Sunday

Saturday

sci-chemistry/acpype

AnteChamber PYthon Parser interfacE

08 Apr 2015; Michał Górny (mgorny) acpype-389.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
389 ~ ~
374 ~ ~
366 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ambertools

A suite for carrying out complete molecular mechanics investigations

27 Feb 2013; Justin Lecher (jlec) ambertools-1.5-r1.ebuild:
Add missing dep on virtual/pkgconfig
alphaamd64armhppaia64ppcppc64sparcx86
1.5-r1 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/apbs

Evaluation of electrostatic properties of nanoscale biomolecular systems

07 Aug 2015; Justin Lecher (jlec) apbs-1.4.1-r2.ebuild:
Use DISTUTILS_SINGLE_IMPL, hopefully fixing, bug #556916
alphaamd64armhppaia64ppcppc64sparcx86
1.4.1-r2 + + +
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/aqua

Program suite in this distribution calculates restraint violations

19 Oct 2012; Justin Lecher (jlec) aqua-3.2-r2.ebuild,
metadata.xml:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
3.2-r2 ~ ~
sci-chemistry Homepage procheck ChangeLog Metadata Similar Bugs Forums

sci-chemistry/aria

Automated NOE assignment and NMR structure calculation

08 Apr 2015; Michał Górny (mgorny) aria-2.3.2_p20130826.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2_p20130826 ~ ~
sci-chemistry Homepage cns ChangeLog Metadata Similar Bugs Forums

sci-chemistry/arp-warp-bin

Improvement and interpretation of crystallographic electron density maps

*arp-warp-bin-7.5 (11 Mar 2015)
11 Mar 2015; Justin Lecher (jlec) +arp-warp-bin-7.5.ebuild,
-arp-warp-bin-7.1-r1.ebuild, -arp-warp-bin-7.1-r2.ebuild,
-arp-warp-bin-7.3.ebuild, -files/7.1-setup-2.patch, -files/7.1-setup.patch:
Version Bump; Drop old with unavailable upstream sources, #542758
alphaamd64armhppaia64ppcppc64sparcx86
7.5 + +
sci-chemistry Homepage ArpWarp ChangeLog Metadata Similar Bugs Forums

sci-chemistry/autodock

A suite of automated docking tools

13 Apr 2015; Justin Lecher (jlec) -autodock-4.2.3-r1.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
4.2.6 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/autodock_vina

Program for drug discovery, molecular docking and virtual screening

No changelog entry available
alphaamd64armhppaia64ppcppc64sparcx86
1.1.2 + +
sci-chemistry Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/avogadro

Advanced molecular editor that uses Qt4 and OpenGL

29 Jun 2015; Justin Lecher (jlec) avogadro-1.0.3-r2.ebuild:
Drop ppc64 due to revdep breakage
alphaamd64armhppaia64ppcppc64sparcx86
1.1.0 ~ ~ ~
1.0.3-r2 ~ ~ ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/azara

A suite of programmes to process and view NMR data

08 Apr 2015; Michał Górny (mgorny) azara-2.8-r5.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
2.8-r5 ~ ~
2.8-r4 ~ ~
sci-chemistry Homepage AZARA ChangeLog Metadata Similar Bugs Forums

sci-chemistry/babel

Interconvert file formats used in molecular modeling

16 Apr 2014; Ulrich Müller (ulm) babel-1.6-r1.ebuild:
Fix LICENSE, add mirror and bindist restrictions, bug 470780.
alphaamd64armhppaia64ppcppc64sparcx86
1.6-r1 + + +
sci-chemistry Homepage all-rights-reserved ChangeLog Metadata Similar Bugs Forums

sci-chemistry/balbes

Automated molecular replacement (MR) pipeline

19 Oct 2012; Justin Lecher (jlec) balbes-1.0.0_p100317-r2.ebuild:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
1.0.0_p100317-r2 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ball

Biochemical Algorithms Library

05 May 2015; Justin Lecher (jlec)
+files/ball-1.4.2-underlinking.patch, ball-1.4.2.ebuild:
Fix linking problems, bug #547522
alphaamd64armhppaia64ppcppc64sparcx86
1.4.2 ~ ~
sci-chemistry Homepage LGPL-2 GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/bkchem

Chemical drawing program

*bkchem-0.14.0_pre2-r1 (20 Feb 2015)
20 Feb 2015; Justin Lecher (jlec) +bkchem-0.14.0_pre2-r1.ebuild,
+files/bkchem-0.14.0_pre2-nolauncher.patch, -bkchem-0.14.0_pre1-r2.ebuild,
-bkchem-0.14.0_pre2.ebuild, metadata.xml:
Drop old; move to EAPI=5 and new pythen eclasses
alphaamd64armhppaia64ppcppc64sparcx86
0.14.0_pre2-r1 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/bodr

The Blue Obelisk Data Repository listing element and isotope properties

*bodr-10 (06 Jan 2014)
06 Jan 2014; Justin Lecher (jlec) bodr-9-r1.ebuild,
+bodr-10.ebuild:
Version Bump; punt base.eclass
alphaamd64armhppaia64ppcppc64sparcx86
10 ~ ~
9-r1 ~ ~
sci-chemistry Homepage MIT ChangeLog Metadata Similar Bugs Forums

sci-chemistry/burrow-owl

Visualize multidimensional nuclear magnetic resonance (NMR) spectra

03 Feb 2014; Justin Lecher (jlec) burrow-owl-1.5.1.ebuild:
Bumpt to EAPI=5
alphaamd64armhppaia64ppcppc64sparcx86
1.5.1 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/cara-bin

Analysis of NMR spectra and Computer Aided Resonance Assignment

31 Jul 2015; Justin Lecher (jlec) -cara-bin-1.8.4.ebuild,
cara-bin-1.8.4-r1.ebuild:
Fix for non-multilib on prefix
alphaamd64armhppaia64ppcppc64sparcx86
1.8.4-r1 ~ ~
sci-chemistry Homepage CARA ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ccp4

Protein X-ray crystallography toolkit -- meta package

19 Oct 2012; Justin Lecher (jlec) ccp4-6.1.3-r1.ebuild:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
6.1.3-r1 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ccp4-apps

