Tuesday

Monday

sci-chemistry/acpype

AnteChamber PYthon Parser interfacE

29 May 2013; Justin Lecher (jlec) acpype-389.ebuild:
Fix usage of new python r1 eclasses (missing PYTHON_REQUIRED_USE,
PYTHON_DEPS)
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

21 Aug 2014; Justin Lecher (jlec) apbs-1.4.1.ebuild,
+files/apbs-1.4.1-manip.patch, files/apbs-1.4.1-multilib.patch:
Fix build failure with USE=tools, #520126
alphaamd64armhppaia64ppcppc64sparcx86
1.4.1 ~ ~ ~
1.3-r3 ~ ~ ~
1.2.1b-r4 + + +
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

06 Jan 2014; Justin Lecher (jlec) aria-2.3.2-r3.ebuild:
Punt base.eclass
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2_p20130826 ~ ~
sci-chemistry Homepage cns ChangeLog Metadata Similar Bugs Forums

sci-chemistry/arp-warp-bin

Software for improvement and interpretation of crystallographic electron density maps

04 Jun 2013; Justin Lecher (jlec) arp-warp-bin-7.1-r2.ebuild:
Fix for correct usage of new python eclasses
alphaamd64armhppaia64ppcppc64sparcx86
7.3 ~ ~
7.1-r2 ~ ~
7.1-r1 + +
sci-chemistry Homepage ArpWarp ChangeLog Metadata Similar Bugs Forums

sci-chemistry/autodock

A suite of automated docking tools

26 Jun 2011; Justin Lecher (jlec) autodock-4.2.3-r1.ebuild:
Straight out QA issues
alphaamd64armhppaia64ppcppc64sparcx86
4.2.3-r1 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/autodock_vina

Program for drug discovery, molecular docking and virtual screening

19 Aug 2013; Justin Lecher (jlec) -autodock_vina-1.1.1-r1.ebuild:
Drop old fixes problems with boost-1.52, #460264
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

*avogadro-1.0.3-r2 (06 Jan 2014)
06 Jan 2014; Justin Lecher (jlec) -avogadro-1.0.3-r1.ebuild,
+avogadro-1.0.3-r2.ebuild, avogadro-1.1.0.ebuild:
Punt base.eclass; bump to python-single-r1.eclass
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

06 Jul 2014; Justin Lecher (jlec) azara-2.8-r4.ebuild,
azara-2.8-r5.ebuild:
Add missing dep on x11-libs/motif, #515000
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

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 (12 Aug 2010)
12 Aug 2010; Justin Lecher (jlec) +bkchem-0.14.0_pre2.ebuild:
Version BUmp
alphaamd64armhppaia64ppcppc64sparcx86
0.14.0_pre2 ~ ~
0.14.0_pre1-r2 ~ ~
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

15 Oct 2014; Pacho Ramos (pacho) cara-bin-1.8.4-r1.ebuild,
cara-bin-1.8.4.ebuild:
Support multilib providers for deps. Bump to EAPI=5.
alphaamd64armhppaia64ppcppc64sparcx86
1.8.4-r1 ~ ~
1.8.4 ~ ~
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

27 Feb 2013; Justin Lecher (jlec) files/6.1.3-lapack.patch,
ccp4-apps-6.1.3-r11.ebuild, ccp4-apps-6.1.3-r12.ebuild:
Use PKG_CONFIG instead of generic pkg-config
alphaamd64armhppaia64ppcppc64sparcx86
6.1.3-r12 ~ ~ ~
6.1.3-r11 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ccp4i

Protein X-ray crystallography toolkit -- graphical interface

06 Jan 2014; Justin Lecher (jlec) ccp4i-6.1.3-r3.ebuild:
Punt base.eclass
alphaamd64armhppaia64ppcppc64sparcx86
6.1.3-r3 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/ccpn

The Collaborative Computing Project for NMR

*ccpn-2.4.1_p141020 (20 Oct 2014)
20 Oct 2014; Justin Lecher (jlec) +ccpn-2.4.1_p141020.ebuild:
Todays python patches
alphaamd64armhppaia64ppcppc64sparcx86
2.4.1_p141020 ~ ~
2.4.1_p141008 ~ ~
2.4.1 ~ ~
2.4.0_p140925 ~ ~
2.4.0_p140917 ~ ~
2.4.0_p140915 ~ ~
2.3.1_p140425 ~ ~
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

