Difference between revisions of "Chemistry"
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|p5-Chemistry-InternalCoords | |p5-Chemistry-InternalCoords | ||
|Represent the position of an atom using internal coordinates | |Represent the position of an atom using internal coordinates | ||
| − | |[[ | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-InternalCoords/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-InternalCoords]] |
|- | |- | ||
|p5-Chemistry-Isotope | |p5-Chemistry-Isotope | ||
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|pcmsolver | |pcmsolver | ||
|API for the Polarizable Continuum Model | |API for the Polarizable Continuum Model | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/pcmsolver/pkg-descr?revision=HEAD]] [[https://github.com/PCMSolver/pcmsolver]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/pcmsolver/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/PCMSolver/pcmsolver]] |
|- | |- | ||
|py27-MDAnalysis | |py27-MDAnalysis | ||
|Python library to analyze molecular dynamics trajectories | |Python library to analyze molecular dynamics trajectories | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-MDAnalysis/pkg-descr?revision=HEAD]] [[https://www.mdanalysis.org]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-MDAnalysis/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.mdanalysis.org]] |
|- | |- | ||
|py27-MDAnalysisTests | |py27-MDAnalysisTests | ||
|Test code and the trajectory data for test cases of MDAnalysis | |Test code and the trajectory data for test cases of MDAnalysis | ||
| − | |[[https://www.mdanalysis.org]] | + | |[[File:1329059652.png|35px|link=https://www.mdanalysis.org]] |
|- | |- | ||
|py27-PyQuante | |py27-PyQuante | ||
|Quantum chemistry in Python | |Quantum chemistry in Python | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-PyQuante/pkg-descr?revision=HEAD]] [[http://pyquante.sourceforge.net/]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-PyQuante/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://pyquante.sourceforge.net/]] |
|- | |- | ||
|py27-pymol | |py27-pymol | ||
|OpenGL-based molecular visualization system | |OpenGL-based molecular visualization system | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-pymol/pkg-descr?revision=HEAD]] [[https://pymol.org/2/]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-pymol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://pymol.org/2/]] |
|- | |- | ||
|py37-MDAnalysis | |py37-MDAnalysis | ||
|Python library to analyze molecular dynamics trajectories | |Python library to analyze molecular dynamics trajectories | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-MDAnalysis/pkg-descr?revision=HEAD]] [[https://www.mdanalysis.org]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-MDAnalysis/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.mdanalysis.org]] |
|- | |- | ||
|py37-MDAnalysisTests | |py37-MDAnalysisTests | ||
|Test code and the trajectory data for test cases of MDAnalysis | |Test code and the trajectory data for test cases of MDAnalysis | ||
| − | |[[https://www.mdanalysis.org]] | + | |[[File:1329059652.png|35px|link=https://www.mdanalysis.org]] |
|- | |- | ||
|py37-avogadrolibs | |py37-avogadrolibs | ||
|Python bindings for Avogadro2 chemistry libraries | |Python bindings for Avogadro2 chemistry libraries | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-avogadrolibs/pkg-descr?revision=HEAD]] [[https://www.openchemistry.org/projects/avogadro2/]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-avogadrolibs/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.openchemistry.org/projects/avogadro2/]] |
|- | |- | ||
|py37-chainer-chemistry | |py37-chainer-chemistry | ||
|Library for deep learning in biology and chemistry | |Library for deep learning in biology and chemistry | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-chainer-chemistry/pkg-descr?revision=HEAD]] [[https://github.com/pfnet-research/chainer-chemistry]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-chainer-chemistry/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/pfnet-research/chainer-chemistry]] |
|- | |- | ||