Protein X-ray crystallography toolkit

alphaamd64armhppaia64ppcppc64sparcx86
6.1.3-r13 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ccp4i

Protein X-ray crystallography toolkit -- graphical interface

27 Mar 2015; Justin Lecher (jlec) -ccp4i-6.1.3-r3.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
6.1.3-r4 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ccpn

The Collaborative Computing Project for NMR

*ccpn-2.4.2_p150421 (21 Apr 2015)
21 Apr 2015; Justin Lecher (jlec) +ccpn-2.4.2_p150421.ebuild:
Today's python patches
alphaamd64armhppaia64ppcppc64sparcx86
2.4.2_p150421 ~ ~
2.4.2_p150413 ~ ~
2.4.2_p150325 ~ ~
2.4.2 ~ ~
2.4.1_p150226 ~ ~
sci-chemistry Homepage || ( CCPN LGPL-2.1 ) ChangeLog Metadata Similar Bugs Forums

sci-chemistry/chemical-mime-data

A collection of data files to add support for chemical MIME types

10 Aug 2014; Sergei Trofimovich (slyfox)
chemical-mime-data-0.1.94-r1.ebuild, chemical-mime-data-0.1.94-r2.ebuild,
chemical-mime-data-0.1.94.ebuild:
QA: drop trailing '.' from DESCRIPTION
alphaamd64armhppaia64ppcppc64sparcx86
0.1.94-r2 ~ ~
0.1.94-r1 ~ ~
0.1.94 + +
sci-chemistry Homepage LGPL-2.1 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/chemtool

A GTK program for drawing organic molecules

alphaamd64armhppaia64ppcppc64sparcx86
1.6.14 ~ ~ ~
1.6.13 + + +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/clashlist

Build lists of van der Waals clashes from an input PDB file

26 Apr 2015; Pacho Ramos (pacho) clashlist-3.17-r1.ebuild:
x86 stable wrt bug #547384
alphaamd64armhppaia64ppcppc64sparcx86
3.17-r1 ~ +
3.17 + +
sci-chemistry Homepage richardson ChangeLog Metadata Similar Bugs Forums

sci-chemistry/cluster

Build lists of collections of interacting items

*cluster-1.3.081231 (21 May 2015)
21 May 2015; Justin Lecher (jlec) +cluster-1.3.081231.ebuild:
Reinstate old version due to broken revdeps
alphaamd64armhppaia64ppcppc64sparcx86
1.3.081231-r1 + +
1.3.081231 + +
sci-chemistry Homepage richardson ChangeLog Metadata Similar Bugs Forums

sci-chemistry/cns

Crystallography and NMR System

09 Jun 2014; Justin Lecher (jlec) cns-1.2.1-r8.ebuild:
Readd Stable keyowrds, #512792
alphaamd64armhppaia64ppcppc64sparcx86
1.3_p7-r1 ~ ~
1.2.1-r8 + +
sci-chemistry Homepage cns ChangeLog Metadata Similar Bugs Forums

sci-chemistry/coot

Crystallographic Object-Oriented Toolkit for model building, completion and validation

06 Aug 2015; Agostino Sarubbo (ago) coot-0.7.2.ebuild:
Stable for amd64, wrt bug #529518
alphaamd64armhppaia64ppcppc64sparcx86
0.7.2 + ~
0.7.1-r1 ~ ~
0.7 + +
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/cyana

Combined assignment and dynamics algorithm for NMR applications

04 Aug 2015; Justin Lecher (jlec) cyana-2.1.ebuild:
Update HOMEPAGE
alphaamd64armhppaia64ppcppc64sparcx86
2.1 ~ ~
sci-chemistry Homepage CYANA ChangeLog Metadata Similar Bugs Forums

sci-chemistry/dssp

The protein secondary structure standard

No changelog entry available
alphaamd64armhppaia64ppcppc64sparcx86
2.2.1-r1 + +
sci-chemistry Homepage Boost-1.0 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/easychem

Chemical structure drawing program - focused on presentation

10 Oct 2014; Justin Lecher (jlec) -easychem-0.6.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
0.6-r1 + ~ +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/eden

A crystallographic real-space electron-density refinement and optimization program

20 Apr 2015; Justin Lecher (jlec) -eden-5.3-r1.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
5.3-r2 + +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/elem

periodic table of the elements

21 Jul 2013; Pacho Ramos (pacho) metadata.xml:
Cleanup due #473480
alphaamd64armhppaia64ppcppc64sparcx86
1.0.3-r2 ~ ~ ~
1.0.3-r1 + + +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/freeon

An experimental suite of programs for linear scaling quantum chemistry

*freeon-1.0.10 (26 Jun 2015)
26 Jun 2015; Nicolas Bock (nicolasbock) +freeon-1.0.10.ebuild:
Version bump.
alphaamd64armhppaia64ppcppc64sparcx86
1.0.10 ~ ~
1.0.8-r1 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gabedit

GUI for computational chemistry packages

*gabedit-2.4.8 (24 Apr 2014)
24 Apr 2014; Justin Lecher (jlec) +gabedit-2.4.8.ebuild:
Version Bump, #508388
alphaamd64armhppaia64ppcppc64sparcx86
2.4.8 ~ ~
2.4.7 ~ ~
2.4.6 + +
sci-chemistry Homepage MIT ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gamess

A powerful quantum chemistry package

27 Feb 2013; Justin Lecher (jlec) gamess-20110811.1.ebuild,
files/gamess-20110811.1.gentoo.patch, metadata.xml:
Use PKG_CONFIG instead of generic pkg-config
alphaamd64armhppaia64ppcppc64sparcx86
20110811.1 ~ ~ ~
sci-chemistry Homepage gamess ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gamessq

Simple job manager for GAMESS-US

06 Jan 2014; Justin Lecher (jlec) gamessq-1.2.ebuild,
metadata.xml:
Punt base.eclass
alphaamd64armhppaia64ppcppc64sparcx86
1.2 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gelemental

Periodic table viewer that provides detailed information on the chemical elements

