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Comment: Added adun.app, moved gdpc to output visualization
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Added note on GAMESS redistribution
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Deletions are marked like this. | Additions are marked like this. |
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|| ''[http://www.msg.ameslab.gov/GAMESS/GAMESS.html GAMESS]'' || || || || || | || ''[http://www.msg.ameslab.gov/GAMESS/GAMESS.html GAMESS]'' || || || || From the free academic license description on the GAMESS homepage: "The license acknowledges the Gordon group's exclusive distribution rights to GAMESS, and also prohibits you from making copies of the GAMESS code for any purpose except use at your own institution." so it is unlikely that Debian could distribute a package.|| |
Chemistry in Debian Science
The [http://cdd.alioth.debian.org/science/tasks/chemistry.html Sentinel page] gathers chemistry packages.
See [http://alioth.debian.org/projects/debichem debichem project on Alioth] - our [http://svn.debian.org/wsvn/debichem SVN] - Join us, if you want to help.
Chemistry tools included in Debian
Viewers/Editors
2D Viewers/Editors
[http://packages.debian.org/unstable/science/bkchem bkchem] Python based chemical structures editor
[http://packages.debian.org/unstable/science/chemtool chemtool] Chemical structures drawing program
[http://packages.debian.org/unstable/science/easychem easychem] Draw high-quality molecules and 2D chemical formulas
[http://packages.debian.org/unstable/science/gchempaint gchempaint] 2D chemical structures editor for the GNOME2 desktop
[http://packages.debian.org/unstable/science/xdrawchem xdrawchem] Chemical structures and reactions editor
3D Structure Viewers
[http://packages.debian.org/unstable/science/garlic garlic] A visualization program for biomolecules
[http://packages.debian.org/unstable/science/gcrystal gcrystal] lightweight crystal structures visualizer
[http://packages.debian.org/unstable/science/gdis gdis] molecular display
[http://packages.debian.org/unstable/science/rasmol rasmol] Visualize biological macromolecules
[http://packages.debian.org/unstable/science/v-sim v-sim] Visualize atomic structures
[http://packages.debian.org/unstable/science/xbs xbs] 3-d models and movies of molecules
[http://packages.debian.org/unstable/science/xmakemol xmakemol] A program for visualizing atomic and molecular systems
3D Viewers and Calculation Output Visualization
[http://packages.debian.org/unstable/science/adun.app adun.app] Molecular Simulator for GNUstep
[http://packages.debian.org/unstable/science/gabedit gabedit] graphical user interface to Ab Initio packages
[http://packages.debian.org/unstable/science/gausssum gausssum] parse and display Gaussian, GAMESS, and etc's output
[http://packages.debian.org/unstable/science/gdpc gdpc] visualiser of molecular dynamic simulations
[http://packages.debian.org/unstable/science/viewmol viewmol] A graphical front end for computational chemistry programs
3D Molecular Modelling and Visualization
[http://packages.debian.org/unstable/science/avogadro avogadro] advanced molecular editor
[http://packages.debian.org/unstable/gnome/ghemical ghemical] A GNOME molecular modelling environment
[http://packages.debian.org/unstable/science/pymol pymol] Molecular Graphics System
Calculations
Molecular Mechanics
[http://packages.debian.org/unstable/science/adun.app adun.app] Molecular Simulator for GNUstep
[http://packages.debian.org/unstable/science/avogadro avogadro] advanced molecular editor
[http://packages.debian.org/unstable/gnome/ghemical ghemical] A GNOME molecular modelling environment
[http://packages.debian.org/unstable/science/gromacs gromacs] Molecular dynamics simulator, with building and analysis tools
Semi Empirical
[http://packages.debian.org/unstable/science/mopac7-bin mopac7] Semi-empirical Quantum Chemistry Library
AbInitio
[http://packages.debian.org/unstable/science/mpqc mpqc] The Massively Parallel Quantum Chemistry Program
[http://packages.debian.org/unstable/science/psi3 psi3] Quantum Chemical Program Suite
[http://packages.qa.debian.org/a/abinit.html abinit ] A package for electronic structure calculations.
[http://packages.debian.org/unstable/openmx ?OpenMx] Package for nano-scale material simulations.
Other
[http://packages.debian.org/unstable/science/apbs apbs] Adaptive Poisson Boltzmann Solver
Utils
[http://packages.debian.org/unstable/science/openbabel openbabel] Chemical toolbox utilities
Other
[http://packages.debian.org/unstable/science/bodr bodr] Blue Obelisk Data Repository
[http://packages.debian.org/unstable/tex/chemeq chemeq] Parser for chemical formula and equilibria
[http://packages.debian.org/unstable/misc/chemical-mime-data chemical-mime-data] chemical MIME and file type support for desktops
[http://packages.debian.org/unstable/math/galculator galculator] A GTK+ 2.0 based calculator
[http://packages.debian.org/unstable/science/gcu-bin gcu-bin] GNOME chemistry utils (helper applications)
[http://packages.debian.org/unstable/science/gelemental gelemental] Periodic Table viewer
[http://packages.debian.org/unstable/science/gperiodic gperiodic] periodic table application
[http://packages.debian.org/unstable/science/kalzium kalzium] chemistry teaching tool for KDE
[http://packages.debian.org/unstable/games/katomic katomic] Atomic Entertainment game for KDE
[http://packages.debian.org/unstable/libs/libcdk-java libcdk-java] Chemistry Development Kit (CDK) Java libraries
[http://packages.debian.org/unstable/science/polyxmass polyxmass] Mass spectrometry software framework
Chemistry tools that could be considered for inclusion in Debian
[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..chemistry;users=debian-science@lists.debian.org Packages being worked on].
Package |
ITP |
alioth.d.o |
third party |
note |
[http://bioclipse.sourceforge.net bioclipse] |
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[http://wiki.bioclipse.net/index.php?title=Bioclipse_packaging_and_deployment bioclipse Wiki] |
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[http://www.cgl.ucsf.edu/chimera/ chimera] |
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From the free academic license description on the GAMESS homepage: "The license acknowledges the Gordon group's exclusive distribution rights to GAMESS, and also prohibits you from making copies of the GAMESS code for any purpose except use at your own institution." so it is unlikely that Debian could distribute a package. |
|
[http://www.csc.fi/gopenmol gopenmol] |
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unsure |
[http://jchempaint.sourceforge.net jchempaint] |
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main/contrib |
[http://jmol.sourceforge.net jmol] |
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GPL 2 vs ASL (not compatible) |
[http://mitglied.lycos.de/PageOfMH/ kmovisto] |
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dead upstream |
General overview for chemistry related software
http://sourceforge.net/softwaremap/trove_list.php?form_cat=384
http://rpmseek.com/cat/Applications/Scientific/Chemistry.html?hl=com&cx=2093
Useful resources
- See also [:Edutainment#chemistry:more...]