|py37-chempy | |py37-chempy | ||
|Package useful for solving problems in chemistry | |Package useful for solving problems in chemistry | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-chempy/pkg-descr?revision=HEAD]] [[https://github.com/bjodah/chempy]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-chempy/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/bjodah/chempy]] |
|- | |- | ||
|py37-gpaw | |py37-gpaw | ||
|DFT and beyond within the projector-augmented wave method in chemistry | |DFT and beyond within the projector-augmented wave method in chemistry | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-gpaw/pkg-descr?revision=HEAD]] [[https://wiki.fysik.dtu.dk/gpaw/]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-gpaw/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://wiki.fysik.dtu.dk/gpaw/]] |
|- | |- | ||
|py37-molmod | |py37-molmod | ||
|Collection of molecular modelling tools for python | |Collection of molecular modelling tools for python | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-molmod/pkg-descr?revision=HEAD]] [[https://github.com/molmod/molmod]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-molmod/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/molmod/molmod]] |
|- | |- | ||
|py37-qcelemental | |py37-qcelemental | ||
|Essentials for quantum chemistry | |Essentials for quantum chemistry | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-qcelemental/pkg-descr?revision=HEAD]] [[https://github.com/MolSSI/QCElemental]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-qcelemental/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/MolSSI/QCElemental]] |
|- | |- | ||
|py37-qcengine | |py37-qcengine | ||
|Quantum chemistry program executor and IO standardizer (QCSchema) | |Quantum chemistry program executor and IO standardizer (QCSchema) | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-qcengine/pkg-descr?revision=HEAD]] [[https://github.com/MolSSI/QCEngine]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-qcengine/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/MolSSI/QCEngine]] |
|- | |- | ||
|py37-qspin | |py37-qspin | ||
|Learn quantum spin and entanglement | |Learn quantum spin and entanglement | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-qspin/pkg-descr?revision=HEAD]] [[https://bitbucket.org/donald_gavel/qspin]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-qspin/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://bitbucket.org/donald_gavel/qspin]] |
|- | |- | ||
|py37-rmf | |py37-rmf | ||
|Library to support reading and writing of Rich Molecular Format files | |Library to support reading and writing of Rich Molecular Format files | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-rmf/pkg-descr?revision=HEAD]] [[https://integrativemodeling.org/rmf/]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-rmf/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://integrativemodeling.org/rmf/]] |
|- | |- | ||
|py37-scoria | |py37-scoria | ||
|Lightweight molecule manipulation codebase | |Lightweight molecule manipulation codebase | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/py-scoria/pkg-descr?revision=HEAD]] [[https://git.durrantlab.com/jdurrant/scoria]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-scoria/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://git.durrantlab.com/jdurrant/scoria]] |
|- | |- | ||
|qbox | |qbox | ||
|First-principles molecular dynamics code | |First-principles molecular dynamics code | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/qbox/pkg-descr?revision=HEAD]] [[http://qboxcode.org/]] | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/qbox/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://qboxcode.org/]] |
|- | |- | ||
|qmcpack | |qmcpack | ||
|Many-body ab initio Quantum Monte Carlo code for quantum chemstry | |Many-body ab initio Quantum Monte Carlo code for quantum chemstry | ||
| − | |[[https://svnweb.freebsd.org/ports/head/science/qmcpack/pkg-descr?revision=HEAD]] [[https://www.qmcpack.org/ | + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/qmcpack/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.qmcpack.org/]] |