*gelemental-1.2.0-r1 (31 Jul 2012)
31 Jul 2012; Justin Lecher (jlec) +gelemental-1.2.0-r1.ebuild:
Apply all debian patches
alphaamd64armhppaia64ppcppc64sparcx86
1.2.0-r1 ~ ~
1.2.0 + +
sci-chemistry Homepage GPL-3 MIT ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ghemical

Chemical quantum mechanics and molecular mechanics

10 Jul 2014; Patrick Lauer (patrick) metadata.xml:
Remove unneeded useflag description from metadata.xml
alphaamd64armhppaia64ppcppc64sparcx86
3.0.0 ~ ~ ~
2.99.2-r2 + + +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gopenmol

Tool for the visualization and analysis of molecular structures

08 Apr 2015; Michał Górny (mgorny) gopenmol-3.00-r3.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
3.00-r3 ~ ~
3.00-r2 ~ ~
sci-chemistry Homepage all-rights-reserved ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gperiodic

Periodic table application for Linux

05 Sep 2012; Justin Lecher (jlec) gperiodic-2.0.10.ebuild,
gperiodic-2.0.10-r2.ebuild:
Bump EAPI to 4; fix desktop file
alphaamd64armhppaia64ppcppc64sparcx86
2.0.10-r2 + +
2.0.10 + +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gromacs

The ultimate molecular dynamics simulation package

*gromacs-5.0.6 (02 Aug 2015)
02 Aug 2015; Alexey Shvetsov (alexxy) +gromacs-5.0.6.ebuild:
Version bump. This one seems to be last version for 5.0.x series
alphaamd64armhppaia64ppcppc64sparcx86
5.1 ~ ~ ~ ~ ~ ~
5.0.6 ~ ~ ~ ~ ~ ~
5.0.5 ~ ~ ~ ~ ~ ~
5.0.4-r1 ~ ~ ~ ~ ~ ~
5.0.4 ~ + + + ~ +
sci-chemistry Homepage LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD ) ChangeLog Metadata Similar Bugs Forums

sci-chemistry/GromacsWrapper

Python framework for Gromacs

08 Apr 2015; Michał Górny (mgorny) GromacsWrapper-0.3.1.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
0.3.2 ~ ~
0.3.1 ~ ~
sci-chemistry Homepage GPL-3 LGPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gsim

Programm for visualisation and processing of experimental and simulated NMR spectra

20 Feb 2015; Justin Lecher (jlec) -gsim-0.20.1.ebuild,
-gsim-21.0.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
21.3 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/gtk-gamess

GUI for GAMESS, a General Atomic and Molecular Electronic Structure System

17 Jan 2015; Manuel Rüger (mrueg) gtk-gamess-2.00.ebuild:
Add ~amd64 keyword. Bump to EAPI=5.
alphaamd64armhppaia64ppcppc64sparcx86
2.00 ~ ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/hollow

Production of surface images of proteins

21 Mar 2015; Justin Lecher (jlec) -hollow-1.1.ebuild,
-hollow-1.2.ebuild, hollow-1.2-r1.ebuild:
use esvn_clean; clean old
alphaamd64armhppaia64ppcppc64sparcx86
1.2-r1 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/icm

MolSoft LCC ICM Pro

14 Jun 2015; Ulrich Müller (ulm) icm-3.7.2e.ebuild,
icm-3.7.3b.ebuild:
[QA] Remove emul-linux-x86-* from dependencies.
alphaamd64armhppaia64ppcppc64sparcx86
3.7.3b ~ ~
3.7.2e ~ ~
sci-chemistry Homepage MolSoft ChangeLog Metadata Similar Bugs Forums

sci-chemistry/icm-browser

MolSoft LCC ICM Browser

14 Jun 2015; Ulrich Müller (ulm) icm-browser-3.6.1i.ebuild:
[QA] Remove emul-linux-x86-* from dependencies.
alphaamd64armhppaia64ppcppc64sparcx86
3.6.1i ~ ~
sci-chemistry Homepage MolSoft ChangeLog Metadata Similar Bugs Forums

sci-chemistry/imosflm

A new GUI for the Mosflm crystallographic data processing tool

07 Aug 2015; Justin Lecher (jlec) -imosflm-1.0.5.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
1.0.7-r1 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/jmol

Java molecular viever for 3-D chemical structures

*jmol-12.0.45-r1 (06 Aug 2014)
*jmol-12.2.27-r1 (06 Aug 2014)
06 Aug 2014; Chris Reffett (creffett) +jmol-12.0.45-r1.ebuild,
+jmol-12.2.27-r1.ebuild, -jmol-12.0.45.ebuild, -jmol-12.2.27.ebuild:
[QA] EAPI/revision bump, drop old
alphaamd64armhppaia64ppcppc64sparcx86
12.2.27-r1 ~ ~
12.0.45-r1 ~ ~
sci-chemistry Homepage LGPL-2.1 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ksdssp

An open source implementation of sci-chemistry/dssp

19 Jun 2013; Sébastien Fabbro (bicatali) metadata.xml:
Changed herd to sci-chemistry
alphaamd64armhppaia64ppcppc64sparcx86
040728-r1 ~ ~
040728 ~ ~
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/makecif

PDB --> CIF convertor

03 Feb 2013; Agostino Sarubbo (ago) makecif-5.6.6-r1.ebuild:
Stable for ppc, wrt bug #454310
alphaamd64armhppaia64ppcppc64sparcx86
5.6.6-r1 ~ + ~
5.6.6 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mars

Robust automatic backbone assignment of proteins

19 Jun 2013; Sébastien Fabbro (bicatali) metadata.xml:
Changed herd to sci-chemistry
alphaamd64armhppaia64ppcppc64sparcx86
1.2 ~ ~
sci-chemistry Homepage all-rights-reserved ChangeLog Metadata Similar Bugs Forums

sci-chemistry/massxpert

Software suite to predict/analyze mass spectrometric data on (bio)polymers

10 Aug 2014; Sergei Trofimovich (slyfox) massxpert-2.0.5.ebuild:
QA: drop trailing '.' from DESCRIPTION
alphaamd64armhppaia64ppcppc64sparcx86
3.4.0 ~ ~
2.0.5 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mdanalysis

