structure; that is, to number the atoms in a unique way regardless of the
input order.
WWW: http://search.cpan.org/dist/Chemistry-Canonicalize/
PR: ports/145143
Submitted by: Steve Wills <steve at mouf.net>
its 3D coordinates by using simple cutoffs, and for guessing the formal bond
orders.
WWW: http://search.cpan.org/dist/Chemistry-Bond-Find/
PR: ports/145143
Submitted by: Steve Wills <steve at mouf.net>
files, a Java package providing an object-oriented interface to HDF data
objects, and Java Native Interfaces to the standard HDF libraries.
WWW: http://www.hdfgroup.org/hdf-java-html/index.html
PR: ports/143859
Submitted by: rfarmer at predatorlabs.net
PyQt-4.7 for FreeBSD. The official update notes can be found at
http://www.riverbankcomputing.com
We'd like to say thanks to all helpers, testers and submitters.
software package developed at MIT to model electromagnetic systems,
along with our MPB eigenmode package.
WWW: http://ab-initio.mit.edu/wiki/index.php/Meep
PR: ports/142158
Submitted by: Stas Timokhin <devel@stasyan.com>
Approved by: portmgr (miwi)
audio/ccaudio||2010-01-18|Has expired: has been broken for 4 months
audio/py-libmpdclient||2010-01-18|Has expired: has been broken for 3 months
chinese/gbk2uni||2010-01-18|Has expired: has been broken for 6 months
chinese/iiimf-le-xcin||2010-01-18|Has expired: has been broken for 3 months
devel/adabindx||2010-01-18|Has expired: has been broken for 3 months
devel/agide||2010-01-18|Has expired: has been broken for 6 months
devel/asis||2010-01-18|Has expired: has been broken for 3 months
devel/callgrind||2010-01-18|Has expired: Included in devel/valgrind
devel/florist||2010-01-18|Has expired: has been broken for 3 months
editors/xml2rfc-xxe||2010-01-18|Has expired: has been broken for 4 months
graphics/gephex||2010-01-18|Has expired: has been broken for 3 months
graphics/irit||2010-01-18|Has expired: has been broken for 3 months
graphics/pixieplus||2010-01-18|Has expired: has been broken for 6 months
japanese/expect||2010-01-18|Has expired: has been broken for 3 months
lang/pnetc||2010-01-18|Has expired: has been broken for 5 months
mail/libnewmail||2010-01-18|Has expired: has been broken for 3 months
net-mgmt/flowscan||2010-01-18|Has expired: has been broken for 5 months
net/astmanproxy||2010-01-18|Has expired: has been broken for 3 months
palm/prc-tools||2010-01-18|Has expired: has been broken for 4 months
print/latex-msc||2010-01-18|Has expired: has been broken for 3 months
science/xloops-ginac||2010-01-18|Has expired: has been broken for 3 months
shells/bush||2010-01-18|Has expired: has been broken for 3 months
textproc/iiimf-gnome-im-switcher||2010-01-18|Has expired: has been broken for 4 months
textproc/iiimf-gtk||2010-01-18|Has expired: has been broken for 3 months
x11-toolkits/gtkada-devel||2010-01-18|Has expired: has been broken for 3 months
x11-toolkits/gtkada||2010-01-18|Has expired: has been broken for 3 months
x11-wm/ion-2||2010-01-18|Has expired: has been broken for 4 months
United States Geological Survey's web server. You provide the latitude
and longitude in degrees, with south latitude and west longitude being
negative. The return is typically a hash containing the data you want.
Query errors are exceptions by default, though the object can be configured
to signal an error by an undef response, with the error retrievable from
the 'error' attribute.
WWW: http://search.cpan.org/dist/Geo-WebService-Elevation-USGS/
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>
