113 Packages in sci-chemistry

Portage Tree » sci-chemistry

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Modified molscript that uses POV-Ray, does thermal ellipsoids, and more - Versions: (glut molscript)
GromacsWrapper
Python framework for Gromacs - Versions: 0.3.1, 0.3.2, 0.5.1 (GPL-3 LGPL-3)
PyMca
X-ray Fluorescence Toolkit - Versions: 4.6.2-r1 (GPL-2)
acpype
AnteChamber PYthon Parser interfacE - Versions: 389 (GPL-3)
ambertools
A suite for carrying out complete molecular mechanics investigations - Versions: 1.5-r1 (GPL-2)
apbs
Evaluation of electrostatic properties of nanoscale biomolecular systems - Versions: 1.4.1-r2 (BSD)
aqua
Program suite in this distribution calculates restraint violations - Versions: 3.2-r2 (procheck)
aria
Automated NOE assignment and NMR structure calculation - Versions: 2.3.2_p20130826 (cns)
autodock
A suite of automated docking tools - Versions: 4.2.6 (GPL-2)
autodock_vina
Program for drug discovery, molecular docking and virtual screening - Versions: 1.1.2 (Apache-2.0)
avogadro
Advanced molecular editor that uses Qt4 and OpenGL - Versions: 1.1.0, 1.0.3-r2, 1.1.1 (GPL-2)
avogadro2
Advanced molecule editor and visualizer 2 - Versions: 0.7.2, 0.8.0 (BSD GPL-2+)
azara
A suite of programmes to process and view NMR data - Versions: 2.8-r5 (AZARA)
ball
Biochemical Algorithms Library - Versions: 1.4.2-r1 (LGPL-2 GPL-3)
bkchem
Chemical drawing program - Versions: 0.14.0_pre2-r1 (GPL-2)
bodr
The Blue Obelisk Data Repository listing element and isotope properties - Versions: 10, 9-r1 (MIT)
burrow-owl
Visualize multidimensional nuclear magnetic resonance (NMR) spectra - Versions: 1.5.1 (GPL-2)
cara-bin
Analysis of NMR spectra and Computer Aided Resonance Assignment - Versions: 1.8.4-r1 (CARA)
ccpn
The Collaborative Computing Project for NMR - Versions: 2.4.2, 2.4.1_p150226, 2.4.2_p150325, 2.4.2_p150413, 2.4.2_p150421 (|| ( CCPN LGPL-2.1 ))
chemical-mime-data
A collection of data files to add support for chemical MIME types - Versions: 0.1.94-r3, 0.1.94-r2 (LGPL-2.1)
chemtool
A GTK program for drawing organic molecules - Versions: 1.6.14, 1.6.13 (GPL-2)
clashlist
Build lists of van der Waals clashes from an input PDB file - Versions: 3.17-r1 (richardson)
cluster
Build lists of collections of interacting items - Versions: 1.3.081231-r1, 1.3.081231 (richardson)
cns
Crystallography and NMR System - Versions: 1.3_p7-r1, 1.2.1-r8 (cns)
coot
Crystallographic Object-Oriented Toolkit - Versions: 0.8.2-r1 (GPL-3)
cyana
Combined assignment and dynamics algorithm for NMR applications - Versions: 2.1 (CYANA)
dssp
The protein secondary structure standard - Versions: 2.2.1-r1 (Boost-1.0)
easychem
Chemical structure drawing program - focused on presentation - Versions: 0.6-r1 (GPL-2)
eden
A crystallographic real-space electron-density refinement and optimization program - Versions: 5.3-r2 (GPL-2)
elem
periodic table of the elements - Versions: 1.0.3-r1, 1.0.3-r2 (GPL-2)
freeon
An experimental suite of programs for linear scaling quantum chemistry - Versions: 1.0.8-r1, 1.0.10 (GPL-3)
gabedit
GUI for computational chemistry packages - Versions: 2.4.6, 2.4.8, 2.4.7 (MIT)
gamess
A powerful quantum chemistry package - Versions: 20110811.1 (gamess)
gamessq
Simple job manager for GAMESS-US - Versions: 1.2 (GPL-3)
gelemental
Periodic table viewer with detailed information on the chemical elements - Versions: 1.2.0-r1 (GPL-3 MIT)
ghemical
Chemical quantum mechanics and molecular mechanics - Versions: 2.99.2-r2, 3.0.0 (GPL-2)
gperiodic
Periodic table application for Linux - Versions: 2.0.10-r2, 3.0.1 (GPL-2)
gromacs
The ultimate molecular dynamics simulation package - Versions: 2016, 2016.1, 4.6.9999, 2016.3, 5.0.9999, 2016.2, 5.1.3, 2016.9999, 9999, 5.0.4, 5.1.9999 (LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD ))