A python library to analyze and manipulate molecular dynamics trajectories

08 Apr 2015; Michał Górny (mgorny) mdanalysis-0.7.7.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
0.7.7 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mead

Macroscopic Electrostatics with Atomic Detail

*mead-2.2.7-r1 (19 Apr 2010)
19 Apr 2010; Justin Lecher (jlec) mead-2.2.7.ebuild,
+mead-2.2.7-r1.ebuild, +files/mead-2.2.7-respect-flags.patch,
-files/respect-cflags.patch:
respect LDFLAGS, #316059
alphaamd64armhppaia64ppcppc64sparcx86
2.2.7-r1 ~
2.2.7 ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mm-align

Protein Complex Structural Alignment

20 May 2013; Justin Lecher (jlec) mm-align-20120321.ebuild,
metadata.xml:
Fix license, #470786
alphaamd64armhppaia64ppcppc64sparcx86
20120321 ~ ~
sci-chemistry Homepage tm-align ChangeLog Metadata Similar Bugs Forums

sci-chemistry/molden

Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac

alphaamd64armhppaia64ppcppc64sparcx86
5.0 ~ ~
4.8-r2 + +
sci-chemistry Homepage MOLDEN ChangeLog Metadata Similar Bugs Forums

sci-chemistry/moldy

Molecular dynamics simulations platform

22 Jun 2012; Justin Lecher (jlec) moldy-2.16e-r2.ebuild:
Don't alter configure.ac needlessly to avoid autoreconf, #422871
alphaamd64armhppaia64ppcppc64sparcx86
2.16e-r2 + + +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/molequeue

Abstract, manage and coordinate execution of tasks

01 Aug 2015; Justin Lecher (jlec) -molequeue-0.6.1-r1.ebuild,
molequeue-0.7.1.ebuild:
Use subslots
alphaamd64armhppaia64ppcppc64sparcx86
0.7.1 ~ ~
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/molmol

Publication-quality molecular visualization package

24 Jul 2014; Justin Lecher (jlec) files/wild.patch:
Fix patch to work with current stable version of patch as well, #517940
alphaamd64armhppaia64ppcppc64sparcx86
2k_p2-r5 ~ ~ ~
2k_p2-r4 ~ ~ ~
2k_p2-r3 ~ ~ ~
2k_p2-r2 + + +
sci-chemistry Homepage molmol ChangeLog Metadata Similar Bugs Forums

sci-chemistry/molrep

molecular replacement program

21 Feb 2013; Justin Lecher (jlec) molrep-11.0.02.ebuild,
-molrep-11.0.03.ebuild, molrep-11.0.03-r1.ebuild, metadata.xml:
Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config;
drop old
alphaamd64armhppaia64ppcppc64sparcx86
11.0.03-r1 ~ ~ ~
11.0.02 + + +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/molscript

Display molecular 3D structures, such as proteins, in both schematic and detailed representations

28 May 2015; Justin Lecher (jlec) -molscript-2.1.2-r1.ebuild,
molscript-2.1.2-r2.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
2.1.2-r2 + + +
sci-chemistry Homepage glut molscript ChangeLog Metadata Similar Bugs Forums

sci-chemistry/molsketch

A drawing tool for 2D molecular structures

*molsketch-0.3.0 (29 Jun 2015)
29 Jun 2015; Justin Lecher (jlec)
+files/molsketch-0.3.0-_DEFAULT_SOURCE.patch,
+files/molsketch-0.3.0-desktop.patch, +files/molsketch-0.3.0-no-quotes.patch,
+molsketch-0.3.0.ebuild, molsketch-0.2.0-r1.ebuild:
Version Bump; fix version of openbabel in deps, bug #553512
alphaamd64armhppaia64ppcppc64sparcx86
0.3.0 ~ ~
0.2.0-r1 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mongochem

Application for managing large collections of chemical data

*mongochem-0.7.0 (03 Feb 2014)
03 Feb 2014; Justin Lecher (jlec) +mongochem-0.7.0.ebuild,
+metadata.xml:
Nre ebuild, written by me
alphaamd64armhppaia64ppcppc64sparcx86
0.7.0 ~ ~
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mopac7

Autotooled, updated version of a powerful, fast semi-empirical package

*mopac7-1.15-r1 (05 Mar 2015)
05 Mar 2015; Justin Lecher (jlec) +mopac7-1.15-r1.ebuild,
-mopac7-1.10-r1.ebuild, metadata.xml:
Drop old; EAPI bump
alphaamd64armhppaia64ppcppc64sparcx86
1.15-r1 ~ ~ ~
1.15 + + +
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sci-chemistry/mosflm

A program for integrating single crystal diffraction data from area detectors

15 May 2015; Justin Lecher (jlec) -mosflm-7.0.6-r2.ebuild,
-mosflm-7.0.7-r2.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
7.0.9 + + +
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sci-chemistry/mpqc

The Massively Parallel Quantum Chemistry Program

27 Feb 2013; Justin Lecher (jlec) mpqc-2.3.1-r1.ebuild,
mpqc-2.3.1-r2.ebuild, mpqc-2.3.1-r3.ebuild:
Add missing dep on virtual/pkgconfig
alphaamd64armhppaia64ppcppc64sparcx86
2.3.1-r3 + + + +
2.3.1-r2 ~ ~ ~ +
2.3.1-r1 + + + +
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mrbump

An automated scheme for Molecular Replacement

14 Apr 2012; Andreas Schuerch (nativemad) mrbump-0.4.4.ebuild:
x86 stable, see bug 375917, thanks all.
alphaamd64armhppaia64ppcppc64sparcx86
0.4.4 + ~ +
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sci-chemistry/msms-bin

MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces

23 May 2012; Justin Lecher (jlec) msms-bin-2.6.1-r1.ebuild:
Move to EAPI=4, use QA_PREBUILT instead of QA_DT_HASH
alphaamd64armhppaia64ppcppc64sparcx86
2.6.1-r1 ~ ~
sci-chemistry Homepage MSMS ChangeLog Metadata Similar Bugs Forums

sci-chemistry/mustang

MUltiple STructural AligNment AlGorithm

29 Apr 2012; Justin Lecher (jlec) mustang-3.2.1.ebuild,
+files/mustang-3.2.1-gcc-4.7.patch:
Fix for gcc-4.7, #413945
alphaamd64armhppaia64ppcppc64sparcx86
3.2.1 + +
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/namd

