
format and *nucleicxstal* allows for the one-letter NA code that follows
the PDB Database code.
* HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply
stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the
new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
* removed CHO and EAM (formyl and ethanol termini of gA in CHARMM)
from the set of residues recognized as protein (collision with
commonly used CHO for cholesterol)
* PrimitivePDBWriter: special segid SYSTEM is translated to empty
chainID
* In order to write multi frame PDB files, the multiframe=True
keyword must be supplied or use the MultiPDBWriter
* empty AtomGroup can be constructed or can result from a selection
without matches; it does *not* raise NoDataError anymore (Issue 12)
* all single frame readers denote the first (and only) frame as
frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is
consistent with the way this is is handled with real trajectories
* requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
* Atom.type is always stored as a string.
Fixes
* HydrogenBondAnalysis: NH1 and NH2 were not recognized
* GROWriter: enforce maximum resname and atomname length of 5 chars
* Universe.load_new() raised a NameError (thanks to JiyongPark.77)
* fixed Issue 105 (trajectory snapshots could not be written to PDB)
* fixed Issue 107 (NAMD/VMD space delimited PSF files can be
autodetected and read); important when using CGENFF atom types
(thanks to JiyongPark.77 for initial patch)
* fixed Issue 101 (could not write single frame to trr file)
* fixed: permissive=True flag was ignored in Universe and hence the
PrimitivePDBReader was always selected even if the Biopython one
was desired
* fixed Issue 112 (used removed Biopython constructs in
MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri
for a test case and fix)
* fixed failing 'type' selection for topology formats that read an
atom type as an integer (such as the AMBER parser)
* fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
* fixed Issue 113 (replaced outdated Biopython to call ClustalW)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
Enhancements
* Universe() got new keywords topology_format and format to allow
the user to specify the file formats instead of deriving it from the
extensions (does not work with "chained" files at the moment); thanks to
Michael Lerner for the suggestion
* Chain trajectory reader allows frame indexing.
* Issue 75: additional donors and acceptors keywords for H-bond analysis
* structural alignment functions alignto() and rms_fit_traj() can also take a
list of selection strings in order to define atom groups with fixed atom
order and alignto() preserves the order of supplied AtomGroups for the
special select values "all" and None.
* new set_* methods for AtomGroup allows changing of Atom attributes
for all members of the group (such as the segid) (EXPERIMENTAL)
* new Atom and Residue attribute resnum that can be used to store
the canonical PDB residue number (EXPERIMENTAL)
Fixes
* fixed Issue 74 (bug in AMBER topology parser which would show up for
certain numbers of input lines; thanks to htaoyu1)
* fix for Issue 48 (sparse contact_matrix in distances.py was slow when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): order of mobile and reference
selection was reversed when supplied as a tuple (sel1, sel2)
Changes
* replaced analysis.util.progress_meter() with class core.log.ProgressMeter
* Issue 28: split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package MDAnalysisTestData, which is
required to run the UnitTests from release 0.7.4 onwards. Numbering matches
the earliest MDAnalysis release for which the data is needed. Any later
releases of MDAnalysis will also use these test data unless a
MDAnalysisTestData package with a higher release number is available.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
Removals
* completely removed the old core.rms_fitting module (and thus we also do not
depend on the LAPACK library anymore, which should simplify installation);
use the functions accessible through MDAnalysis.analysis.align (which are
faster and use QCPROT)
Enhancements
* PDBQT (autodock) format added (reading and writing of single frames)
* new attributes universe.trajectory.frame and universe.trajectory.frame:
report the current frame number and time (e.g. in ps) of the current frame
of the trajectory
* new attribute Timestep.volume (unit cell volume)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* HELANAL helix analysis in MDAnalysis.analysis.helanal; Python
implementation of helanal.f from
http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin
Hall, used under GPL v2+)
* hydrogen bonds analysis in MDAnalysis.analysis.hbonds
* MDAnalysis.analysis.distances.dist() for calculating distances between
matching atoms in two groups
* MDAnalysis logo by Christian Beckstein (and a reformatting of the
online docs to match the logo theme)
Change of behaviour
* alignto() and rms_fit_trj(): changed keyword 'select' default from
'backbone' to 'all'
Fixes
* fixed alignto() (raised KeyError)
* fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
* use spaces everywhere and no TABs and tell emacs and vim to keep it that
way (Issue 69)
* fixed Issue 70 (problems with instant atom selections)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
2014-01-03 22:28:42 +01:00
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${PYSITELIB}/MDAnalysis/analysis/x3dna.py
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${PYSITELIB}/MDAnalysis/analysis/x3dna.pyc
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${PYSITELIB}/MDAnalysis/analysis/x3dna.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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------------------------------------------------------------------------------
??/??/13 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin
* 0.8.0
Enhancements
* Merge AtomGroups into a new Universe (Issue 157)
* TPR parser (currently limited to versions 58, 73 and 83 of the
Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
* fast XTC seeking (Issue 127)
* changing resid (set_resid()) or segid (set_segid()) changes the
topology and lists of resids/segids can be assigned to
groups of objects (AtomGroup, ResidueGroup)
* helanal: additional output of local bend and unit twist angles
(Issue 133)
* added support for reading DMS files (DESRES molecular structure)
* bond connectivity information can be guessed from a PDB file if
the bond=True keyword is set in Universe (Issue 23)
* MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
* Plugin to generate nucleic acid helicoidal parameters using X3DNA;
(must install working version 2.1 of X3DNA independently)
* can use advanced slicing (with arbitrary lists or arrays) at all
levels of the hierarchy (Issue 148)
* coordinate readers and writers can be used as context managers
with the 'with' statement
* Can load multiple trajectories as Universe(topology, traj2, traj2,
...) in addition to providing all trajectories as a list,
i.e. Universe(topology, [traj1, traj2, ...])
* added support for YASP and IBIsCO formats (.trz) (Issue 152)
* new methods for AtomGroup: packintobox() (only orthorhombic boxes)
* added non-standard "extended" PDB format (XPDB) that reads
five-digit residue numbers
* util.convert_aa_code() recognizes non-standard residue names such
as HSE, GLUH, GLH, ...
* added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
* added TopologyDict and TopologyGroup classes for bond analysis
Changes
* dropped support for Python 2.5; minimum requirement is Python 2.6
(Issue 130)
* almost all methods of AtomGroup return NumPy arrays
* slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
SegmentGroup will now always return an appropriate object and
never a simple list
* removed Timeseries.principleAxis (probably was never working)
* dependent on Biopython >= 1.59 (Issue 147)
* Hydrogen bond analysis defaults to updating selection 1 and 2 for
every timestep in order to avoid unexpected behavior (Issue 138)
Fixes
* fixed incorrect computation of distances in serial and parallel
distance_array() with PBC (Issue 151)
* fixed Issue 129 (hole.py module pipe/file closure)
* fixed array comparison bug in MDAnalysis.analysis.helanal
and various enhancements to the helanal module
* fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
if ref_frame != 0
* alignto() now checks that the two selections describe the same
atoms (fixes Issue 143)
* slicing of ResidueGroup will now produce a ResidueGroup, and
slicing of a SegmentGroup will produce a SegmentGroup, not a list
as before (fixes Issue 135)
* detect OpenMP-capable compiler during setup (Issue 145), which should allow
users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
C-compiler (clang) (Issue 142) although they will not get a parallel
version of distance_array.
* PDB with blank lines gave IndexError (Issue 158)
12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi, sebastien.buchoux
* 0.7.7
Enhancements
* multithreaded distance_array() (Issue 80, experimental); see the
new core.parallel.distance module
* MDAnalysis.analysis.rms for simple RMSD analysis
* format of input coordinates can be set as (filename, format)
tuples (Issue 76)
* new AtomGroup.asphericity() and AtomGroup.shapeParameter()
methods to compute shape descriptors.
* access to forces (AtomGroup.forces with get_forces() and set_forces();
the default unit for force is kJ/(mol*A) and it is automatically
converted from/to native). Currently, only the TRR Reader/Writer
support forces.
* all element masses
* logger reports current version when starting
Fixes
* fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
* fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
* fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
* fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
* fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
* Issue 122 (made installation of netCDF4 library optional, which
means that users of the AMBER netcdf Reader/Writer will have to
manually install the library and its dependencies netcdf and HDF5,
see https://code.google.com/p/mdanalysis/wiki/netcdf)
06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0, danny.parton
* 0.7.6
Enhancements
* GRO file velocities may be accessed as AtomGroup.velocities()
or Atom.velocity (Issue 102)
* PrimitivePDBReader can be sliced
* AMBER NetCDF (binary trajectory) reader and writer, supporting
coordinates and velocities; requires netcdf4-python (Issue 109)
* additional attributes and methods for AtomGroup to consolidate
the interface to the Timestep: attribute 'positions' and
'get_positions()' can be used instead of the 'coordinates()'
method. get/set methods for both positions and velocities.
* almost all Readers now support some form of slicing; unsupported
slicing operations will raise a TypeError
* additional analysis for Nucleic Acid order parameters
(MDAnalysis.analysis.nuclinfo)
* AMBER TOPParser now able to do both amber10 and amber12 formats
(Issue 100)
Changes
* selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
*nucleic* includes the two-letter NA code that follows gromacs topolgy
format and *nucleicxstal* allows for the one-letter NA code that follows
the PDB Database code.
* HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply
stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the
new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
* removed CHO and EAM (formyl and ethanol termini of gA in CHARMM)
from the set of residues recognized as protein (collision with
commonly used CHO for cholesterol)
* PrimitivePDBWriter: special segid SYSTEM is translated to empty
chainID
* In order to write multi frame PDB files, the multiframe=True
keyword must be supplied or use the MultiPDBWriter
* empty AtomGroup can be constructed or can result from a selection
without matches; it does *not* raise NoDataError anymore (Issue 12)
* all single frame readers denote the first (and only) frame as
frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is
consistent with the way this is is handled with real trajectories
* requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
* Atom.type is always stored as a string.
Fixes
* HydrogenBondAnalysis: NH1 and NH2 were not recognized
* GROWriter: enforce maximum resname and atomname length of 5 chars
* Universe.load_new() raised a NameError (thanks to JiyongPark.77)
* fixed Issue 105 (trajectory snapshots could not be written to PDB)
* fixed Issue 107 (NAMD/VMD space delimited PSF files can be
autodetected and read); important when using CGENFF atom types
(thanks to JiyongPark.77 for initial patch)
* fixed Issue 101 (could not write single frame to trr file)
* fixed: permissive=True flag was ignored in Universe and hence the
PrimitivePDBReader was always selected even if the Biopython one
was desired
* fixed Issue 112 (used removed Biopython constructs in
MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri
for a test case and fix)
* fixed failing 'type' selection for topology formats that read an
atom type as an integer (such as the AMBER parser)
* fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
* fixed Issue 113 (replaced outdated Biopython to call ClustalW)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
Enhancements
* Universe() got new keywords topology_format and format to allow
the user to specify the file formats instead of deriving it from the
extensions (does not work with "chained" files at the moment); thanks to
Michael Lerner for the suggestion
* Chain trajectory reader allows frame indexing.
* Issue 75: additional donors and acceptors keywords for H-bond analysis
* structural alignment functions alignto() and rms_fit_traj() can also take a
list of selection strings in order to define atom groups with fixed atom
order and alignto() preserves the order of supplied AtomGroups for the
special select values "all" and None.
* new set_* methods for AtomGroup allows changing of Atom attributes
for all members of the group (such as the segid) (EXPERIMENTAL)
* new Atom and Residue attribute resnum that can be used to store
the canonical PDB residue number (EXPERIMENTAL)
Fixes
* fixed Issue 74 (bug in AMBER topology parser which would show up for
certain numbers of input lines; thanks to htaoyu1)
* fix for Issue 48 (sparse contact_matrix in distances.py was slow when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): order of mobile and reference
selection was reversed when supplied as a tuple (sel1, sel2)
Changes
* replaced analysis.util.progress_meter() with class core.log.ProgressMeter
* Issue 28: split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package MDAnalysisTestData, which is
required to run the UnitTests from release 0.7.4 onwards. Numbering matches
the earliest MDAnalysis release for which the data is needed. Any later
releases of MDAnalysis will also use these test data unless a
MDAnalysisTestData package with a higher release number is available.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
Removals
* completely removed the old core.rms_fitting module (and thus we also do not
depend on the LAPACK library anymore, which should simplify installation);
use the functions accessible through MDAnalysis.analysis.align (which are
faster and use QCPROT)
Enhancements
* PDBQT (autodock) format added (reading and writing of single frames)
* new attributes universe.trajectory.frame and universe.trajectory.frame:
report the current frame number and time (e.g. in ps) of the current frame
of the trajectory
* new attribute Timestep.volume (unit cell volume)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* HELANAL helix analysis in MDAnalysis.analysis.helanal; Python
implementation of helanal.f from
http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin
Hall, used under GPL v2+)
* hydrogen bonds analysis in MDAnalysis.analysis.hbonds
* MDAnalysis.analysis.distances.dist() for calculating distances between
matching atoms in two groups
* MDAnalysis logo by Christian Beckstein (and a reformatting of the
online docs to match the logo theme)
Change of behaviour
* alignto() and rms_fit_trj(): changed keyword 'select' default from
'backbone' to 'all'
Fixes
* fixed alignto() (raised KeyError)
* fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
* use spaces everywhere and no TABs and tell emacs and vim to keep it that
way (Issue 69)
* fixed Issue 70 (problems with instant atom selections)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
2014-01-03 22:28:42 +01:00
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${PYSITELIB}/MDAnalysis/coordinates/DMS.py
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${PYSITELIB}/MDAnalysis/coordinates/DMS.pyc
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${PYSITELIB}/MDAnalysis/coordinates/DMS.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/coordinates/GMS.py
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${PYSITELIB}/MDAnalysis/coordinates/GMS.pyc
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${PYSITELIB}/MDAnalysis/coordinates/GMS.pyo
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2012-09-04 00:59:11 +02:00
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${PYSITELIB}/MDAnalysis/coordinates/GRO.py
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${PYSITELIB}/MDAnalysis/coordinates/GRO.pyc
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${PYSITELIB}/MDAnalysis/coordinates/GRO.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/coordinates/INPCRD.py
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${PYSITELIB}/MDAnalysis/coordinates/INPCRD.pyc
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${PYSITELIB}/MDAnalysis/coordinates/INPCRD.pyo
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2012-09-04 00:59:11 +02:00
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${PYSITELIB}/MDAnalysis/coordinates/LAMMPS.py
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${PYSITELIB}/MDAnalysis/coordinates/LAMMPS.pyc
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${PYSITELIB}/MDAnalysis/coordinates/LAMMPS.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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Update new version
------------------------------------------------------------------------------
??/??/13 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin
* 0.8.0
Enhancements
* Merge AtomGroups into a new Universe (Issue 157)
* TPR parser (currently limited to versions 58, 73 and 83 of the
Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
* fast XTC seeking (Issue 127)
* changing resid (set_resid()) or segid (set_segid()) changes the
topology and lists of resids/segids can be assigned to
groups of objects (AtomGroup, ResidueGroup)
* helanal: additional output of local bend and unit twist angles
(Issue 133)
* added support for reading DMS files (DESRES molecular structure)
* bond connectivity information can be guessed from a PDB file if
the bond=True keyword is set in Universe (Issue 23)
* MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
* Plugin to generate nucleic acid helicoidal parameters using X3DNA;
(must install working version 2.1 of X3DNA independently)
* can use advanced slicing (with arbitrary lists or arrays) at all
levels of the hierarchy (Issue 148)
* coordinate readers and writers can be used as context managers
with the 'with' statement
* Can load multiple trajectories as Universe(topology, traj2, traj2,
...) in addition to providing all trajectories as a list,
i.e. Universe(topology, [traj1, traj2, ...])
* added support for YASP and IBIsCO formats (.trz) (Issue 152)
* new methods for AtomGroup: packintobox() (only orthorhombic boxes)
* added non-standard "extended" PDB format (XPDB) that reads
five-digit residue numbers
* util.convert_aa_code() recognizes non-standard residue names such
as HSE, GLUH, GLH, ...
* added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
* added TopologyDict and TopologyGroup classes for bond analysis
Changes
* dropped support for Python 2.5; minimum requirement is Python 2.6
(Issue 130)
* almost all methods of AtomGroup return NumPy arrays
* slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
SegmentGroup will now always return an appropriate object and
never a simple list
* removed Timeseries.principleAxis (probably was never working)
* dependent on Biopython >= 1.59 (Issue 147)
* Hydrogen bond analysis defaults to updating selection 1 and 2 for
every timestep in order to avoid unexpected behavior (Issue 138)
Fixes
* fixed incorrect computation of distances in serial and parallel
distance_array() with PBC (Issue 151)
* fixed Issue 129 (hole.py module pipe/file closure)
* fixed array comparison bug in MDAnalysis.analysis.helanal
and various enhancements to the helanal module
* fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
if ref_frame != 0
* alignto() now checks that the two selections describe the same
atoms (fixes Issue 143)
* slicing of ResidueGroup will now produce a ResidueGroup, and
slicing of a SegmentGroup will produce a SegmentGroup, not a list
as before (fixes Issue 135)
* detect OpenMP-capable compiler during setup (Issue 145), which should allow
users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
C-compiler (clang) (Issue 142) although they will not get a parallel
version of distance_array.
* PDB with blank lines gave IndexError (Issue 158)
12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi, sebastien.buchoux
* 0.7.7
Enhancements
* multithreaded distance_array() (Issue 80, experimental); see the
new core.parallel.distance module
* MDAnalysis.analysis.rms for simple RMSD analysis
* format of input coordinates can be set as (filename, format)
tuples (Issue 76)
* new AtomGroup.asphericity() and AtomGroup.shapeParameter()
methods to compute shape descriptors.
* access to forces (AtomGroup.forces with get_forces() and set_forces();
the default unit for force is kJ/(mol*A) and it is automatically
converted from/to native). Currently, only the TRR Reader/Writer
support forces.
* all element masses
* logger reports current version when starting
Fixes
* fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
* fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
* fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
* fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
* fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
* Issue 122 (made installation of netCDF4 library optional, which
means that users of the AMBER netcdf Reader/Writer will have to
manually install the library and its dependencies netcdf and HDF5,
see https://code.google.com/p/mdanalysis/wiki/netcdf)
06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0, danny.parton
* 0.7.6
Enhancements
* GRO file velocities may be accessed as AtomGroup.velocities()
or Atom.velocity (Issue 102)
* PrimitivePDBReader can be sliced
* AMBER NetCDF (binary trajectory) reader and writer, supporting
coordinates and velocities; requires netcdf4-python (Issue 109)
* additional attributes and methods for AtomGroup to consolidate
the interface to the Timestep: attribute 'positions' and
'get_positions()' can be used instead of the 'coordinates()'
method. get/set methods for both positions and velocities.