24 Mar 2014; Agostino Sarubbo (ago) chemtool-1.6.13.ebuild:
Stable for ppc, wrt bug #501046
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

13 Jun 2012; Jeff Horelick (jdhore) clashlist-3.17.ebuild:
marked x86 per bug 419867
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

13 Jun 2012; Jeff Horelick (jdhore) cluster-1.3.081231.ebuild:
marked x86 per bug 419861
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

12 Oct 2014; Justin Lecher (jlec) coot-0.7.ebuild,
coot-0.7.1-r1.ebuild, coot-0.7.2.ebuild:
Fix Slot of mmdb dep
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

19 Jun 2013; Sébastien Fabbro (bicatali) metadata.xml:
Changed herd to sci-chemistry
alphaamd64armhppaia64ppcppc64sparcx86
2.1 ~ ~
sci-chemistry Homepage CYANA ChangeLog Metadata Similar Bugs Forums

sci-chemistry/dssp

The protein secondary structure standard

*dssp-2.2.1-r1 (25 Jun 2014)
25 Jun 2014; Justin Lecher (jlec) -dssp-2.2.1.ebuild,
+dssp-2.2.1-r1.ebuild:
Fix evil typo
alphaamd64armhppaia64ppcppc64sparcx86
2.2.1-r1 ~ ~
2.1.0 ~ ~
2.0.4 ~ ~
0.70831 + +
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

19 Feb 2013; Justin Lecher (jlec) eden-5.3-r1.ebuild,
metadata.xml:
Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
alphaamd64armhppaia64ppcppc64sparcx86
5.3-r1 + +
5.3 +
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

10 Aug 2014; Sergei Trofimovich (slyfox) freeon-1.0.8-r1.ebuild:
QA: drop trailing '.' from DESCRIPTION
alphaamd64armhppaia64ppcppc64sparcx86
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

*ghemical-3.0.0 (02 Feb 2013)
02 Feb 2013; Patrick Lauer (patrick) +ghemical-3.0.0.ebuild:
Bump
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

*gopenmol-3.00-r3 (04 Jul 2013)
04 Jul 2013; Justin Lecher (jlec) gopenmol-3.00-r2.ebuild,
+gopenmol-3.00-r3.ebuild, +files/3.00-impl-dec.patch,
+files/3.00-tcl8.6.patch, metadata.xml:
Bump to EAPI=5 and new python eclass, fix for tcl8.6; fix implicit
declarations; restrict license, #470782
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-5.0.2-r1 (21 Oct 2014)
21 Oct 2014; Christoph Junghans (ottxor) +gromacs-5.0.2-r1.ebuild:
fix bash completion (bug #526318)
alphaamd64armhppaia64ppcppc64sparcx86
5.0.2-r1 ~ ~ ~ ~ ~ ~
5.0.2 ~ ~ ~ ~ ~ ~
5.0.1 ~ ~ ~ ~ ~ ~
5.0 ~ ~ ~ ~ ~ ~
4.6.7 ~ ~ ~ ~ ~ ~
4.6.6 ~ ~ ~ ~ ~ ~
4.6.5 ~ + + + ~ +
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

*GromacsWrapper-0.3.2 (13 May 2014)
13 May 2014; Justin Lecher (jlec) +GromacsWrapper-0.3.2.ebuild:
Version Bump
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

*gsim-21.3 (09 Nov 2013)
09 Nov 2013; Justin Lecher (jlec) +gsim-21.3.ebuild,
+files/gsim-21.3-build.conf.patch:
Vesion Bump
alphaamd64armhppaia64ppcppc64sparcx86
21.3 ~ ~
21.0 ~ ~
0.20.1 ~ ~
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

04 May 2012; Jeff Horelick (jdhore) gtk-gamess-2.00.ebuild:
dev-util/pkgconfig -> virtual/pkgconfig
alphaamd64armhppaia64ppcppc64sparcx86
2.00 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/hollow

Production of surface images of proteins

*hollow-1.2 (03 Nov 2011)
03 Nov 2011; Justin Lecher (jlec) +hollow-1.2.ebuild,
metadata.xml:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
1.2 ~ ~
1.1 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/icm