A powerful and highly parallelized molecular dynamics code

26 Jun 2015; Nicolas Bock (nicolasbock) metadata.xml:
Updated metadata.xml
alphaamd64armhppaia64ppcppc64sparcx86
2.10 ~
2.9-r1 ~
sci-chemistry Homepage namd ChangeLog Metadata Similar Bugs Forums

sci-chemistry/nmrglue

A module for working with NMR data in Python

*nmrglue-0.5-r1 (04 Mar 2015)
04 Mar 2015; Justin Lecher (jlec) +files/nmrglue-0.5-nohyper.patch,
+nmrglue-0.5-r1.ebuild, -nmrglue-0.5.ebuild:
Backport fix for agilent data conversion
alphaamd64armhppaia64ppcppc64sparcx86
0.5-r1 ~ ~
0.4 ~ ~
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/numbat

new user-friendly method built for automatic dX-tensor determination

*numbat-0.999-r1 (22 May 2013)
22 May 2013; Justin Lecher (jlec) -numbat-0.999.ebuild,
+numbat-0.999-r1.ebuild, +files/numbat-0.999-gnuplot.patch:
Add fix for gnuplot
alphaamd64armhppaia64ppcppc64sparcx86
0.999-r1 ~ ~
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sci-chemistry/oasis

A direct-method program for SAD/SIR phasing

09 Mar 2015; Justin Lecher (jlec) -oasis-4.0-r2.ebuild,
oasis-4.0-r3.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
4.0-r3 + ~ +
sci-chemistry Homepage ccp4 oasis ChangeLog Metadata Similar Bugs Forums

sci-chemistry/openbabel

Interconverts file formats used in molecular modeling

28 Jun 2015; Justin Lecher (jlec) metadata.xml:
Drop unused local USE-description: 'swig'
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2 + ~ + +
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sci-chemistry/openbabel-perl

Perl bindings for OpenBabel

28 Jun 2015; Mikle Kolyada (zlogene) openbabel-perl-2.3.2.ebuild:
x86 stable wrt bug #534620
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2 + ~ + +
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sci-chemistry/openbabel-python

Python bindings for OpenBabel (including Pybel)

28 Jun 2015; Mikle Kolyada (zlogene) openbabel-python-2.3.2.ebuild:
x86 stable wrt bug #534618
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2 + ~ + +
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sci-chemistry/ortep3

Thermal ellipsoid plot program for crystal structure illustrations

19 Oct 2012; Justin Lecher (jlec) ortep3-1.0.3-r1.ebuild,
metadata.xml:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
1.0.3-r1 ~ ~
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sci-chemistry/p3d

Python module for structural bioinformatics

26 Jun 2011; Justin Lecher (jlec) p3d-0.4.3.ebuild,
p3d-9999.ebuild, metadata.xml:
migrate from 'git' to 'git-2'
alphaamd64armhppaia64ppcppc64sparcx86
9999
0.4.3 ~ ~
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sci-chemistry/parassign

Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)

08 Apr 2015; Michał Górny (mgorny) parassign-20130522.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
20130522 ~ ~
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sci-chemistry/pdb-extract

Tools for extracting mmCIF data from structure determination applications

*pdb-extract-3.11 (23 Jun 2012)
23 Jun 2012; Justin Lecher (jlec) +pdb-extract-3.11.ebuild,
+files/pdb-extract-3.11-cflags-install.patch,
+files/pdb-extract-3.11-gcc-4.7.patch:
Version Bump, #379159
alphaamd64armhppaia64ppcppc64sparcx86
3.11 ~ ~ ~
3.004-r2 + ~ +
sci-chemistry Homepage PDB ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pdb-tools

Tools for manipulating and doing calculations on wwPDB macromolecule structure files

08 Apr 2015; Michał Górny (mgorny) pdb-tools-0.2.1-r1.ebuild,
pdb-tools-0.2.1-r2.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
0.2.1-r2 ~ ~
0.2.1-r1 ~ ~
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sci-chemistry/pdb2pqr

An automated pipeline for performing Poisson-Boltzmann electrostatics calculations

alphaamd64armhppaia64ppcppc64sparcx86
1.9.0-r1 + + +
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pdbcat

Manipulate and process PDB files using commonly available tools such as Perl, awk, etc

18 Jul 2013; Justin Lecher (jlec) pdbcat-1.3.ebuild, metadata.xml:
Fix usage of cmake-utils.eclass, #477236
alphaamd64armhppaia64ppcppc64sparcx86
1.3 ~ ~
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sci-chemistry/pdbcns

Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back

*pdbcns-2.0.010504 (01 Mar 2012)
01 Mar 2012; Justin Lecher (jlec) +pdbcns-2.0.010504.ebuild,
+metadata.xml:
New addition
alphaamd64armhppaia64ppcppc64sparcx86
2.0.010504 ~ ~
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pdbmat

Calculate Tirion's model from pdb structures

21 May 2013; Justin Lecher (jlec) pdbmat-3.89.ebuild,
metadata.xml:
Correct license to CeCILL-2, #470788
alphaamd64armhppaia64ppcppc64sparcx86
3.89 ~ ~
sci-chemistry Homepage CeCILL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/phaser

A program for phasing macromolecular crystal structures

08 Apr 2015; Michał Górny (mgorny) phaser-2.1.4.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
2.1.4
sci-chemistry Homepage || ( phaser phaser-com ccp4 ) ChangeLog Metadata Similar Bugs Forums

sci-chemistry/platon

Versatile, SHELX-97 compatible, multipurpose crystallographic tool

19 Oct 2012; Justin Lecher (jlec) platon-20110126.ebuild,
metadata.xml:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
20110126 ~ ~ ~
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sci-chemistry/pointless