* almost all Readers now support some form of slicing; unsupported
slicing operations will raise a TypeError
* additional analysis for Nucleic Acid order parameters
(MDAnalysis.analysis.nuclinfo)
* AMBER TOPParser now able to do both amber10 and amber12 formats
(Issue 100)
Changes
* selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
*nucleic* includes the two-letter NA code that follows gromacs topolgy
format and *nucleicxstal* allows for the one-letter NA code that follows
the PDB Database code.
* HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply
stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the
new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
* removed CHO and EAM (formyl and ethanol termini of gA in CHARMM)
from the set of residues recognized as protein (collision with
commonly used CHO for cholesterol)
* PrimitivePDBWriter: special segid SYSTEM is translated to empty
chainID
* In order to write multi frame PDB files, the multiframe=True
keyword must be supplied or use the MultiPDBWriter
* empty AtomGroup can be constructed or can result from a selection
without matches; it does *not* raise NoDataError anymore (Issue 12)
* all single frame readers denote the first (and only) frame as
frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is
consistent with the way this is is handled with real trajectories
* requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
* Atom.type is always stored as a string.
Fixes
* HydrogenBondAnalysis: NH1 and NH2 were not recognized
* GROWriter: enforce maximum resname and atomname length of 5 chars
* Universe.load_new() raised a NameError (thanks to JiyongPark.77)
* fixed Issue 105 (trajectory snapshots could not be written to PDB)
* fixed Issue 107 (NAMD/VMD space delimited PSF files can be
autodetected and read); important when using CGENFF atom types
(thanks to JiyongPark.77 for initial patch)
* fixed Issue 101 (could not write single frame to trr file)
* fixed: permissive=True flag was ignored in Universe and hence the
PrimitivePDBReader was always selected even if the Biopython one
was desired
* fixed Issue 112 (used removed Biopython constructs in
MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri
for a test case and fix)
* fixed failing 'type' selection for topology formats that read an
atom type as an integer (such as the AMBER parser)
* fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
* fixed Issue 113 (replaced outdated Biopython to call ClustalW)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
Enhancements
* Universe() got new keywords topology_format and format to allow
the user to specify the file formats instead of deriving it from the
extensions (does not work with "chained" files at the moment); thanks to
Michael Lerner for the suggestion
* Chain trajectory reader allows frame indexing.
* Issue 75: additional donors and acceptors keywords for H-bond analysis
* structural alignment functions alignto() and rms_fit_traj() can also take a
list of selection strings in order to define atom groups with fixed atom
order and alignto() preserves the order of supplied AtomGroups for the
special select values "all" and None.
* new set_* methods for AtomGroup allows changing of Atom attributes
for all members of the group (such as the segid) (EXPERIMENTAL)
* new Atom and Residue attribute resnum that can be used to store
the canonical PDB residue number (EXPERIMENTAL)
Fixes
* fixed Issue 74 (bug in AMBER topology parser which would show up for
certain numbers of input lines; thanks to htaoyu1)
* fix for Issue 48 (sparse contact_matrix in distances.py was slow when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): order of mobile and reference
selection was reversed when supplied as a tuple (sel1, sel2)
Changes
* replaced analysis.util.progress_meter() with class core.log.ProgressMeter
* Issue 28: split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package MDAnalysisTestData, which is
required to run the UnitTests from release 0.7.4 onwards. Numbering matches
the earliest MDAnalysis release for which the data is needed. Any later
releases of MDAnalysis will also use these test data unless a
MDAnalysisTestData package with a higher release number is available.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
Removals
* completely removed the old core.rms_fitting module (and thus we also do not
depend on the LAPACK library anymore, which should simplify installation);
use the functions accessible through MDAnalysis.analysis.align (which are
faster and use QCPROT)
Enhancements
* PDBQT (autodock) format added (reading and writing of single frames)
* new attributes universe.trajectory.frame and universe.trajectory.frame:
report the current frame number and time (e.g. in ps) of the current frame
of the trajectory
* new attribute Timestep.volume (unit cell volume)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* HELANAL helix analysis in MDAnalysis.analysis.helanal; Python
implementation of helanal.f from
http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin
Hall, used under GPL v2+)
* hydrogen bonds analysis in MDAnalysis.analysis.hbonds
* MDAnalysis.analysis.distances.dist() for calculating distances between
matching atoms in two groups
* MDAnalysis logo by Christian Beckstein (and a reformatting of the
online docs to match the logo theme)
Change of behaviour
* alignto() and rms_fit_trj(): changed keyword 'select' default from
'backbone' to 'all'
Fixes
* fixed alignto() (raised KeyError)
* fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
* use spaces everywhere and no TABs and tell emacs and vim to keep it that
way (Issue 69)
* fixed Issue 70 (problems with instant atom selections)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
2014-01-03 22:28:42 +01:00
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${PYSITELIB}/MDAnalysis/coordinates/TRZ.py
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${PYSITELIB}/MDAnalysis/coordinates/TRZ.pyc
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${PYSITELIB}/MDAnalysis/coordinates/TRZ.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/core/log.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/exceptions.pyo
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${PYSITELIB}/MDAnalysis/lib/NeighborSearch.py
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${PYSITELIB}/MDAnalysis/lib/_transformations.so
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${PYSITELIB}/MDAnalysis/lib/c_distances.so
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${PYSITELIB}/MDAnalysis/lib/c_distances_openmp.so
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${PYSITELIB}/MDAnalysis/lib/distances.py
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${PYSITELIB}/MDAnalysis/lib/formats/__init__.py
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${PYSITELIB}/MDAnalysis/lib/formats/__init__.pyc
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${PYSITELIB}/MDAnalysis/lib/formats/cython_util.so
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${PYSITELIB}/MDAnalysis/lib/formats/libmdaxdr.so
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${PYSITELIB}/MDAnalysis/lib/log.pyo
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${PYSITELIB}/MDAnalysis/lib/mdamath.pyc
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${PYSITELIB}/MDAnalysis/lib/mdamath.pyo
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${PYSITELIB}/MDAnalysis/lib/transformations.pyo
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${PYSITELIB}/MDAnalysis/migration/fixes/__init__.pyo
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_agcountmethods.py
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_agmethods.pyo
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_calctorsions.py
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_numframes.pyc
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_numframes.pyo
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_selectatoms.py
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_selectatoms.pyc
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_selectatoms.pyo
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsionclasses.py
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsionclasses.pyc
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsionclasses.pyo
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsions.py
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_torsions.pyo
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_writer.py
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_writer.pyc
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${PYSITELIB}/MDAnalysis/migration/fixes/fix_writer.pyo
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${PYSITELIB}/MDAnalysis/migration/ten2eleven.pyc
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${PYSITELIB}/MDAnalysis/migration/ten2eleven.pyo
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${PYSITELIB}/MDAnalysis/migration/test_dummy_old_MDA_code.py
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${PYSITELIB}/MDAnalysis/migration/test_dummy_torsion.py
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2012-09-04 00:59:11 +02:00
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${PYSITELIB}/MDAnalysis/selections/__init__.py
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${PYSITELIB}/MDAnalysis/selections/gromacs.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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??/??/13 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin
* 0.8.0
Enhancements
* Merge AtomGroups into a new Universe (Issue 157)
* TPR parser (currently limited to versions 58, 73 and 83 of the
Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
* fast XTC seeking (Issue 127)
* changing resid (set_resid()) or segid (set_segid()) changes the
topology and lists of resids/segids can be assigned to
groups of objects (AtomGroup, ResidueGroup)
* helanal: additional output of local bend and unit twist angles
(Issue 133)
* added support for reading DMS files (DESRES molecular structure)
* bond connectivity information can be guessed from a PDB file if
the bond=True keyword is set in Universe (Issue 23)
* MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
* Plugin to generate nucleic acid helicoidal parameters using X3DNA;
(must install working version 2.1 of X3DNA independently)
* can use advanced slicing (with arbitrary lists or arrays) at all
levels of the hierarchy (Issue 148)
* coordinate readers and writers can be used as context managers
with the 'with' statement
* Can load multiple trajectories as Universe(topology, traj2, traj2,
...) in addition to providing all trajectories as a list,
i.e. Universe(topology, [traj1, traj2, ...])
* added support for YASP and IBIsCO formats (.trz) (Issue 152)
* new methods for AtomGroup: packintobox() (only orthorhombic boxes)
* added non-standard "extended" PDB format (XPDB) that reads
five-digit residue numbers
* util.convert_aa_code() recognizes non-standard residue names such
as HSE, GLUH, GLH, ...