MolSoft LCC ICM Pro

15 Oct 2014; Pacho Ramos (pacho) icm-3.7.2e.ebuild,
icm-3.7.3b.ebuild:
Support multilib providers for deps. Bump to EAPI=5.
alphaamd64armhppaia64ppcppc64sparcx86
3.7.3b ~ ~
3.7.2e ~ ~
sci-chemistry Homepage MolSoft ChangeLog Metadata Similar Bugs Forums

sci-chemistry/icm-browser

MolSoft LCC ICM Browser

16 Oct 2014; Pacho Ramos (pacho) icm-browser-3.6.1i.ebuild:
Support multilib providers for deps. Bump to EAPI=5.
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

*imosflm-1.0.7-r1 (08 Apr 2014)
08 Apr 2014; Samuli Suominen (ssuominen)
+files/1.0.7-libpng16.patch, +imosflm-1.0.7-r1.ebuild:
Fix broken embedded .png file for libpng16 wrt #467036 by Johan Hattne. The
patch has been applied also in upstream.
alphaamd64armhppaia64ppcppc64sparcx86
1.0.7-r1 ~ ~ ~
1.0.7 ~ ~ ~
1.0.5 + ~ +
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

*mdanalysis-0.7.7 (04 Jul 2013)
04 Jul 2013; Justin Lecher (jlec) +mdanalysis-0.7.7.ebuild,
+metadata.xml:
New addition written by me
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

16 Jan 2014; Justin Lecher (jlec) molequeue-0.7.1.ebuild:
Fix usex usage
alphaamd64armhppaia64ppcppc64sparcx86
0.7.1 ~ ~
0.6.1-r1 ~ ~
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

*molscript-2.1.2-r2 (14 Oct 2014)
14 Oct 2014; Justin Lecher (jlec) +molscript-2.1.2-r2.ebuild,
metadata.xml:
Bump to EAPI=5
alphaamd64armhppaia64ppcppc64sparcx86
2.1.2-r2 ~ ~ ~
2.1.2-r1 + + +
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sci-chemistry/molsketch

A drawing tool for 2D molecular structures

17 Sep 2014; Justin Lecher (jlec) molsketch-0.2.0-r1.ebuild:
Build with -DCMAKE_DISABLE_FIND_PACKAGE_KDE4=ON, #523020
alphaamd64armhppaia64ppcppc64sparcx86
0.2.0-r1 ~ ~
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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 ~ ~
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sci-chemistry/mopac7

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

03 Jan 2014; Ulrich Müller (ulm) mopac7-1.10-r1.ebuild,
mopac7-1.15.ebuild:
Fix LICENSE, bug 496688.
alphaamd64armhppaia64ppcppc64sparcx86
1.15 + + +
1.10-r1 ~ + +
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sci-chemistry/mosflm

A program for integrating single crystal diffraction data from area detectors

19 Jun 2013; Sébastien Fabbro (bicatali) metadata.xml:
Changed herd to sci-chemistry
alphaamd64armhppaia64ppcppc64sparcx86
7.0.9 ~ ~ ~
7.0.7-r2 ~ ~ ~
7.0.6-r2 + ~ +
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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 + + + +
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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 + +
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sci-chemistry/namd

A powerful and highly parallelized molecular dynamics code

13 Dec 2013; Nicolas Bock (nicolasbock) metadata.xml:
sci-chemistry/namd: Updated maintainer email to gentoo.org
alphaamd64armhppaia64ppcppc64sparcx86
2.9-r1 ~
2.9 ~
2.7_beta2-r1 ~
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sci-chemistry/nmrglue

A module for working with NMR data in Python

*nmrglue-0.4 (04 Apr 2013)
04 Apr 2013; Justin Lecher (jlec) +nmrglue-0.4.ebuild,
+metadata.xml:
New addition
alphaamd64armhppaia64ppcppc64sparcx86
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

24 Dec 2013; Agostino Sarubbo (ago) oasis-4.0-r3.ebuild:
Stable for x86, wrt bug #485944
alphaamd64armhppaia64ppcppc64sparcx86
4.0-r3 + ~ +
4.0-r2 + ~ +
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sci-chemistry/openbabel

Interconverts file formats used in molecular modeling

20 Feb 2013; Agostino Sarubbo (ago) openbabel-2.3.2.ebuild:
Add ~arm, wrt bug #455960
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2 ~ ~ ~ ~
2.3.1 ~ ~
2.3.0 ~ ~
2.2.3 + + + +
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sci-chemistry/openbabel-perl