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!colspan="3"| | !colspan="3"| | ||
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!colspan="3"| | !colspan="3"| | ||
|- | |- | ||
| − | !colspan="3"|'''Back to | + | !colspan="3"|'''Back to ''' [[image:Icon Disti GhostBSD.png|50px|link=Science and Engineering]] '''Science and Engineering''' |
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|} | |} | ||
[[Category:Station]] | [[Category:Station]] | ||
Latest revision as of 13:20, 20 January 2020
Welcome to the Chemistry
|
| App/Package | Abstract | Addition or Link |
|---|---|---|
| CheMPS2 | Spin-adapted implementation of DMRG for ab initio quantum chemistry |  
|
| Jmol | Java 3D viewer for chemical structures |
|
| MolScript | Display 3D molecules in schematic and detailed representations |
|
| atom-chemistry | Program for DFT calculations in atoms |
|
| avogadro2 | Chemical editor and visualization application |
|
| avogadrolibs | Avogadro2 libraries for chemical editor and visualization applications |
|
| bagel | Brilliantly Advanced General Electronic-structure Library |
|
| bodr | Chemistry data like element and isotope properties, atomic radii, etc |
|
| cdk-chemistry | Chemistry Development Kit |
|
| checkmol | Analyze molecules for the presence of functional groups |
|
| chemical-mime-data | Collection of chemical MIME types for UNIX desktops |
|
| chemtool | Draw organic molecules easily and store them |
|
| cp2k | Quantum chemistry and solid state physics software package |
|
| dalton | Powerful molecular electronic structure program for quantum chemistry |
|
| datawarrior | Chemistry-aware multi-purpose data visualization and analysis program |
|
| dkh | Wolf, Reiher, and Hess's Douglas-Kroll-Hess relativistic correction |
|
| dlpolyclassic | Molecular dynamics simulation package |
|
| elk-chemistry- | All-electron full-potential linearised augmented-planewave code |
|
| epte | Electronic Periodic Table of the Elements |
|
| erd | AcesIII electron repulsion integrals |
|
| erkale | Quantum chemistry program to solve the electronic structure of atoms |
|
| erkale-pseudopotentials | Pseudopotentials for Erkale, the quantum chemistry program |
|
| erkale-serial | Quantum chemistry program to solve the electronic structure of atoms |
|
| fleur | FLAPW code for atomic computations in quantum chemistry and physics |
|
| gabedit | Graphical user interface for several chemistry software packages |
|
| gamess-us | General Atomic and Molecular Electronic Structure System (US) |
|
| gchemutils | C++ classes and Gtk3 widgets related to chemistry |
|
| gdma | Anthony Stone's Gaussian Distributed Multipole Analysis |
|
| ghemical | Computational chemistry software package |
|
| gpaw-setups | Setups (data files) for py-gpaw, the DFT quantum chemistry software |
|
| gromacs | Compute molecular dynamics |
|
| iboview | Program for analyzing molecular electronic structure |
|
| jdftx | Software for joint density functional theory in chemistry |
|
| kalzium | Periodic table of elements for KDE 4 |
|
| kim-api | Framework for reliable, reproducible, portable molecular simulations |
|
| lammps | Classical molecular dynamics code with a focus on materials modeling |
|
| latte | Quantum chemistry: Density functional tight binding molecular dynamics |
|
| libccp4 | Protein X-ray crystallography toolkit |
|
| libcint | General GTO integrals for quantum chemistry |
|
| libefp | Effective fragment potential method in quantum chemistry |
|
| libgridxc | Library to compute the exchange and correlation energy and potentials |
|
| libint | Evaluate the integrals in modern atomic and molecular theory |
|
| liboglappth | Support libraries of science/ghemical port |
|
| libssm | C++ toolkit for superposition of macromolecules |
|
| lm-uiuc | Software for sampling trajectories of the reaction-diffusion equations |
|
| luscus | Molecular editor and viewer |
|
| madness | Multiresolution adaptive numeric environment for scientific simulation |
|
| massxpert | massXpert software for (bio)chemists |
|
| mdynamix | General purpose molecular dynamics code |
|
| mmdb2 | C++ toolkit for working with macromolecular coordinate files |