* added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
* added TopologyDict and TopologyGroup classes for bond analysis
Changes
* dropped support for Python 2.5; minimum requirement is Python 2.6
(Issue 130)
* almost all methods of AtomGroup return NumPy arrays
* slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
SegmentGroup will now always return an appropriate object and
never a simple list
* removed Timeseries.principleAxis (probably was never working)
* dependent on Biopython >= 1.59 (Issue 147)
* Hydrogen bond analysis defaults to updating selection 1 and 2 for
every timestep in order to avoid unexpected behavior (Issue 138)
Fixes
* fixed incorrect computation of distances in serial and parallel
distance_array() with PBC (Issue 151)
* fixed Issue 129 (hole.py module pipe/file closure)
* fixed array comparison bug in MDAnalysis.analysis.helanal
and various enhancements to the helanal module
* fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
if ref_frame != 0
* alignto() now checks that the two selections describe the same
atoms (fixes Issue 143)
* slicing of ResidueGroup will now produce a ResidueGroup, and
slicing of a SegmentGroup will produce a SegmentGroup, not a list
as before (fixes Issue 135)
* detect OpenMP-capable compiler during setup (Issue 145), which should allow
users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
C-compiler (clang) (Issue 142) although they will not get a parallel
version of distance_array.
* PDB with blank lines gave IndexError (Issue 158)
12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi, sebastien.buchoux
* 0.7.7
Enhancements
* multithreaded distance_array() (Issue 80, experimental); see the
new core.parallel.distance module
* MDAnalysis.analysis.rms for simple RMSD analysis
* format of input coordinates can be set as (filename, format)
tuples (Issue 76)
* new AtomGroup.asphericity() and AtomGroup.shapeParameter()
methods to compute shape descriptors.
* access to forces (AtomGroup.forces with get_forces() and set_forces();
the default unit for force is kJ/(mol*A) and it is automatically
converted from/to native). Currently, only the TRR Reader/Writer
support forces.
* all element masses
* logger reports current version when starting
Fixes
* fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
* fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
* fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
* fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
* fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
* Issue 122 (made installation of netCDF4 library optional, which
means that users of the AMBER netcdf Reader/Writer will have to
manually install the library and its dependencies netcdf and HDF5,
see https://code.google.com/p/mdanalysis/wiki/netcdf)
06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0, danny.parton
* 0.7.6
Enhancements
* GRO file velocities may be accessed as AtomGroup.velocities()
or Atom.velocity (Issue 102)
* PrimitivePDBReader can be sliced
* AMBER NetCDF (binary trajectory) reader and writer, supporting
coordinates and velocities; requires netcdf4-python (Issue 109)
* additional attributes and methods for AtomGroup to consolidate
the interface to the Timestep: attribute 'positions' and
'get_positions()' can be used instead of the 'coordinates()'
method. get/set methods for both positions and velocities.
* almost all Readers now support some form of slicing; unsupported
slicing operations will raise a TypeError
* additional analysis for Nucleic Acid order parameters
(MDAnalysis.analysis.nuclinfo)
* AMBER TOPParser now able to do both amber10 and amber12 formats
(Issue 100)
Changes
* selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
*nucleic* includes the two-letter NA code that follows gromacs topolgy
format and *nucleicxstal* allows for the one-letter NA code that follows
the PDB Database code.
* HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply
stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the
new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
* removed CHO and EAM (formyl and ethanol termini of gA in CHARMM)
from the set of residues recognized as protein (collision with
commonly used CHO for cholesterol)
* PrimitivePDBWriter: special segid SYSTEM is translated to empty
chainID
* In order to write multi frame PDB files, the multiframe=True
keyword must be supplied or use the MultiPDBWriter
* empty AtomGroup can be constructed or can result from a selection
without matches; it does *not* raise NoDataError anymore (Issue 12)
* all single frame readers denote the first (and only) frame as
frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is
consistent with the way this is is handled with real trajectories
* requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
* Atom.type is always stored as a string.
Fixes
* HydrogenBondAnalysis: NH1 and NH2 were not recognized
* GROWriter: enforce maximum resname and atomname length of 5 chars
* Universe.load_new() raised a NameError (thanks to JiyongPark.77)
* fixed Issue 105 (trajectory snapshots could not be written to PDB)
* fixed Issue 107 (NAMD/VMD space delimited PSF files can be
autodetected and read); important when using CGENFF atom types
(thanks to JiyongPark.77 for initial patch)
* fixed Issue 101 (could not write single frame to trr file)
* fixed: permissive=True flag was ignored in Universe and hence the
PrimitivePDBReader was always selected even if the Biopython one
was desired
* fixed Issue 112 (used removed Biopython constructs in
MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri
for a test case and fix)
* fixed failing 'type' selection for topology formats that read an
atom type as an integer (such as the AMBER parser)
* fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
* fixed Issue 113 (replaced outdated Biopython to call ClustalW)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
Enhancements
* Universe() got new keywords topology_format and format to allow
the user to specify the file formats instead of deriving it from the
extensions (does not work with "chained" files at the moment); thanks to
Michael Lerner for the suggestion
* Chain trajectory reader allows frame indexing.
* Issue 75: additional donors and acceptors keywords for H-bond analysis
* structural alignment functions alignto() and rms_fit_traj() can also take a
list of selection strings in order to define atom groups with fixed atom
order and alignto() preserves the order of supplied AtomGroups for the
special select values "all" and None.
* new set_* methods for AtomGroup allows changing of Atom attributes
for all members of the group (such as the segid) (EXPERIMENTAL)
* new Atom and Residue attribute resnum that can be used to store
the canonical PDB residue number (EXPERIMENTAL)
Fixes
* fixed Issue 74 (bug in AMBER topology parser which would show up for
certain numbers of input lines; thanks to htaoyu1)
* fix for Issue 48 (sparse contact_matrix in distances.py was slow when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): order of mobile and reference
selection was reversed when supplied as a tuple (sel1, sel2)
Changes
* replaced analysis.util.progress_meter() with class core.log.ProgressMeter
* Issue 28: split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package MDAnalysisTestData, which is
required to run the UnitTests from release 0.7.4 onwards. Numbering matches
the earliest MDAnalysis release for which the data is needed. Any later
releases of MDAnalysis will also use these test data unless a
MDAnalysisTestData package with a higher release number is available.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
Removals
* completely removed the old core.rms_fitting module (and thus we also do not
depend on the LAPACK library anymore, which should simplify installation);
use the functions accessible through MDAnalysis.analysis.align (which are
faster and use QCPROT)
Enhancements
* PDBQT (autodock) format added (reading and writing of single frames)
* new attributes universe.trajectory.frame and universe.trajectory.frame:
report the current frame number and time (e.g. in ps) of the current frame
of the trajectory
* new attribute Timestep.volume (unit cell volume)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* HELANAL helix analysis in MDAnalysis.analysis.helanal; Python
implementation of helanal.f from
http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin
Hall, used under GPL v2+)
* hydrogen bonds analysis in MDAnalysis.analysis.hbonds
* MDAnalysis.analysis.distances.dist() for calculating distances between
matching atoms in two groups
* MDAnalysis logo by Christian Beckstein (and a reformatting of the
online docs to match the logo theme)
Change of behaviour
* alignto() and rms_fit_trj(): changed keyword 'select' default from
'backbone' to 'all'
Fixes
* fixed alignto() (raised KeyError)
* fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
* use spaces everywhere and no TABs and tell emacs and vim to keep it that
way (Issue 69)
* fixed Issue 70 (problems with instant atom selections)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
2014-01-03 22:28:42 +01:00
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${PYSITELIB}/MDAnalysis/topology/DMSParser.pyc
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${PYSITELIB}/MDAnalysis/topology/DMSParser.pyo
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${PYSITELIB}/MDAnalysis/topology/ExtendedPDBParser.py
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${PYSITELIB}/MDAnalysis/topology/ExtendedPDBParser.pyc
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${PYSITELIB}/MDAnalysis/topology/ExtendedPDBParser.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/topology/GMSParser.py
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${PYSITELIB}/MDAnalysis/topology/GMSParser.pyc
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${PYSITELIB}/MDAnalysis/topology/GMSParser.pyo
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2012-09-04 00:59:11 +02:00
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${PYSITELIB}/MDAnalysis/topology/GROParser.py
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${PYSITELIB}/MDAnalysis/topology/GROParser.pyc
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${PYSITELIB}/MDAnalysis/topology/GROParser.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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Update new version
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??/??/13 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin
* 0.8.0
Enhancements
* Merge AtomGroups into a new Universe (Issue 157)
* TPR parser (currently limited to versions 58, 73 and 83 of the
Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
* fast XTC seeking (Issue 127)
* changing resid (set_resid()) or segid (set_segid()) changes the
topology and lists of resids/segids can be assigned to
groups of objects (AtomGroup, ResidueGroup)
* helanal: additional output of local bend and unit twist angles
(Issue 133)
* added support for reading DMS files (DESRES molecular structure)
* bond connectivity information can be guessed from a PDB file if
the bond=True keyword is set in Universe (Issue 23)
* MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
* Plugin to generate nucleic acid helicoidal parameters using X3DNA;
(must install working version 2.1 of X3DNA independently)
* can use advanced slicing (with arbitrary lists or arrays) at all
levels of the hierarchy (Issue 148)
* coordinate readers and writers can be used as context managers
with the 'with' statement
* Can load multiple trajectories as Universe(topology, traj2, traj2,
...) in addition to providing all trajectories as a list,
i.e. Universe(topology, [traj1, traj2, ...])
* added support for YASP and IBIsCO formats (.trz) (Issue 152)
* new methods for AtomGroup: packintobox() (only orthorhombic boxes)
* added non-standard "extended" PDB format (XPDB) that reads
five-digit residue numbers
* util.convert_aa_code() recognizes non-standard residue names such
as HSE, GLUH, GLH, ...