Perl bindings for OpenBabel

20 Feb 2013; Agostino Sarubbo (ago) openbabel-perl-2.3.2.ebuild:
Add ~arm, wrt bug #455960
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2 ~ ~ ~ ~
2.3.1 ~ ~
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sci-chemistry/openbabel-python

Python bindings for OpenBabel (including Pybel)

13 Oct 2013; Pacho Ramos (pacho) openbabel-python-2.3.2.ebuild:
Also compatible with python3_3
alphaamd64armhppaia64ppcppc64sparcx86
2.3.2 ~ ~ ~ ~
2.3.1 ~ ~
2.3.0 ~ ~
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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)

04 Jun 2013; Justin Lecher (jlec) parassign-20130522.ebuild:
Fix deps for new python eclasses
alphaamd64armhppaia64ppcppc64sparcx86
20130522 ~ ~
sci-chemistry Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

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

31 Mar 2014; Michał Górny (mgorny) pdb-tools-0.2.1-r1.ebuild:
Add support for the new PyPy slotting.
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

19 Oct 2012; Justin Lecher (jlec) pdb2pqr-1.5.0-r2.ebuild,
pdb2pqr-1.7.0.ebuild, pdb2pqr-1.7.0-r2.ebuild:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
1.7.0-r2 ~ ~ ~
1.7.0 ~ ~ ~
1.5.0-r2 + + +
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

06 Jan 2014; Justin Lecher (jlec) phaser-2.1.4.ebuild,
metadata.xml:
Bump to EAPI=5; punt base.eclass; Bump to python-single-r1.eclass
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

16 Aug 2013; Justin Lecher (jlec) pointless-1.6.14-r1.ebuild:
Add back python eclass
alphaamd64armhppaia64ppcppc64sparcx86
1.6.14-r1 ~ ~ ~
1.6.14 ~ ~ ~
1.6.2 + ~ +
sci-chemistry Homepage ccp4 ChangeLog Metadata Similar Bugs Forums

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

alphaamd64armhppaia64ppcppc64sparcx86
2.13.110909 ~ ~ ~
2.12.110413 + + +
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sci-chemistry/procheck

Checks the stereochemical quality of a protein structure

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

sci-chemistry/prodecomp

Decomposition-based analysis of NMR projections

*prodecomp-3.0 (20 Oct 2010)
20 Oct 2010; Justin Lecher (jlec) +prodecomp-3.0.ebuild,
+metadata.xml:
Initital addition
alphaamd64armhppaia64ppcppc64sparcx86
3.0 ~ ~
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sci-chemistry/propka

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

30 Jun 2014; Mike Gilbert (floppym) propka-3.1_p140511.ebuild:
Depend on setuptools.
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

19 Jun 2013; Sébastien Fabbro (bicatali) metadata.xml:
Changed herd to sci-chemistry
alphaamd64armhppaia64ppcppc64sparcx86
4.6.2-r1 ~ ~
4.6.2 ~ ~
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sci-chemistry/pymol

A Python-extensible molecular graphics system

*pymol-1.7.3.2 (20 Oct 2014)
20 Oct 2014; Justin Lecher (jlec) +pymol-1.7.3.2.ebuild,
+files/pymol-9999-listing.patch, +files/pymol-9999-options.patch:
Version Bump
alphaamd64armhppaia64ppcppc64sparcx86
1.7.3.2 ~ ~ ~
1.7.3.1 ~ ~ ~
1.7.3.0 ~ ~ ~
1.7.2.1 ~ ~ ~
1.7.2.0 ~ ~ ~
1.7.1.3 ~ ~ ~
1.7.1.1 ~ ~ ~
1.7.0.4-r1 ~ ~ ~
1.7.0.4 ~ ~ ~
1.7.0.1 + ~ +
1.7.0.0 ~ ~ ~
1.6.0.0-r2 ~ ~ ~
1.6.0.0-r1 ~ ~ ~
1.6.0.0 ~ ~ ~
1.6.0_rc1 ~ ~ ~
1.5.0.3-r2 ~ ~ ~
1.5.0.3-r1 + + +
sci-chemistry Homepage PSF-2.2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/pymol-apbs-plugin