gsim
Visualisation and processing of experimental and simulated NMR spectra - Versions: 21.3-r1, 21.3 (GPL-2)
gtk-gamess
GUI for GAMESS, a General Atomic and Molecular Electronic Structure System - Versions: 2.00 (GPL-2)
hollow
Production of surface images of proteins - Versions: 1.2-r1 (GPL-3)
icm
MolSoft LCC ICM Pro - Versions: 3.7.2e, 3.7.3b (MolSoft)
jmol
Java molecular viever for 3-D chemical structures - Versions: 12.2.27-r1, 12.0.45-r1 (LGPL-2.1)
ksdssp
ksdssp is an open source implementation of dssp - Versions: 040728, 040728-r1 (BSD)
mars
Robust automatic backbone assignment of proteins - Versions: 1.2 (all-rights-reserved)
massxpert
Software suite to predict/analyze mass spectrometric data on (bio)polymers - Versions: 3.4.0 (GPL-3)
mdanalysis
A python library to analyze and manipulate molecular dynamics trajectories - Versions: 0.7.7 (GPL-2)
mead
Macroscopic Electrostatics with Atomic Detail - Versions: 2.2.7, 2.2.7-r1 (GPL-2)
mm-align
Protein Complex Structural Alignment - Versions: 20120321 (tm-align)
molden
Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac - Versions: 5.5, 4.8-r2, 5.0 (MOLDEN)
moldy
Molecular dynamics simulations platform - Versions: 2.16e-r2 (GPL-2)
molequeue
Abstract, manage and coordinate execution of tasks - Versions: 0.8.0, 0.7.1 (BSD)
molmol
Publication-quality molecular visualization package - Versions: 2k_p2-r5, 2k_p2-r4, 2k_p2-r2, 2k_p2-r3 (molmol)
molscript
Display molecular 3D structures, such as proteins, in both schematic and detailed representations - Versions: 2.1.2-r2 (glut molscript)
molsketch
A drawing tool for 2D molecular structures - Versions: 0.2.0-r1, 0.3.0 (GPL-2)
mongochem
Application for managing large collections of chemical data - Versions: 0.7.0-r1 (BSD)
mopac7
Autotooled, updated version of a powerful, fast semi-empirical package - Versions: 1.15, 1.15-r1 (public-domain)
mpqc
The Massively Parallel Quantum Chemistry Program - Versions: 2.3.1-r4, 2.3.1-r1, 2.3.1-r2, 2.3.1-r3 (GPL-2)
msms-bin
MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces - Versions: 2.6.1-r1 (MSMS)
mustang
MUltiple STructural AligNment AlGorithm - Versions: 3.2.1, 3.2.2 (BSD)
namd
A powerful and highly parallelized molecular dynamics code - Versions: 2.9-r1, 2.10 (namd)
nmrglue
A module for working with NMR data in Python - Versions: 0.5-r1 (BSD)
numbat
new user-friendly method built for automatic dX-tensor determination - Versions: 0.999-r1 (GPL-3)
openbabel
Interconverts file formats used in molecular modeling - Versions: 2.3.2-r1 (GPL-2)
openbabel-perl
Perl bindings for OpenBabel - Versions: 2.3.2 (GPL-2)
openbabel-python
Python bindings for OpenBabel (including Pybel) - Versions: 2.3.2 (GPL-2)
ortep3
Thermal ellipsoid plot program for crystal structure illustrations - Versions: 1.0.3-r1 (public-domain)
p3d
Python module for structural bioinformatics - Versions: 9999, 0.4.3-r1 (GPL-3)
parassign
Assign protein nuclei solely on the basis of pseudocontact shifts (PCS) - Versions: 20130522 (Apache-2.0)
pdb-tools
Tools for manipulating and doing calculations on wwPDB macromolecule structure files - Versions: 0.2.1-r2, 0.2.1-r1 (GPL-3)
pdb2pqr
An automated pipeline for performing Poisson-Boltzmann electrostatics calculations - Versions: 1.9.0-r1 (BSD)
pdbcat
Manipulate and process PDB files using tools such as Perl, awk, etc - Versions: 1.3 (free-noncomm)
pdbcns
Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back - Versions: 2.0.010504 (BSD)
pdbmat
Calculate Tirion's model from pdb structures - Versions: 3.89 (CeCILL-2)
platon
Versatile, SHELX-97 compatible, multipurpose crystallographic tool - Versions: 20151001 (free-noncomm)
prekin
Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files - Versions: 6.51.081122-r1 (richardson)
probe
Evaluates atomic packing within or between molecules - Versions: 2.13.110909 (richardson)
procheck
Checks the stereochemical quality of a protein structure - Versions: 3.5.4-r1, 3.5.4-r2 (procheck)
prodecomp
Decomposition-based analysis of NMR projections - Versions: 3.0-r1 (GPL-2)
prody
Protein Dynamics Analysis - Versions: 1.6 (MIT)
propka
Prediction of the pKa values of ionizable groups in proteins and protein-ligand complexes - Versions: 3.1_p140511 (all-rights-reserved)
psi
Suite for ab initio quantum chemistry computing various molecular properties - Versions: 3.4.0-r2 (GPL-2)
pymol
A Python-extensible molecular graphics system - Versions: 1.8.4.0-r1 (PSF-2.2)
pymol-plugins-bni-tools
Gives Pymol additional functionalities and presets to the PyMOL GUI - Versions: 0.27 (CNRI)
pymol-plugins-caver
Calculation of pathways from buried cavities to outside solvent in protein structures - Versions: 2.1.2 (CAVER)
pymol-plugins-dssp
DSSP Plugin for PyMOL - Versions: 110430-r1 (BSD pymol)
pymol-plugins-dynamics
Molecular dynamics in Pymol - Versions: 1.2.0, 2.0.4 (GPL-3)
pymol-plugins-emovie
PyMOL plugin for convinient movie creation - Versions: 1.0.4 (GPL-2)
pymol-plugins-msms
GUI for MSMS and displaying its results in PyMOL - Versions: 100415-r1 (BSD pymol)
pymol-plugins-promol
Fast and accurate regognition of active sites - Versions: 3.0.2-r1 (all-rights-reserved)
pymol-plugins-psico
Pymol ScrIpt COllection - Versions: 3.1-r1 (BSD-2)
rasmol
Molecular Graphics Visualisation Tool - Versions: 2.7.5.2-r2 (|| ( GPL-2 RASLIC ))
raster3d
Generation high quality raster images of proteins or other molecules - Versions: 3.0.2, 3.0.3 (Artistic-2)
reduce
Adds hydrogens to a Protein Data Bank (PDB) molecule structure file - Versions: 3.14.080821, 3.16.111118, 3.13.080428-r1 (richardson)
relax
Molecular dynamics by NMR data analysis - Versions: 4.0.0-r1 (GPL-2)
shelx
Programs for crystal structure determination from single-crystal diffraction data - Versions: 20141228 (free-noncomm)
sparky
Graphical NMR assignment and integration program for large polymers - Versions: 3.115-r2 (sparky)
suitename
The ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development - Versions: 0.3.070628 (richardson)
surf
Solvent accesible Surface calculator - Versions: 1.0 (SURF)
theseus
Maximum likelihood superpositioning and analysis of macromolecular structures - Versions: 2.0.6, 3.3.0, 3.0.0 (GPL-3)
threeV
3V: Voss Volume Voxelator - Versions: 1.2 (GPL-2)
tinker
Molecular modeling package that includes force fields, such as AMBER and CHARMM - Versions: 7.1.2 (Tinker)
tm-align
Quick & Accurate Structural Alignment - Versions: 20140601, 20150914 (tm-align)
viewmol
Open-source graphical front end for computational chemistry programs - Versions: 2.4.1-r3 (GPL-2)
vmd
Visual Molecular Dynamics - Versions: 1.9.2 (vmd)
votca-csg
Votca coarse-graining engine - Versions: 9999, 1.4 (Apache-2.0)
votca-csgapps
Extra applications for votca-csg - Versions: 9999, 1.4 (Apache-2.0)
votca-xtp
Votca excitation and charge properties module - Versions: 9999, 1.4 (Apache-2.0)
wxmacmolplt
Chemical 3D graphics program with GAMESS input builder - Versions: 7.5-r1 (GPL-2)
xds-bin
Software for processing single-crystal X-ray monochromatic diffraction data - Versions: 20170430 (free-noncomm)
xdsgui
GUI for XDS that is supposed to help both novice and experienced users - Versions: 0_p130530 (GPL-2)
xdsstat-bin
Prints various statistics (that are not available from XDS itself) - Versions: 140225 (all-rights-reserved)
xyza2pipe
Cross conversion environment of NMR spectra - Versions: 20101129, 20121001 (olivia)
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