* added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
* added TopologyDict and TopologyGroup classes for bond analysis
Changes
* dropped support for Python 2.5; minimum requirement is Python 2.6
(Issue 130)
* almost all methods of AtomGroup return NumPy arrays
* slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
SegmentGroup will now always return an appropriate object and
never a simple list
* removed Timeseries.principleAxis (probably was never working)
* dependent on Biopython >= 1.59 (Issue 147)
* Hydrogen bond analysis defaults to updating selection 1 and 2 for
every timestep in order to avoid unexpected behavior (Issue 138)
Fixes
* fixed incorrect computation of distances in serial and parallel
distance_array() with PBC (Issue 151)
* fixed Issue 129 (hole.py module pipe/file closure)
* fixed array comparison bug in MDAnalysis.analysis.helanal
and various enhancements to the helanal module
* fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
if ref_frame != 0
* alignto() now checks that the two selections describe the same
atoms (fixes Issue 143)
* slicing of ResidueGroup will now produce a ResidueGroup, and
slicing of a SegmentGroup will produce a SegmentGroup, not a list
as before (fixes Issue 135)
* detect OpenMP-capable compiler during setup (Issue 145), which should allow
users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
C-compiler (clang) (Issue 142) although they will not get a parallel
version of distance_array.
* PDB with blank lines gave IndexError (Issue 158)
12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi, sebastien.buchoux
* 0.7.7
Enhancements
* multithreaded distance_array() (Issue 80, experimental); see the
new core.parallel.distance module
* MDAnalysis.analysis.rms for simple RMSD analysis
* format of input coordinates can be set as (filename, format)
tuples (Issue 76)
* new AtomGroup.asphericity() and AtomGroup.shapeParameter()
methods to compute shape descriptors.
* access to forces (AtomGroup.forces with get_forces() and set_forces();
the default unit for force is kJ/(mol*A) and it is automatically
converted from/to native). Currently, only the TRR Reader/Writer
support forces.
* all element masses
* logger reports current version when starting
Fixes
* fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
* fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
* fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
* fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
* fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
* Issue 122 (made installation of netCDF4 library optional, which
means that users of the AMBER netcdf Reader/Writer will have to
manually install the library and its dependencies netcdf and HDF5,
see https://code.google.com/p/mdanalysis/wiki/netcdf)
06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0, danny.parton
* 0.7.6
Enhancements
* GRO file velocities may be accessed as AtomGroup.velocities()
or Atom.velocity (Issue 102)
* PrimitivePDBReader can be sliced
* AMBER NetCDF (binary trajectory) reader and writer, supporting
coordinates and velocities; requires netcdf4-python (Issue 109)
* additional attributes and methods for AtomGroup to consolidate
the interface to the Timestep: attribute 'positions' and
'get_positions()' can be used instead of the 'coordinates()'
method. get/set methods for both positions and velocities.
* almost all Readers now support some form of slicing; unsupported
slicing operations will raise a TypeError
* additional analysis for Nucleic Acid order parameters
(MDAnalysis.analysis.nuclinfo)
* AMBER TOPParser now able to do both amber10 and amber12 formats
(Issue 100)
Changes
* selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
*nucleic* includes the two-letter NA code that follows gromacs topolgy
format and *nucleicxstal* allows for the one-letter NA code that follows
the PDB Database code.
* HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply
stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the
new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
* removed CHO and EAM (formyl and ethanol termini of gA in CHARMM)
from the set of residues recognized as protein (collision with
commonly used CHO for cholesterol)
* PrimitivePDBWriter: special segid SYSTEM is translated to empty
chainID
* In order to write multi frame PDB files, the multiframe=True
keyword must be supplied or use the MultiPDBWriter
* empty AtomGroup can be constructed or can result from a selection
without matches; it does *not* raise NoDataError anymore (Issue 12)
* all single frame readers denote the first (and only) frame as
frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is
consistent with the way this is is handled with real trajectories
* requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
* Atom.type is always stored as a string.
Fixes
* HydrogenBondAnalysis: NH1 and NH2 were not recognized
* GROWriter: enforce maximum resname and atomname length of 5 chars
* Universe.load_new() raised a NameError (thanks to JiyongPark.77)
* fixed Issue 105 (trajectory snapshots could not be written to PDB)
* fixed Issue 107 (NAMD/VMD space delimited PSF files can be
autodetected and read); important when using CGENFF atom types
(thanks to JiyongPark.77 for initial patch)
* fixed Issue 101 (could not write single frame to trr file)
* fixed: permissive=True flag was ignored in Universe and hence the
PrimitivePDBReader was always selected even if the Biopython one
was desired
* fixed Issue 112 (used removed Biopython constructs in
MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri
for a test case and fix)
* fixed failing 'type' selection for topology formats that read an
atom type as an integer (such as the AMBER parser)
* fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
* fixed Issue 113 (replaced outdated Biopython to call ClustalW)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
Enhancements
* Universe() got new keywords topology_format and format to allow
the user to specify the file formats instead of deriving it from the
extensions (does not work with "chained" files at the moment); thanks to
Michael Lerner for the suggestion
* Chain trajectory reader allows frame indexing.
* Issue 75: additional donors and acceptors keywords for H-bond analysis
* structural alignment functions alignto() and rms_fit_traj() can also take a
list of selection strings in order to define atom groups with fixed atom
order and alignto() preserves the order of supplied AtomGroups for the
special select values "all" and None.
* new set_* methods for AtomGroup allows changing of Atom attributes
for all members of the group (such as the segid) (EXPERIMENTAL)
* new Atom and Residue attribute resnum that can be used to store
the canonical PDB residue number (EXPERIMENTAL)
Fixes
* fixed Issue 74 (bug in AMBER topology parser which would show up for
certain numbers of input lines; thanks to htaoyu1)
* fix for Issue 48 (sparse contact_matrix in distances.py was slow when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): order of mobile and reference
selection was reversed when supplied as a tuple (sel1, sel2)
Changes
* replaced analysis.util.progress_meter() with class core.log.ProgressMeter
* Issue 28: split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package MDAnalysisTestData, which is
required to run the UnitTests from release 0.7.4 onwards. Numbering matches
the earliest MDAnalysis release for which the data is needed. Any later
releases of MDAnalysis will also use these test data unless a
MDAnalysisTestData package with a higher release number is available.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
Removals
* completely removed the old core.rms_fitting module (and thus we also do not
depend on the LAPACK library anymore, which should simplify installation);
use the functions accessible through MDAnalysis.analysis.align (which are
faster and use QCPROT)
Enhancements
* PDBQT (autodock) format added (reading and writing of single frames)
* new attributes universe.trajectory.frame and universe.trajectory.frame:
report the current frame number and time (e.g. in ps) of the current frame
of the trajectory
* new attribute Timestep.volume (unit cell volume)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* HELANAL helix analysis in MDAnalysis.analysis.helanal; Python
implementation of helanal.f from
http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin
Hall, used under GPL v2+)
* hydrogen bonds analysis in MDAnalysis.analysis.hbonds
* MDAnalysis.analysis.distances.dist() for calculating distances between
matching atoms in two groups
* MDAnalysis logo by Christian Beckstein (and a reformatting of the
online docs to match the logo theme)
Change of behaviour
* alignto() and rms_fit_trj(): changed keyword 'select' default from
'backbone' to 'all'
Fixes
* fixed alignto() (raised KeyError)
* fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
* use spaces everywhere and no TABs and tell emacs and vim to keep it that
way (Issue 69)
* fixed Issue 70 (problems with instant atom selections)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
2014-01-03 22:28:42 +01:00
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${PYSITELIB}/MDAnalysis/topology/LAMMPSParser.py
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${PYSITELIB}/MDAnalysis/topology/LAMMPSParser.pyc
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${PYSITELIB}/MDAnalysis/topology/LAMMPSParser.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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Update new version
------------------------------------------------------------------------------
??/??/13 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin
* 0.8.0
Enhancements
* Merge AtomGroups into a new Universe (Issue 157)
* TPR parser (currently limited to versions 58, 73 and 83 of the
Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
* fast XTC seeking (Issue 127)
* changing resid (set_resid()) or segid (set_segid()) changes the
topology and lists of resids/segids can be assigned to
groups of objects (AtomGroup, ResidueGroup)
* helanal: additional output of local bend and unit twist angles
(Issue 133)
* added support for reading DMS files (DESRES molecular structure)
* bond connectivity information can be guessed from a PDB file if
the bond=True keyword is set in Universe (Issue 23)
* MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
* Plugin to generate nucleic acid helicoidal parameters using X3DNA;
(must install working version 2.1 of X3DNA independently)
* can use advanced slicing (with arbitrary lists or arrays) at all
levels of the hierarchy (Issue 148)
* coordinate readers and writers can be used as context managers
with the 'with' statement
* Can load multiple trajectories as Universe(topology, traj2, traj2,
...) in addition to providing all trajectories as a list,
i.e. Universe(topology, [traj1, traj2, ...])
* added support for YASP and IBIsCO formats (.trz) (Issue 152)
* new methods for AtomGroup: packintobox() (only orthorhombic boxes)
* added non-standard "extended" PDB format (XPDB) that reads
five-digit residue numbers
* util.convert_aa_code() recognizes non-standard residue names such
as HSE, GLUH, GLH, ...