APBS plugin for pymol

13 Aug 2014; Andreas Schuerch (nativemad)
pymol-apbs-plugin-2.1_p26-r1.ebuild:
x86 stable, see bug 507142
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

*pymol-plugins-caver-2.1.2 (18 Mar 2011)
*pymol-plugins-caver-2.1.1 (18 Mar 2011)
18 Mar 2011; Justin Lecher (jlec)
+pymol-plugins-caver-2.1.1.ebuild, +pymol-plugins-caver-2.1.2.ebuild,
+metadata.xml:
Moved from sci-chemistry/caver to sci-chemistry/pymol-plugins-caver, Version
Bump
alphaamd64armhppaia64ppcppc64sparcx86
2.1.2 ~ ~ ~
2.1.1 ~ ~ ~
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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

29 May 2013; Justin Lecher (jlec)
pymol-plugins-dynamics-1.2.0.ebuild:
Fix usage of new python r1 eclasses (missing PYTHON_REQUIRED_USE,
PYTHON_DEPS)
alphaamd64armhppaia64ppcppc64sparcx86
1.2.0 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

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 ~ ~
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sci-chemistry/pymol-plugins-promol

Fast and accurate regognition of active sites

29 May 2013; Justin Lecher (jlec)
pymol-plugins-promol-3.0.2-r1.ebuild:
Fix usage of new python r1 eclasses (missing PYTHON_REQUIRED_USE)
alphaamd64armhppaia64ppcppc64sparcx86
3.0.2-r1 ~ ~
3.0.2 ~ ~
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sci-chemistry/pymol-plugins-psico

Pymol ScrIpt COllection

06 Nov 2012; Justin Lecher (jlec) pymol-plugins-psico-3.0.ebuild,
pymol-plugins-psico-3.1.ebuild:
Correct for moving of mmtk from sci-chemistry to sci-libs
alphaamd64armhppaia64ppcppc64sparcx86
3.1 ~ ~
3.0 ~ ~
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sci-chemistry/rasmol

Molecular Graphics Visualisation Tool

20 Dec 2012; Justin Lecher (jlec) -rasmol-2.7.5.1.ebuild,
metadata.xml:
Drop old version; fixes 438428
alphaamd64armhppaia64ppcppc64sparcx86
2.7.5.2 + + +
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-3.3.1 (10 Oct 2014)
10 Oct 2014; Justin Lecher (jlec) +relax-3.3.1.ebuild:
Version BUmp
alphaamd64armhppaia64ppcppc64sparcx86
9999
3.3.1 ~ ~
3.3.0 ~ ~
3.2.3 ~ ~
3.2.2 ~ ~
3.2.1 ~ ~
3.2.0 ~ ~
3.1.7-r1 ~ ~
3.1.7 ~ ~
3.1.6 ~ ~
3.1.5 ~ ~
3.1.4 ~ ~
3.1.3 ~ ~
3.1.2 ~ ~
3.1.1-r1 ~ ~
3.1.0-r2 ~ ~
3.0.2-r2 ~ ~
3.0.1 ~ ~
2.2.5 ~ ~
2.2.1 ~ ~
2.1.0 ~ ~
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sci-chemistry/scala

Scale together multiple observations of reflections

17 Dec 2012; Justin Lecher (jlec) -scala-3.3.18-r2.ebuild,
metadata.xml:
Drop old
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

*shelx-20140326 (19 May 2014)
19 May 2014; Justin Lecher (jlec) +shelx-20140326.ebuild:
Version BUmp
alphaamd64armhppaia64ppcppc64sparcx86
20140326 ~ ~ ~
20060317-r2 ~ ~ ~
20060317-r1 + + +
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sci-chemistry/solve-resolve-bin

Automated crystallographic structure solution for MIR, SAD, and MAD

03 Feb 2012; Justin Lecher (jlec) solve-resolve-bin-2.13.ebuild,
metadata.xml:
Correct QA_* , stable x86 tested by me
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

11 Nov 2013; Justin Lecher (jlec) sparky-3.115-r1.ebuild:
It also works with python 2.7
alphaamd64armhppaia64ppcppc64sparcx86
3.115-r1 ~ ~
3.115 ~ ~
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 ~ ~
sci-chemistry Homepage richardson ChangeLog Metadata Similar Bugs Forums