|
| mmtf-cpp | C++ MMTF format API, decoder and encoder, for molecular structures |
|
| mol2ps | Read molecular structure files and generate Postscript output |
|
| molgif | Tool to create GIF animations of molecules |
|
| molsketch | 2D molecule editor |
|
| mpqc | Massively Parallel Quantum Chemistry Program | 
|
| msms | Program to efficiently compute molecular surfaces |
|
| multiwfn | Multifunctional wavefunction analysis for quantum chemistry |
|
| namd | Computer software for molecular dynamics simulation |
|
| nwchem | High-performance computational chemistry software |
|
| nwchem-data | Data for NWChem, the computational chemistry software |
|
| openbabel | Chemical toolbox designed to speak the many languages of chemical data |
|
| openkim | Knowledgebase of Interatomic Models |
|
| openkim-models | Open Knowledgebase of Interatomic Models |
|
| opsin | Open Parser for Systematic IUPAC Nomenclature of chemical names |
|
| p5-Chemistry-3DBuilder | Generate 3D coordinates from a connection table |
|
| p5-Chemistry-Bond-Find | Detect bonds in a molecule and assign formal bond orders |
|
| p5-Chemistry-Canonicalize | Number the atoms in a molecule in a unique way |
|
| p5-Chemistry-Elements | Perl extension for working with Chemical Elements |
|
| p5-Chemistry-File-MDLMol | MDL molfile reader/write |
|
| p5-Chemistry-File-Mopac | MOPAC 6 input file reader/writer |
|
| p5-Chemistry-File-PDB | Perl module to read and write PDB files |
|
| p5-Chemistry-File-SLN | SLN linear notation parser/writer |
|
| p5-Chemistry-File-SMARTS | SMARTS chemical substructure pattern linear notation parser |
|
| p5-Chemistry-File-SMILES | SMILES linear notation parser/writer |
|
| p5-Chemistry-File-VRML | Generate VRML models for molecules |
|
| p5-Chemistry-File-XYZ | XYZ molecule format reader/writer |
|
| p5-Chemistry-FormulaPattern | Match molecule by formula |
|
| p5-Chemistry-InternalCoords | Represent the position of an atom using internal coordinates |
|
| p5-Chemistry-Isotope | Table of the isotopes exact mass data |
|
| p5-Chemistry-MacroMol | Perl toolkit to describe macromolecules |
|
| p5-Chemistry-MidasPattern | Select atoms in macromolecules |
|
| p5-Chemistry-Mok | Molecular awk interpreter |
|
| p5-Chemistry-Mol | Perl toolkit to describe molecules |
|
| p5-Chemistry-Pattern | Chemical substructure pattern matching |
|
| p5-Chemistry-Reaction | Represent a ring as a substructure of a molecule |
|
| p5-Chemistry-Ring | Represent a ring as a substructure of a molecule |
|
| p5-PerlMol | Perl modules for molecular chemistry |
|
| packmol | Pack molecules in defined regions of space |
|
| pcmsolver | API for the Polarizable Continuum Model |
|
| py27-MDAnalysis | Python library to analyze molecular dynamics trajectories |
|
| py27-MDAnalysisTests | Test code and the trajectory data for test cases of MDAnalysis |
|
| py27-PyQuante | Quantum chemistry in Python |
|
| py27-pymol | OpenGL-based molecular visualization system |
|
| py37-MDAnalysis | Python library to analyze molecular dynamics trajectories |
|
| py37-MDAnalysisTests | Test code and the trajectory data for test cases of MDAnalysis |
|
| py37-avogadrolibs | Python bindings for Avogadro2 chemistry libraries |
|
| py37-chainer-chemistry | Library for deep learning in biology and chemistry |
|
| py37-chempy | Package useful for solving problems in chemistry |
|
| py37-gpaw | DFT and beyond within the projector-augmented wave method in chemistry |
|
| py37-molmod | Collection of molecular modelling tools for python |
|
| py37-qcelemental | Essentials for quantum chemistry |
|
| py37-qcengine | Quantum chemistry program executor and IO standardizer (QCSchema) |
|
| py37-qspin | Learn quantum spin and entanglement |
|
| py37-rmf | Library to support reading and writing of Rich Molecular Format files |
|
| py37-scoria | Lightweight molecule manipulation codebase |
|
| qbox | First-principles molecular dynamics code |
|
| qmcpack | Many-body ab initio Quantum Monte Carlo code for quantum chemstry |
|
| If you don't find a package, you are looking for, we recommend to search the  Ports Collection.
| ||
Back to  Science and Engineering
| ||