Scores crystallographic Laue and space groups

08 Apr 2015; Michał Górny (mgorny) pointless-1.6.14-r1.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
1.6.14-r1 ~ ~ ~
1.6.14 ~ ~ ~
1.6.2 + ~ +
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sci-chemistry/povscript+

Modified molscript that uses POV-Ray, does thermal ellipsoids, and more

*povscript+-2.1.2.2.20 (12 Jul 2013)
12 Jul 2013; Justin Lecher (jlec) -povscript+-2.1.2.2.18.ebuild,
povscript+-2.1.2.2.19.ebuild, +povscript+-2.1.2.2.20.ebuild, metadata.xml:
Version Bump; drop old; fix upstreams new webpresents, #476582
alphaamd64armhppaia64ppcppc64sparcx86
2.1.2.2.20 ~ ~ ~
2.1.2.2.19 ~ ~ ~
sci-chemistry Homepage glut molscript ChangeLog Metadata Similar Bugs Forums

sci-chemistry/prekin

Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files

24 Oct 2012; Ulrich Müller (ulm) prekin-6.51.081122-r1.ebuild:
Update dependency after package move from x11-libs/openmotif to
x11-libs/motif.
alphaamd64armhppaia64ppcppc64sparcx86
6.51.081122-r1 ~ ~ ~
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sci-chemistry/probe

Evaluates atomic packing within or between molecules

06 Aug 2015; Agostino Sarubbo (ago) probe-2.13.110909.ebuild:
Stable for amd64, wrt bug #556816
alphaamd64armhppaia64ppcppc64sparcx86
2.13.110909 + ~ ~
2.12.110413 + + +
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sci-chemistry/procheck

Checks the stereochemical quality of a protein structure

*procheck-3.5.4-r2 (05 Jan 2015)
05 Jan 2015; Justin Lecher (jlec) +procheck-3.5.4-r2.ebuild,
+files/procheck-3.5.4-close.patch, metadata.xml:
Add patch to fix problems with newer gfortran, thanks xarthisius for the
patch
alphaamd64armhppaia64ppcppc64sparcx86
3.5.4-r2 ~ ~
3.5.4-r1 + +
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sci-chemistry/prodecomp

Decomposition-based analysis of NMR projections

15 Apr 2015; Justin Lecher (jlec) metadata.xml,
prodecomp-3.0.ebuild:
Drop old; Bump EAPI and python eclasses
alphaamd64armhppaia64ppcppc64sparcx86
3.0-r1 ~ ~
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sci-chemistry/propka

Prediction of the pKa values of ionizable groups in proteins and protein-ligand complexes

11 Feb 2015; Justin Lecher (jlec) propka-3.1_p140511.ebuild:
Add RESTRICT="mirror bindist", #539784
alphaamd64armhppaia64ppcppc64sparcx86
3.1_p140511 ~ ~
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sci-chemistry/psi

Suite of ab initio quantum chemistry programs to compute various molecular properties

19 Feb 2013; Justin Lecher (jlec) psi-3.4.0-r2.ebuild:
Add missing dep on virtual/pkgconfig
alphaamd64armhppaia64ppcppc64sparcx86
3.4.0-r2 + +
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sci-chemistry/PyMca

X-ray Fluorescence Toolkit

08 Apr 2015; Michał Górny (mgorny) PyMca-4.6.2-r1.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
4.6.2-r1 ~ ~
4.6.2 ~ ~
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sci-chemistry/pymol

A Python-extensible molecular graphics system

26 May 2015; Justin Lecher (jlec) pymol-1.7.0.1.ebuild:
Move to virtual
alphaamd64armhppaia64ppcppc64sparcx86
1.7.6.0 ~ ~ ~
1.7.4.0 ~ ~ ~
1.7.0.1 + ~ +
sci-chemistry Homepage PSF-2.2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-apbs-plugin

APBS plugin for pymol

08 Apr 2015; Michał Górny (mgorny)
pymol-apbs-plugin-2.1_p26.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
2.1_p26-r1 + ~ +
2.1_p26 + ~ ~
2.1_p24 ~ ~ ~
0_p18 + ~ +
0_p15 ~ ~ +
sci-chemistry Homepage pymol ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-plugins-bni-tools

Gives Pymol additional functionalities and presets to the PyMOL GUI

*pymol-plugins-bni-tools-0.27 (15 Jul 2013)
15 Jul 2013; Justin Lecher (jlec)
+pymol-plugins-bni-tools-0.27.ebuild, metadata.xml:
Version Bump; move to new python eclasses
alphaamd64armhppaia64ppcppc64sparcx86
0.27 ~ ~
0.25.1 ~ ~
sci-chemistry Homepage CNRI ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-plugins-caver

Calculation of pathways from buried cavities to outside solvent in protein structures

15 Apr 2015; Justin Lecher (jlec)
-pymol-plugins-caver-2.1.1.ebuild, metadata.xml,
pymol-plugins-caver-2.1.2.ebuild:
Drop old; Bump EAPI and python eclasses
alphaamd64armhppaia64ppcppc64sparcx86
2.1.2 ~ ~ ~
sci-chemistry Homepage CAVER ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-plugins-dssp

DSSP Plugin for PyMOL

*pymol-plugins-dssp-110430-r1 (02 Dec 2013)
02 Dec 2013; Justin Lecher (jlec)
-pymol-plugins-dssp-110412.ebuild, -pymol-plugins-dssp-110413.ebuild,
+pymol-plugins-dssp-110430-r1.ebuild, metadata.xml:
Bump to python-r1.eclass; drop old
alphaamd64armhppaia64ppcppc64sparcx86
110430-r1 ~ ~
110430 ~ ~
sci-chemistry Homepage BSD pymol ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-plugins-dynamics