* added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
* added TopologyDict and TopologyGroup classes for bond analysis
Changes
* dropped support for Python 2.5; minimum requirement is Python 2.6
(Issue 130)
* almost all methods of AtomGroup return NumPy arrays
* slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
SegmentGroup will now always return an appropriate object and
never a simple list
* removed Timeseries.principleAxis (probably was never working)
* dependent on Biopython >= 1.59 (Issue 147)
* Hydrogen bond analysis defaults to updating selection 1 and 2 for
every timestep in order to avoid unexpected behavior (Issue 138)
Fixes
* fixed incorrect computation of distances in serial and parallel
distance_array() with PBC (Issue 151)
* fixed Issue 129 (hole.py module pipe/file closure)
* fixed array comparison bug in MDAnalysis.analysis.helanal
and various enhancements to the helanal module
* fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
if ref_frame != 0
* alignto() now checks that the two selections describe the same
atoms (fixes Issue 143)
* slicing of ResidueGroup will now produce a ResidueGroup, and
slicing of a SegmentGroup will produce a SegmentGroup, not a list
as before (fixes Issue 135)
* detect OpenMP-capable compiler during setup (Issue 145), which should allow
users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
C-compiler (clang) (Issue 142) although they will not get a parallel
version of distance_array.
* PDB with blank lines gave IndexError (Issue 158)
12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi, sebastien.buchoux
* 0.7.7
Enhancements
* multithreaded distance_array() (Issue 80, experimental); see the
new core.parallel.distance module
* MDAnalysis.analysis.rms for simple RMSD analysis
* format of input coordinates can be set as (filename, format)
tuples (Issue 76)
* new AtomGroup.asphericity() and AtomGroup.shapeParameter()
methods to compute shape descriptors.
* access to forces (AtomGroup.forces with get_forces() and set_forces();
the default unit for force is kJ/(mol*A) and it is automatically
converted from/to native). Currently, only the TRR Reader/Writer
support forces.
* all element masses
* logger reports current version when starting
Fixes
* fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
* fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
* fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
* fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
* fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
* Issue 122 (made installation of netCDF4 library optional, which
means that users of the AMBER netcdf Reader/Writer will have to
manually install the library and its dependencies netcdf and HDF5,
see https://code.google.com/p/mdanalysis/wiki/netcdf)
06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0, danny.parton
* 0.7.6
Enhancements
* GRO file velocities may be accessed as AtomGroup.velocities()
or Atom.velocity (Issue 102)
* PrimitivePDBReader can be sliced
* AMBER NetCDF (binary trajectory) reader and writer, supporting
coordinates and velocities; requires netcdf4-python (Issue 109)
* additional attributes and methods for AtomGroup to consolidate
the interface to the Timestep: attribute 'positions' and
'get_positions()' can be used instead of the 'coordinates()'
method. get/set methods for both positions and velocities.
* almost all Readers now support some form of slicing; unsupported
slicing operations will raise a TypeError
* additional analysis for Nucleic Acid order parameters
(MDAnalysis.analysis.nuclinfo)
* AMBER TOPParser now able to do both amber10 and amber12 formats
(Issue 100)
Changes
* selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
*nucleic* includes the two-letter NA code that follows gromacs topolgy
format and *nucleicxstal* allows for the one-letter NA code that follows
the PDB Database code.
* HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply
stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the
new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
* removed CHO and EAM (formyl and ethanol termini of gA in CHARMM)
from the set of residues recognized as protein (collision with
commonly used CHO for cholesterol)
* PrimitivePDBWriter: special segid SYSTEM is translated to empty
chainID
* In order to write multi frame PDB files, the multiframe=True
keyword must be supplied or use the MultiPDBWriter
* empty AtomGroup can be constructed or can result from a selection
without matches; it does *not* raise NoDataError anymore (Issue 12)
* all single frame readers denote the first (and only) frame as
frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is
consistent with the way this is is handled with real trajectories
* requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
* Atom.type is always stored as a string.
Fixes
* HydrogenBondAnalysis: NH1 and NH2 were not recognized
* GROWriter: enforce maximum resname and atomname length of 5 chars
* Universe.load_new() raised a NameError (thanks to JiyongPark.77)
* fixed Issue 105 (trajectory snapshots could not be written to PDB)
* fixed Issue 107 (NAMD/VMD space delimited PSF files can be
autodetected and read); important when using CGENFF atom types
(thanks to JiyongPark.77 for initial patch)
* fixed Issue 101 (could not write single frame to trr file)
* fixed: permissive=True flag was ignored in Universe and hence the
PrimitivePDBReader was always selected even if the Biopython one
was desired
* fixed Issue 112 (used removed Biopython constructs in
MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri
for a test case and fix)
* fixed failing 'type' selection for topology formats that read an
atom type as an integer (such as the AMBER parser)
* fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
* fixed Issue 113 (replaced outdated Biopython to call ClustalW)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
Enhancements
* Universe() got new keywords topology_format and format to allow
the user to specify the file formats instead of deriving it from the
extensions (does not work with "chained" files at the moment); thanks to
Michael Lerner for the suggestion
* Chain trajectory reader allows frame indexing.
* Issue 75: additional donors and acceptors keywords for H-bond analysis
* structural alignment functions alignto() and rms_fit_traj() can also take a
list of selection strings in order to define atom groups with fixed atom
order and alignto() preserves the order of supplied AtomGroups for the
special select values "all" and None.
* new set_* methods for AtomGroup allows changing of Atom attributes
for all members of the group (such as the segid) (EXPERIMENTAL)
* new Atom and Residue attribute resnum that can be used to store
the canonical PDB residue number (EXPERIMENTAL)
Fixes
* fixed Issue 74 (bug in AMBER topology parser which would show up for
certain numbers of input lines; thanks to htaoyu1)
* fix for Issue 48 (sparse contact_matrix in distances.py was slow when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): order of mobile and reference
selection was reversed when supplied as a tuple (sel1, sel2)
Changes
* replaced analysis.util.progress_meter() with class core.log.ProgressMeter
* Issue 28: split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package MDAnalysisTestData, which is
required to run the UnitTests from release 0.7.4 onwards. Numbering matches
the earliest MDAnalysis release for which the data is needed. Any later
releases of MDAnalysis will also use these test data unless a
MDAnalysisTestData package with a higher release number is available.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
Removals
* completely removed the old core.rms_fitting module (and thus we also do not
depend on the LAPACK library anymore, which should simplify installation);
use the functions accessible through MDAnalysis.analysis.align (which are
faster and use QCPROT)
Enhancements
* PDBQT (autodock) format added (reading and writing of single frames)
* new attributes universe.trajectory.frame and universe.trajectory.frame:
report the current frame number and time (e.g. in ps) of the current frame
of the trajectory
* new attribute Timestep.volume (unit cell volume)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* HELANAL helix analysis in MDAnalysis.analysis.helanal; Python
implementation of helanal.f from
http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin
Hall, used under GPL v2+)
* hydrogen bonds analysis in MDAnalysis.analysis.hbonds
* MDAnalysis.analysis.distances.dist() for calculating distances between
matching atoms in two groups
* MDAnalysis logo by Christian Beckstein (and a reformatting of the
online docs to match the logo theme)
Change of behaviour
* alignto() and rms_fit_trj(): changed keyword 'select' default from
'backbone' to 'all'
Fixes
* fixed alignto() (raised KeyError)
* fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
* use spaces everywhere and no TABs and tell emacs and vim to keep it that
way (Issue 69)
* fixed Issue 70 (problems with instant atom selections)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
2014-01-03 22:28:42 +01:00
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${PYSITELIB}/MDAnalysis/topology/TPRParser.py
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${PYSITELIB}/MDAnalysis/topology/TPRParser.pyc
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${PYSITELIB}/MDAnalysis/topology/TPRParser.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/topology/XYZParser.pyc
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${PYSITELIB}/MDAnalysis/topology/XYZParser.pyo
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${PYSITELIB}/MDAnalysis/topology/__init__.pyc
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${PYSITELIB}/MDAnalysis/topology/__init__.pyo
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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------------------------------------------------------------------------------
??/??/13 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin
* 0.8.0
Enhancements
* Merge AtomGroups into a new Universe (Issue 157)
* TPR parser (currently limited to versions 58, 73 and 83 of the
Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
* fast XTC seeking (Issue 127)
* changing resid (set_resid()) or segid (set_segid()) changes the
topology and lists of resids/segids can be assigned to
groups of objects (AtomGroup, ResidueGroup)
* helanal: additional output of local bend and unit twist angles
(Issue 133)
* added support for reading DMS files (DESRES molecular structure)
* bond connectivity information can be guessed from a PDB file if
the bond=True keyword is set in Universe (Issue 23)
* MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
* Plugin to generate nucleic acid helicoidal parameters using X3DNA;
(must install working version 2.1 of X3DNA independently)
* can use advanced slicing (with arbitrary lists or arrays) at all
levels of the hierarchy (Issue 148)
* coordinate readers and writers can be used as context managers
with the 'with' statement
* Can load multiple trajectories as Universe(topology, traj2, traj2,
...) in addition to providing all trajectories as a list,
i.e. Universe(topology, [traj1, traj2, ...])
* added support for YASP and IBIsCO formats (.trz) (Issue 152)
* new methods for AtomGroup: packintobox() (only orthorhombic boxes)
* added non-standard "extended" PDB format (XPDB) that reads
five-digit residue numbers
* util.convert_aa_code() recognizes non-standard residue names such
as HSE, GLUH, GLH, ...