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-2.0.6 (06 Jun 2013)
06 Jun 2013; Justin Lecher (jlec) +theseus-2.0.6.ebuild:
Version BUmp; fix double prefix
alphaamd64armhppaia64ppcppc64sparcx86
2.0.6 ~ ~
2.0.3 ~ ~
2.0.1-r1 ~ ~
1.6.2-r1 ~ ~
sci-chemistry Homepage GPL-3 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/threeV

3V: Voss Volume Voxelator

30 Oct 2010; Justin Lecher (jlec) threeV-1.2.ebuild:
Keyworded for ~-linux prefix
alphaamd64armhppaia64ppcppc64sparcx86
1.2 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/tinker

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

19 Oct 2012; Justin Lecher (jlec) tinker-5.1.09.ebuild,
tinker-6.ebuild, metadata.xml:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
updated fortran-2.eclass
alphaamd64armhppaia64ppcppc64sparcx86
6 ~ ~
5.1.09 ~ ~
sci-chemistry Homepage Tinker ChangeLog Metadata Similar Bugs Forums

sci-chemistry/tm-align

Quick & Accurate Structural Alignment

*tm-align-20130511 (12 May 2013)
12 May 2013; Justin Lecher (jlec) -tm-align-20130508.ebuild,
+tm-align-20130511.ebuild:
Version BUmp, remove broken version
alphaamd64armhppaia64ppcppc64sparcx86
20130511 ~ ~ ~
20120707 ~ ~ ~
20120124 ~ ~
sci-chemistry Homepage tm-align ChangeLog Metadata Similar Bugs Forums

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

*vmd-1.9.1-r3 (21 Aug 2014)
21 Aug 2014; Justin Lecher (jlec) +vmd-1.9.1-r3.ebuild:
Drop arch specific NVCC flags
alphaamd64armhppaia64ppcppc64sparcx86
1.9.1-r3 ~ ~
1.9.1-r2 ~ ~
1.9.1-r1 ~ ~
1.9.1 ~ ~
sci-chemistry Homepage vmd ChangeLog Metadata Similar Bugs Forums

sci-chemistry/votca-csg

Votca coarse-graining engine

*votca-csg-1.2.4 (31 Aug 2014)
31 Aug 2014; Christoph Junghans (ottxor) +votca-csg-1.2.4.ebuild,
-votca-csg-1.2.3-r1.ebuild, -votca-csg-1.2.3.ebuild:
version bump
alphaamd64armhppaia64ppcppc64sparcx86
1.2.4 ~ ~
1.2.2 + +
sci-chemistry Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/votca-csgapps

Extra applications for votca-csg

*votca-csgapps-1.2.4 (31 Aug 2014)
31 Aug 2014; Christoph Junghans (ottxor)
+votca-csgapps-1.2.4.ebuild, -votca-csgapps-1.2.3.ebuild:
version bump
alphaamd64armhppaia64ppcppc64sparcx86
1.2.4 ~ ~
1.2.2 + +
sci-chemistry Homepage Apache-2.0 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/webmo

Web-based interface to computational chemistry packages

27 Jun 2011; Justin Lecher (jlec) webmo-6.1.010.ebuild,
webmo-7.0.003.ebuild, webmo-8.0.010.ebuild:
Added fetch restriction and dropped keywords
alphaamd64armhppaia64ppcppc64sparcx86
8.0.010
7.0.003
6.1.010
sci-chemistry Homepage WebMO 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-20140110 (06 Jul 2014)
06 Jul 2014; Justin Lecher (jlec) -xds-bin-20131111.ebuild,
+xds-bin-20140110.ebuild:
Version Bump, #516390
alphaamd64armhppaia64ppcppc64sparcx86
20140110 ~ ~
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 ~ ~
sci-chemistry Homepage GPL-2 ChangeLog Metadata Similar Bugs Forums

sci-chemistry/xdsi

A crude interface for running the XDS

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

sci-chemistry/xdsstat-bin

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

15 Oct 2014; Pacho Ramos (pacho) xdsstat-bin-140225.ebuild:
Support multilib providers for deps. Bump to EAPI=5.
alphaamd64armhppaia64ppcppc64sparcx86
140225 ~ ~
sci-chemistry Homepage all-rights-reserved ChangeLog Metadata Similar Bugs Forums

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:
21 Oct 2014
23:20 UTC

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