Molecular dynamics in Pymol

08 Apr 2015; Michał Górny (mgorny)
pymol-plugins-dynamics-1.2.0.ebuild:
Drop old Python implementations
alphaamd64armhppaia64ppcppc64sparcx86
1.2.0 ~ ~
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sci-chemistry/pymol-plugins-emovie

eMovie is a plug-in tool for the molecular visualization program PyMOL

*pymol-plugins-emovie-1.0.4 (25 Feb 2010)
25 Feb 2010; Justin Lecher (jlec)
+files/1.0.4-indent.patch, +pymol-plugins-emovie-1.0.4.ebuild,
+metadata.xml:
eMovie is a free tool that makes the creation of molecular movies both
easy and intuitive via a breakthrough storyboard interface, similar in
nature to what is used in the creation of traditional movies. eMovie is a
plug-in for PyMOL, a powerful, open source, and multi-platform molecular
graphics program.
alphaamd64armhppaia64ppcppc64sparcx86
1.0.4 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-plugins-msms

GUI for MSMS and displaying its results in PyMOL

*pymol-plugins-msms-100415-r1 (02 Dec 2013)
02 Dec 2013; Justin Lecher (jlec)
+pymol-plugins-msms-100415-r1.ebuild, metadata.xml:
Bump to python-r1.eclass
alphaamd64armhppaia64ppcppc64sparcx86
100415-r1 ~ ~
100415 ~ ~
sci-chemistry Homepage BSD pymol ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-plugins-promol

Fast and accurate regognition of active sites

12 Feb 2015; Justin Lecher (jlec)
pymol-plugins-promol-3.0.2-r1.ebuild:
Fix typo and fetch from upstream directly, #539786
alphaamd64armhppaia64ppcppc64sparcx86
3.0.2-r1 ~ ~
sci-chemistry Homepage all-rights-reserved ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-plugins-psico

Pymol ScrIpt COllection

*pymol-plugins-psico-3.1-r1 (29 May 2015)
29 May 2015; Justin Lecher (jlec)
+pymol-plugins-psico-3.1-r1.ebuild, -pymol-plugins-psico-3.0.ebuild,
-pymol-plugins-psico-3.1.ebuild, metadata.xml:
Move to EAPI=5 and new python eclasses, bug #544720; thanks Ian Delaney for
the patch
alphaamd64armhppaia64ppcppc64sparcx86
3.1-r1 ~ ~
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sci-chemistry/rasmol

Molecular Graphics Visualisation Tool

17 Jun 2015; Justin Lecher (jlec) -rasmol-2.7.5.2-r1.ebuild,
rasmol-2.7.5.2-r2.ebuild:
Fix compilation problems on ppc, bug #547318; drop old
alphaamd64armhppaia64ppcppc64sparcx86
2.7.5.2-r2 + + +
sci-chemistry Homepage || ( GPL-2 RASLIC ) ChangeLog Metadata Similar Bugs Forums

sci-chemistry/raster3d

Generation high quality raster images of proteins or other molecules

*raster3d-3.0.3 (24 Jul 2014)
24 Jul 2014; Justin Lecher (jlec) +raster3d-3.0.3.ebuild,
metadata.xml:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
3.0.3 ~ ~ ~
3.0.2 + + +
sci-chemistry Homepage Artistic-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/reduce

Adds hydrogens to a Protein Data Bank (PDB) molecule structure file

*reduce-3.16.111118 (07 Dec 2012)
07 Dec 2012; Justin Lecher (jlec) +reduce-3.16.111118.ebuild,
metadata.xml:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
3.16.111118 ~ ~ ~
3.14.080821 ~ ~ ~
3.13.080428-r1 + + +
sci-chemistry Homepage richardson ChangeLog Metadata Similar Bugs Forums

sci-chemistry/refmac

Macromolecular crystallographic refinement program

06 Jan 2014; Justin Lecher (jlec) refmac-5.5.0110-r3.ebuild:
Punt base.eclass
alphaamd64armhppaia64ppcppc64sparcx86
5.5.0110-r3 + + +
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sci-chemistry/relax

Molecular dynamics by NMR data analysis

*relax-3.3.8 (04 Apr 2015)
04 Apr 2015; Justin Lecher (jlec) +relax-3.3.8.ebuild:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
3.3.8 ~ ~
3.3.7 ~ ~
3.3.6 ~ ~
3.3.5 ~ ~
3.3.4 ~ ~
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sci-chemistry/scala

Scale together multiple observations of reflections

04 Jul 2015; Patrice Clement (monsieurp) scala-3.3.20.ebuild:
Update blocker on scala-bin (package has moved to dev-lang/). Fix bug 553912.
alphaamd64armhppaia64ppcppc64sparcx86
3.3.20 + + +
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sci-chemistry/sfcheck

Program for assessing the agreement between the atomic model and X-ray data or EM map

19 Jun 2013; Sébastien Fabbro (bicatali) metadata.xml:
sci-chemistry only
alphaamd64armhppaia64ppcppc64sparcx86
7.03.18-r1 + ~ +
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sci-chemistry/shelx

Programs for crystal structure determination from single-crystal diffraction data

05 Mar 2015; Justin Lecher (jlec) metadata.xml:
Drop unused local USE
alphaamd64armhppaia64ppcppc64sparcx86
20141228 + + +
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sci-chemistry/solve-resolve-bin

Automated crystallographic structure solution for MIR, SAD, and MAD

09 Jan 2015; Justin Lecher (jlec) solve-resolve-bin-2.13.ebuild,
metadata.xml:
Bump EAPI; do some QA
alphaamd64armhppaia64ppcppc64sparcx86
2.13 + +
sci-chemistry Homepage solve ChangeLog Metadata Similar Bugs Forums

sci-chemistry/sparky

Graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers

20 Mar 2015; Justin Lecher (jlec) -sparky-3.115.ebuild,
sparky-3.115-r1.ebuild:
Fix tcl/tk slotting; drop old
alphaamd64armhppaia64ppcppc64sparcx86
3.115-r1 ~ ~
sci-chemistry Homepage sparky ChangeLog Metadata Similar Bugs Forums

sci-chemistry/suitename

The ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development

23 Jul 2012; Justin Lecher (jlec) suitename-0.3.070628.ebuild:
Change order of sed, #427476
alphaamd64armhppaia64ppcppc64sparcx86
0.3.070628 ~ ~
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sci-chemistry/surf