* added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
* added TopologyDict and TopologyGroup classes for bond analysis
Changes
* dropped support for Python 2.5; minimum requirement is Python 2.6
(Issue 130)
* almost all methods of AtomGroup return NumPy arrays
* slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
SegmentGroup will now always return an appropriate object and
never a simple list
* removed Timeseries.principleAxis (probably was never working)
* dependent on Biopython >= 1.59 (Issue 147)
* Hydrogen bond analysis defaults to updating selection 1 and 2 for
every timestep in order to avoid unexpected behavior (Issue 138)
Fixes
* fixed incorrect computation of distances in serial and parallel
distance_array() with PBC (Issue 151)
* fixed Issue 129 (hole.py module pipe/file closure)
* fixed array comparison bug in MDAnalysis.analysis.helanal
and various enhancements to the helanal module
* fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
if ref_frame != 0
* alignto() now checks that the two selections describe the same
atoms (fixes Issue 143)
* slicing of ResidueGroup will now produce a ResidueGroup, and
slicing of a SegmentGroup will produce a SegmentGroup, not a list
as before (fixes Issue 135)
* detect OpenMP-capable compiler during setup (Issue 145), which should allow
users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
C-compiler (clang) (Issue 142) although they will not get a parallel
version of distance_array.
* PDB with blank lines gave IndexError (Issue 158)
12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi, sebastien.buchoux
* 0.7.7
Enhancements
* multithreaded distance_array() (Issue 80, experimental); see the
new core.parallel.distance module
* MDAnalysis.analysis.rms for simple RMSD analysis
* format of input coordinates can be set as (filename, format)
tuples (Issue 76)
* new AtomGroup.asphericity() and AtomGroup.shapeParameter()
methods to compute shape descriptors.
* access to forces (AtomGroup.forces with get_forces() and set_forces();
the default unit for force is kJ/(mol*A) and it is automatically
converted from/to native). Currently, only the TRR Reader/Writer
support forces.
* all element masses
* logger reports current version when starting
Fixes
* fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
* fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
* fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
* fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
* fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
* Issue 122 (made installation of netCDF4 library optional, which
means that users of the AMBER netcdf Reader/Writer will have to
manually install the library and its dependencies netcdf and HDF5,
see https://code.google.com/p/mdanalysis/wiki/netcdf)
06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0, danny.parton
* 0.7.6
Enhancements
* GRO file velocities may be accessed as AtomGroup.velocities()
or Atom.velocity (Issue 102)
* PrimitivePDBReader can be sliced
* AMBER NetCDF (binary trajectory) reader and writer, supporting
coordinates and velocities; requires netcdf4-python (Issue 109)
* additional attributes and methods for AtomGroup to consolidate
the interface to the Timestep: attribute 'positions' and
'get_positions()' can be used instead of the 'coordinates()'
method. get/set methods for both positions and velocities.
* almost all Readers now support some form of slicing; unsupported
slicing operations will raise a TypeError
* additional analysis for Nucleic Acid order parameters
(MDAnalysis.analysis.nuclinfo)
* AMBER TOPParser now able to do both amber10 and amber12 formats
(Issue 100)
Changes
* selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
*nucleic* includes the two-letter NA code that follows gromacs topolgy
format and *nucleicxstal* allows for the one-letter NA code that follows
the PDB Database code.
* HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply
stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the
new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
* removed CHO and EAM (formyl and ethanol termini of gA in CHARMM)
from the set of residues recognized as protein (collision with
commonly used CHO for cholesterol)
* PrimitivePDBWriter: special segid SYSTEM is translated to empty
chainID
* In order to write multi frame PDB files, the multiframe=True
keyword must be supplied or use the MultiPDBWriter
* empty AtomGroup can be constructed or can result from a selection
without matches; it does *not* raise NoDataError anymore (Issue 12)
* all single frame readers denote the first (and only) frame as
frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is
consistent with the way this is is handled with real trajectories
* requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
* Atom.type is always stored as a string.
Fixes
* HydrogenBondAnalysis: NH1 and NH2 were not recognized
* GROWriter: enforce maximum resname and atomname length of 5 chars
* Universe.load_new() raised a NameError (thanks to JiyongPark.77)
* fixed Issue 105 (trajectory snapshots could not be written to PDB)
* fixed Issue 107 (NAMD/VMD space delimited PSF files can be
autodetected and read); important when using CGENFF atom types
(thanks to JiyongPark.77 for initial patch)
* fixed Issue 101 (could not write single frame to trr file)
* fixed: permissive=True flag was ignored in Universe and hence the
PrimitivePDBReader was always selected even if the Biopython one
was desired
* fixed Issue 112 (used removed Biopython constructs in
MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri
for a test case and fix)
* fixed failing 'type' selection for topology formats that read an
atom type as an integer (such as the AMBER parser)
* fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
* fixed Issue 113 (replaced outdated Biopython to call ClustalW)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
Enhancements
* Universe() got new keywords topology_format and format to allow
the user to specify the file formats instead of deriving it from the
extensions (does not work with "chained" files at the moment); thanks to
Michael Lerner for the suggestion
* Chain trajectory reader allows frame indexing.
* Issue 75: additional donors and acceptors keywords for H-bond analysis
* structural alignment functions alignto() and rms_fit_traj() can also take a
list of selection strings in order to define atom groups with fixed atom
order and alignto() preserves the order of supplied AtomGroups for the
special select values "all" and None.
* new set_* methods for AtomGroup allows changing of Atom attributes
for all members of the group (such as the segid) (EXPERIMENTAL)
* new Atom and Residue attribute resnum that can be used to store
the canonical PDB residue number (EXPERIMENTAL)
Fixes
* fixed Issue 74 (bug in AMBER topology parser which would show up for
certain numbers of input lines; thanks to htaoyu1)
* fix for Issue 48 (sparse contact_matrix in distances.py was slow when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): order of mobile and reference
selection was reversed when supplied as a tuple (sel1, sel2)
Changes
* replaced analysis.util.progress_meter() with class core.log.ProgressMeter
* Issue 28: split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package MDAnalysisTestData, which is
required to run the UnitTests from release 0.7.4 onwards. Numbering matches
the earliest MDAnalysis release for which the data is needed. Any later
releases of MDAnalysis will also use these test data unless a
MDAnalysisTestData package with a higher release number is available.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
Removals
* completely removed the old core.rms_fitting module (and thus we also do not
depend on the LAPACK library anymore, which should simplify installation);
use the functions accessible through MDAnalysis.analysis.align (which are
faster and use QCPROT)
Enhancements
* PDBQT (autodock) format added (reading and writing of single frames)
* new attributes universe.trajectory.frame and universe.trajectory.frame:
report the current frame number and time (e.g. in ps) of the current frame
of the trajectory
* new attribute Timestep.volume (unit cell volume)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* HELANAL helix analysis in MDAnalysis.analysis.helanal; Python
implementation of helanal.f from
http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin
Hall, used under GPL v2+)
* hydrogen bonds analysis in MDAnalysis.analysis.hbonds
* MDAnalysis.analysis.distances.dist() for calculating distances between
matching atoms in two groups
* MDAnalysis logo by Christian Beckstein (and a reformatting of the
online docs to match the logo theme)
Change of behaviour
* alignto() and rms_fit_trj(): changed keyword 'select' default from
'backbone' to 'all'
Fixes
* fixed alignto() (raised KeyError)
* fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
* use spaces everywhere and no TABs and tell emacs and vim to keep it that
way (Issue 69)
* fixed Issue 70 (problems with instant atom selections)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
2014-01-03 22:28:42 +01:00
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py-mdanalysis: update to 0.15.0
This makes py-mdanalysis fetch and package again.
It needs additional dependencies packaged, which I leave for maintainer.
* 0.15.0
Metadata
* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)
* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes
* rmsd doesn't superimpose by default anymore. The superposition
is controlled by the 'superposition' keyword now. (see issue #562, #822)
Enhancements
* Add conda build scripts (Issue #608)
* Added read-only property giving Universe init kwargs (Issue #292)
* Added 'crdbox' as AMBER Trj format extension (Issue #846)
* Iteration and seeking in PDB files made faster (Issue #848)
Fixes
* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
* rmsd now returns proper value when given array of weights (Issue #814)
* change_release now finds number and dev (Issue #776)
* units.py now correctly prints errors for unknown units.
* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
* MOL2 files without substructure section can now be read (Issue #816)
* MOL2 files can be written without substructure section (Issue #816)
* GRO files with an incomplete set of velocities can now be read (Issue #820)
* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)
* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)
* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes
* Added zero_based indices for HBondsAnalysis. (Issue #807)
* Generalized contact analysis class `Contacts` added. (Issue #702)
* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)
* PDB parsers/readers/writers replaced by "permissive"/"primitive"
counterparts (formerly known as PrimitivePDBReader); the
'permissive' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)
* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)
* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)
* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed
* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
* 0.14.0
API Changes
* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format '.npz'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)
* rotation_matrix now accepts array-likes as input
Enhancement
* XDR file seeking errors now report system errno. (PR #678)
* Offsets reading for xtc/trr files has been sped up. (Issue #441)
* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)
* Performance improvements for the PDBReader of about 10%
* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)
* Trajectories can now be sliced using a boolean array (Issue #725)
Changes
* xdrlib was rebranded libmdaxdr. (Issue #679)
* xdrlib has been ported to cython. (Issue #441)
* util.NamedStream no longer inherits from basestring (Issue #649)
* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)
* PDB doesn't save charge information anymore
* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes
* Syntax error corrected in psa.py (Issue #738)
* XDR file seeking and telling working again for large files (Issue #677).
* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
* The 'atom' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)
* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)
* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
* Fixed NCDFReader not reading dt (Issue #676)
* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
* Fixed cyzone selection failing in orthogonal systems (Issue #710)
* Fixed Error in calculation of average grid density (Issue #716)
* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra
* 0.13.0
API Changes
* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)
* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won't give a warning if the
number of atoms differs between frames.
* GROWriter.fmt strings updated to use format style (Issue #494)
* removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement
* ChainReader now reports times properly summed over sub-readers (Issue #522)
* GRO file reading approximately 50% faster for large files (Issue #212)
* GRO file writing now will write velocities where possible (Issue #494)
* Added bonded selection (Issue #362)
* Spherical layer and spherical zone selections now much faster (Issue #362)
* new keyword "backend" for accelerated functions in MDAnalysis.lib.distances
to select "serial" or "OpenMP"-enabled versions of the code; the default
is "serial" so old code will behave as before (see Issue #530)
* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)
* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
* Added analysis.rdf, with InterRDF tool. (Issue #460)
* Made Reader.check_slice_indices a public method (Issue #604)
* analysis.helanal.helanal_main() now returns results as dict
* Added keyword to update selection every frame in density calculation (Issue #584)
* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.
* MOL2Reader now reads molecule and substructure into ts.data
* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes
* built html doc files are no longer version controlled (Issue #491)
* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)
* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout
* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)
* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.
* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes
* Fixed select_atoms requiring a trajectory be loaded (Issue #270)
* AtomGroup timesteps no longer cached (Issue #606)
* GROWriter now truncates atom numbers over 99999 (Issue #550)
* AMBER netcdf writer now correctly uses float32 precision (Issue #518)
* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)
* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)
* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
* Fixed unpickling errors due to lingering dead universes. (Issue #487)
* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)
* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)
* Fixed non-compliant Amber NCDFWriter (Issue #488)
* Fixed many Timestep methods failing when positions weren't present
(Issue #512)
* Fixed PointSelection using KDTree (Issue #362)
* Fixed GROParser getting tripped up by some file (Issue #548)
* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)
* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)
* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()
* Fixed lib.util.greedy_splitext() (now returns full path)
* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)
* Fixed MOL2Writer rereading frames when writing them (Issue #521)
* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15
* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes
* Fixed OpenMP detection on Linux/OSX #459
* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps
* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=<dt>)
* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)
* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud
* 0.12.0
API Changes
* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)
* Atoms without a Universe now return NoDataError instead of
AttributeError
* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe
* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)
* `PSAnalysis` can now generate annotated heat maps (Issue #438)
* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
* Additional getters added to `Path` and `PSAnalysis` (Issue #438)
* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)
* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with 'MDA_'. Current options are 'use_cython', 'ues_openmp', 'debug_cflags'
Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)
* To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
Fixes
* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn't notice that multiple fragments
had been given. (Issue #445)
* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to '***', breaking the parser (Issue #446)
* Fixed AtomGroup.sequence() (Issue #451)
* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)
* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock
* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes
* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)
* Changed trajectory reader numframes to n_frames (Issue #376)
* Changed Timestep.numatoms to n_atoms (Issue #376)
* Deprecated the use of the 'fullgroup' selection keyword (Issue #268)
* Changed atom.number attribute to atom.index (Issue #372)
* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)
* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)
* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)
* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)
* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)
* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)
* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)
* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)
* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)
* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)
* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)
* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)
* All TopologyObjects now have a "value" method to evaluate them
(Issue #373)
* TopologyGroup now has a "values" methods to evaluate all contained
bonds (Issue #373)
* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)
* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)
* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)
* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)
* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)
* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)
* AtomGroup setters `set_<property>` now plural for consistency with
property names (Issue #385)
* DCDReader no longer supports the "skip" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)
* All Readers have a default "dt" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)
* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements
* Added the 'global' selection keyword (Issue #268)
* Added Jmol selection writer (Issue #356)
* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now
* Tests can now detect memleaks on a per-test basis (Issue #323)
* AtomGroups can now be pickled/unpickled (Issue #293)
* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)
* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)
* Timestep objects now have __eq__ method (Issue #294)
* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)
* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)
* RMSF class added to rms analysis module
* ProgressMeter now outputs every *interval* number of ``update``
calls (Issue #313)
* Created lib.mdamath for common mathematical functions. (Issue #287)
* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)
* Timesteps can now allocate velocities and forces if they weren't
originally created with these through the use of the has_ flags.
(Issue #213)
* Timesteps now store 'dt' and 'time_offset' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)
* MDAnalysis.selection: can also be written to a NamedStream
* Added function lib.mdamath.make_whole to "unbreak" molecules
over periodic boundaries. (Issue #355)
* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)
* Added setter to bfactors property (Issue #372)
* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)
* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes
* numpy >= 1.5 required
* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).
* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)
* Removed FormatError, now replaced by ValueError (Issue #294)
* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)
* Timestep._x _y and _z are now read only (Issue #213)
* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.
* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)
* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)
* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes
* All Writers now refer to time between written Timesteps as "dt",
was previously "delta" in some Writers. (Issue #206)
* Topology files can now be compressed (Issue #336)
* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)
* Amber TRJ and NCDF Reader & Writers now use 'dt' instead of 'delta'
to refer to time elapsed between timesteps. (Issue #350 and #206)
* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)
* ChainReaders no longer cause memory leak (Issue #312)
* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)
* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)
* relative imports are now banned in unit testing modules
(Issue #189)
* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)
* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)
* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)
* Fixed analysis.hole not using CPOINT (Issue #384)
* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)
* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)
* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler
* 0.10.0
Enhancements
* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
* Added the 'same ... as' selection keyword (Issue #217)
* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)
* Added guess_bonds method to AtomGroup. (Issue #245)
* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
* TopologyGroup now has alternate constructor method, .from_indices()
* Added TopologyObject.indices property
* Amber netCDF4 Reader will now read Forces (Issue #257)
* Amber netCDF4 Writer will now write Velocities and Forces
* Added Amber coordinate/restart file reader (Issue #262)
* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.
* new path similarity analysis module MDAnalysis.analysis.psa
* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes
* TopologyGroup can now have zero length, and will evaluate to False
when empty.
* Renamed TopologyGroup.dump_contents to "to_indices"
* Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
* PrimitivePDBReader now requires the numatoms keyword
* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)
* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes
* bynum selections now work from AtomGroup instances (Issue #275)
* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)
* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst
* 0.9.2
Enhancements
* Can now set velocity from Atom object. (Issue 221)
* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)
* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes
* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis
* "applications" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/
* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes
* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin
* 0.9.1
Enhancements
* XYZ file format can be used without an associated topology file.
* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE'' and ``OPTIMIZE'' (work wit both GAMESS-US and Firefly)
Changes
* removed undocumented MDAnalysis.builder module
Fixes
* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux
* 0.9.0
Enhancements
* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)
* docs now use secure mathjax CDN (Issue 182)
* minor improvements to helanal docstring
* Support for reading altloc records in PDB files
* Cap proteins with ACE and NMA terminal caps
* MOL2 read and write support
* 2D streamplot code no longer uses deprecated matplotlib.nxutils module
* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)
* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries
* XYZWriter (write simple XYZ trajectories)
* TRZReader upgrades, seeking and numframes faster
* PQRWriter (write PQR files)
* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)
* TopologyGroup/TopologyDict system overhauled. (Issue 194)
* TopologyObject class created, Bonds/Angles/etc nicer to work with.
* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.
* Added support for improper torsions.
* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups
* Increased performance of topology.core.guess_bonds greatly
* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.
* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_* functions.
* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)
* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)
* Added ability to remove items from Universe cache with _clear_caches.
* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)
* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ
* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)
* Added energy units to core.units (Issue 214)
* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment
* New AtomGroup.sequence() method to extract a protein sequence.
* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)
* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)
* Added atom selections to ContactAnalysis (Issue 169)
Changes
* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).
* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic "TypeError: AtomGroup is not callable" was
raised (see also Issue 173 for detailed explanation)
* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)
* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.
* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to 'SYSTEM').
* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead
* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes
* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!
* fixed creation of residues and segments in Merge()
* resolves Issue 188 regarding Helanal Finish Argument
* fixed Issue 184 (TPR files with double precision)
* fixed Issue 199 (FutureWarning in pyqcprot)
2016-09-11 18:58:21 +02:00
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${PYSITELIB}/MDAnalysis/version.py
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${PYSITELIB}/MDAnalysis/version.pyc
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${PYSITELIB}/MDAnalysis/version.pyo
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${PYSITELIB}/MDAnalysis/visualization/__init__.py
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${PYSITELIB}/MDAnalysis/visualization/__init__.pyc
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${PYSITELIB}/MDAnalysis/visualization/__init__.pyo
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${PYSITELIB}/MDAnalysis/visualization/streamlines.py
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${PYSITELIB}/MDAnalysis/visualization/streamlines.pyc
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${PYSITELIB}/MDAnalysis/visualization/streamlines.pyo
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${PYSITELIB}/MDAnalysis/visualization/streamlines_3D.py
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${PYSITELIB}/MDAnalysis/visualization/streamlines_3D.pyc
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${PYSITELIB}/MDAnalysis/visualization/streamlines_3D.pyo
|