building bioinformatics-related tools and utilities.
Current list of features includes: a Sequence data type supporting
protein and nucleotide sequences and conversion between them.
WWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
PR: ports/142187
Submitted by: Jacula Modyun <jacula(at)gmail.com>
of harmonic inversion - given a discrete-time, finite-length signal
that consists of a sum of finitely-many sinusoids (possibly exponentially
decaying) in a given bandwidth, it determines the frequencies, decay
constants, amplitudes, and phases of those sinusoids.
WWW: http://ab-initio.mit.edu/wiki/index.php/Harminv
PR: ports/142154
Submitted by: Stas Timokhin <devel@stasyan.com>
e-mail addresses from the pkg-descr file that could reasonably
be mistaken for maintainer contact information in order to avoid
confusion on the part of users looking for support. As a pleasant
side effect this also avoids confusion and/or frustration for people
who are no longer maintaining those ports.
It's goal is to offer flexible, easy-to-use yet still powerful
algorithms for Machine Learning Tasks and a variety of
predefined environments to test and compare your algorithms.
PyBrain is short for Python-Based Reinforcement Learning,
Artificial Intelligence and Neural Network Library. In fact,
we came up with the name first and later reverse-engineerer
this quite descriptive "Backronym".
WWW: http://pybrain.org/
parse, generate and operate on KML. It is an implementation
of the OGC KML 2.2 standard.
WWW: http://code.google.com/p/libkml/
Approved by: miwi(mentor)
molecular structure files in different formats and generates
Postscript output for 2D display. The Postscript file can then be used
e.g. for creating a bitmap file, using a Postscript interpreter like
Ghostscript.
WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2ps.html
PR: ports/138673
Feature safe: yes
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar>
structure files in different formats and analyzes the input
molecule for the presence of various functional groups and structural
elements. At present, approx. 200 different functional groups are
recognized. This output can be easily placed into a database table,
permitting the creation of chemical databases with a functional group
search option. Checkmol also outputs a set of statistical values derived
from a given molecule, which can also be used for quick retrieval from a
database. These values include: the number of atoms, bonds, and rings,
the number of differently hybridized carbon, oxgen, and nitrogen atoms,
the number of C=O double bonds, the number of rings of different sizes,
the number of rings containing nitrogen, oxygen, sulfur, the number of
aromatic rings, the number of heterocyclic rings, etc. The combination
of all of these values for a given molecule represents some kind of
"fingerprint" which is useful for rapid pre-selection in a database
structure/substructure search prior to a full atom-by-atom match.
WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html
PR: ports/138670
Feature safe:yes
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar>
- Merge all SF mirrors to MASTER_SITE_SOURCEFORGE, resort according to quick download speed survey
- Fix MASTER_SITES for all port that have used SOURCEFORGE_EXTENTED
Approved by: portmgr (pav)
mechanics, with a special focus laid to quantum computing.
It started as a pure quantum computer simulator, but
support for general quantum simulation has been recently
added.
WWW: http://www.libquantum.de/
PR: ports/137468
Submitted by: Wen Heping <wenheping at gmail.com>
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.
It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.
With help: marcus and kwm
Pointyhat-exp: a few times by pav
Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and
a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by: marcus
Approved by: portmgr
- Split boost port to separate components, with boost-all metaport
PR: ports/137054
Submitted by: Alexander Churanov <churanov.port.maintainer@gmail.com> (maintainer)
correctly detect and depend on it in math/py-numpy
* Replace the old numpy documentation with the new numpy book
* Explicitly tell the distutil to use gnu95 fortran compiler
* Use ${PYTHONPREFIX_SITELIBDIR} rather than ${PYTHON_SITELIBDIR} when
generating the packing list for science/py-scipy
* Bump PORTREVISIONs, for packing lists are changed
PR: ports/136058
Submitted by: Li-Lun Wang (Leland Wang) <llwang AT infor.org> (maintainer)
researchers and developers, written in C++.
Its purpose is to simplify the visualization needs faced by a roboticist
daily - using visualization as a debugging aid or making fancy slides for
a presentation, for example.
Chris Petrik (chris@officialunix.com)
WWW: http://www.peekabot.org
PR: 135892
Submitted by: Chris Petrik <c.petrik.sosa@gmail.com>
modular xorg.
- supply corresponding USE_XORG for all imake-using ports that need it
- USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG
- retire USE_X_PREFIX which is not really used anywhere after the
above change
- a few minor nits like whitespace and SF macro
Tested by: 2 tinderbox runs by pav
Approved by: portmgr (pav)
- Fix WITH_MPICH
- Use LOCALBASE for reference to bits installed by others
- Pass maintainership to the submitter
- Pet portlint(1): IGNORE
PR: ports/133242
Submitted by: Florian Smeets <flo at kasimir.com>
Approved by: Stephen Montgomery-Smith <stephen at math.missouri.edu> (maintainer)
describe macromolecules, a macromolecule is just a molecule that
consists of several "domains". For example, a protein consists
of aminoacid residues, or a nucleic acid consists of bases. Therefore
Chemistry::MacroMol is derived from Chemistry::Mol, with additional
methods to handle the domains.
WWW: http://search.cpan.org/dist/Chemistry-MacroMol/
PR: ports/134609
Submitted by: Wen Heping <wenheping at gmail.com>
is commonly used to describe proteins, particularly those stored in the
Protein Data Bank.
WWW: http://search.cpan.org/dist/Chemistry-File-PDB/
PR: ports/134612
Submitted by: Wen Heping <wenheping at gmail.com>
describe molecules. It consists of several modules: Chemistry::Mol,
Chemistry::Atom, Chemistry::Bond, and Chemistry::File.
WWW: http://search.cpan.org/dist/Chemistry-Mol/
PR: ports/134462
Submitted by: Wen Heping <wenheping at gmail.com>