Solvent accesible Surface calculator

11 Apr 2013; Ulrich Müller (ulm) surf-1.0.ebuild:
Fix LICENSE, see README file.
alphaamd64armhppaia64ppcppc64sparcx86
1.0 ~ ~ ~
sci-chemistry Homepage SURF ChangeLog Metadata Similar Bugs Forums

sci-chemistry/theseus

Maximum likelihood superpositioning and analysis of macromolecular structures

*theseus-3.3.0 (03 Jul 2015)
03 Jul 2015; Justin Lecher (jlec) +theseus-3.3.0.ebuild,
-theseus-1.6.2-r1.ebuild, -theseus-2.0.1-r1.ebuild, -theseus-2.0.3.ebuild,
theseus-2.0.6.ebuild, theseus-3.0.0.ebuild:
Version Bump; drop old
alphaamd64armhppaia64ppcppc64sparcx86
3.3.0 ~ ~
3.0.0 ~ ~
2.0.6 ~ ~
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sci-chemistry/threeV

3V: Voss Volume Voxelator

30 Oct 2010; Justin Lecher (jlec) threeV-1.2.ebuild:
Keyworded for ~-linux prefix
alphaamd64armhppaia64ppcppc64sparcx86
1.2 ~ ~
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sci-chemistry/tinker

Molecular modeling package that includes force fields, such as AMBER and CHARMM

*tinker-7.1.2 (21 Jun 2015)
21 Jun 2015; Justin Lecher (jlec) +files/7.1.2-openmp.patch,
+files/tinker-7.1.2-build.patch, +tinker-7.1.2.ebuild, -tinker-5.1.09.ebuild,
-tinker-6.ebuild:
Version Bump, bug #390165, bug #521292; drop old, obsolets bug #478596, bug
#552712
alphaamd64armhppaia64ppcppc64sparcx86
7.1.2 ~ ~
sci-chemistry Homepage Tinker ChangeLog Metadata Similar Bugs Forums

sci-chemistry/tm-align

Quick & Accurate Structural Alignment

18 May 2015; Justin Lecher (jlec) -tm-align-20130511.ebuild:
Drop old
alphaamd64armhppaia64ppcppc64sparcx86
20140601 + + + +
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sci-chemistry/viewmol

Open-source graphical front end for computational chemistry programs

24 Oct 2012; Ulrich Müller (ulm) viewmol-2.4.1-r2.ebuild:
Update dependency after package move from x11-libs/openmotif to
x11-libs/motif.
alphaamd64armhppaia64ppcppc64sparcx86
2.4.1-r2 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/vmd

Visual Molecular Dynamics

31 Jul 2015; Justin Lecher (jlec) vmd-1.9.2.ebuild:
Depend on newer tk
alphaamd64armhppaia64ppcppc64sparcx86
1.9.2 ~ ~
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sci-chemistry/votca-csg

Votca coarse-graining engine

16 Mar 2015; Agostino Sarubbo (ago) votca-csg-1.2.4-r1.ebuild:
Stable for x86, wrt bug #526968
alphaamd64armhppaia64ppcppc64sparcx86
1.2.4-r1 + +
1.2.2 + +
sci-chemistry Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/votca-csgapps

Extra applications for votca-csg

16 Mar 2015; Agostino Sarubbo (ago) votca-csgapps-1.2.4.ebuild:
Stable for x86, wrt bug #526968
alphaamd64armhppaia64ppcppc64sparcx86
1.2.4 + +
1.2.2 + +
sci-chemistry Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

*wxmacmolplt-7.5 (06 Jan 2014)
06 Jan 2014; Justin Lecher (jlec) +wxmacmolplt-7.5.ebuild,
+files/wxmacmolplt-7.5-glew.patch:
Version Bump, #439438; thanks Reinis Danne <rei4dan@gmail.com> for the ebuild
alphaamd64armhppaia64ppcppc64sparcx86
7.5 ~ ~
7.4.2 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/xds-bin

X-ray Detector Software for processing single-crystal monochromatic diffraction data

*xds-bin-20150301 (03 Mar 2015)
03 Mar 2015; Justin Lecher (jlec) +xds-bin-20150301.ebuild,
-xds-bin-20141119.ebuild:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
20150301 ~ ~
sci-chemistry Homepage free-noncomm ChangeLog Metadata Similar Bugs Forums

sci-chemistry/xdsgui

GUI for XDS that is supposed to help both novice and experienced users

30 May 2013; Justin Lecher (jlec) xdsgui-0_p130530.ebuild:
Block QA Warning as package is prebuilt, add missing deo
alphaamd64armhppaia64ppcppc64sparcx86
0_p130530 ~ ~
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sci-chemistry/xdsi

A crude interface for running the XDS

11 Feb 2015; Justin Lecher (jlec) xdsi-0.92-r1.ebuild:
Add RESTRICT="mirror bindist", #470790
alphaamd64armhppaia64ppcppc64sparcx86
0.92-r1 ~ ~
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sci-chemistry/xdsstat-bin

Prints various statistics (that are not available from XDS itself)

13 Nov 2014; Justin Lecher (jlec) xdsstat-bin-140225.ebuild:
Drop glibc from deps
alphaamd64armhppaia64ppcppc64sparcx86
140225 ~ ~
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sci-chemistry/xia2

An automated data reduction system for crystallography

19 Jun 2013; Sébastien Fabbro (bicatali) metadata.xml:
sci-chemistry only
alphaamd64armhppaia64ppcppc64sparcx86
0.3.4.0 ~ ~ ~
0.3.3.3 ~ ~ ~
0.3.3.1 + ~ +
0.3.1.7 ~ ~ ~
0.3.1.6 ~ ~
0.3.1.0 ~ ~
sci-chemistry Homepage BSD ChangeLog Metadata Similar Bugs Forums

sci-chemistry/xyza2pipe

Cross conversion environment of NMR spectra

*xyza2pipe-20121001 (28 Nov 2013)
28 Nov 2013; Justin Lecher (jlec) +xyza2pipe-20121001.ebuild,
+files/xyza2pipe-20121001-gentoo.patch, metadata.xml:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
20121001 ~ ~
20101129 ~ ~
sci-chemistry Homepage olivia ChangeLog Metadata Similar Bugs Forums

Last update:
30 Aug 2015
02:01 UTC

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