Difference between revisions of "Chemistry"

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(Created page with "{|class="wikitable" style="width:96.5%;background:#FFFFFF; border:2px solid #008000" |- |style="text-align:center;padding: 10px" | '''Welcome to the'''image:Icon Disti Gho...")
 
 
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! scope="col" style="width: 250px;"|'''Addition or Link'''
 
! scope="col" style="width: 250px;"|'''Addition or Link'''
 
|-
 
|-
−
|xxx
+
|CheMPS2
−
|xxx
+
|Spin-adapted implementation of DMRG for ab initio quantum chemistry
−
|xxx
+
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/chemps2/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/SebWouters/CheMPS2]]
 +
|-
 +
|Jmol
 +
|Java 3D viewer for chemical structures
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/jmol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://sourceforge.net/projects/jmol/]]
 +
|-
 +
|MolScript
 +
|Display 3D molecules in schematic and detailed representations
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/molscript/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://avatar.se/molscript/molscript.html]]
 +
|-
 +
|atom-chemistry
 +
|Program for DFT calculations in atoms
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/atom/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://departments.icmab.es/leem/siesta/]]
 +
|-
 +
|avogadro2
 +
|Chemical editor and visualization application
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/avogadro2/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.openchemistry.org/projects/avogadro2/]]
 +
|-
 +
|avogadrolibs
 +
|Avogadro2 libraries for chemical editor and visualization applications
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/avogadrolibs/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.openchemistry.org/projects/avogadro2/]]
 +
|-
 +
|bagel
 +
|Brilliantly Advanced General Electronic-structure Library
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/bagel/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://nubakery.org/]]
 +
|-
 +
|bodr
 +
|Chemistry data like element and isotope properties, atomic radii, etc
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/bodr/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://sourceforge.net/projects/bodr/]]
 +
|-
 +
|cdk-chemistry
 +
|Chemistry Development Kit
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/cdk/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://cdk.github.io/]]
 +
|-
 +
|checkmol
 +
|Analyze molecules for the presence of functional groups
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/checkmol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html]]
 +
|-
 +
|chemical-mime-data
 +
|Collection of chemical MIME types for UNIX desktops
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/chemical-mime-data/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://chemical-mime.sourceforge.net/]]
 +
|-
 +
|chemtool
 +
|Draw organic molecules easily and store them
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/chemtool/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://ruby.chemie.uni-freiburg.de/~martin/chemtool/]]
 +
|-
 +
|cp2k
 +
|Quantum chemistry and solid state physics software package
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/cp2k/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.cp2k.org/]]
 +
|-
 +
|dalton
 +
|Powerful molecular electronic structure program for quantum chemistry
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/dalton/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://daltonprogram.org/]]
 +
|-
 +
|datawarrior
 +
|Chemistry-aware multi-purpose data visualization and analysis program
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/datawarrior/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.openmolecules.org/]]
 +
|-
 +
|dkh
 +
|Wolf, Reiher, and Hess's Douglas-Kroll-Hess relativistic correction
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/dkh/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.reiher.ethz.ch/software/dkh-x2c.html]]
 +
|-
 +
|dlpolyclassic
 +
|Molecular dynamics simulation package
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/dlpoly-classic/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/]]
 +
|-
 +
|elk-chemistry-
 +
|All-electron full-potential linearised augmented-planewave code
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/elk/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://elk.sourceforge.net/]]
 +
|-
 +
|epte
 +
|Electronic Periodic Table of the Elements
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/epte/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.toddmiller.com/epte/]]
 +
|-
 +
|erd
 +
|AcesIII electron repulsion integrals
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/erd/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/psi4/erd]]
 +
|-
 +
|erkale
 +
|Quantum chemistry program to solve the electronic structure of atoms
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/erkale/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/susilehtola/erkale]]
 +
|-
 +
|erkale-pseudopotentials
 +
|Pseudopotentials for Erkale, the quantum chemistry program
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/erkale-pseudopotentials/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/susilehtola/erkale]]
 +
|-
 +
|erkale-serial
 +
|Quantum chemistry program to solve the electronic structure of atoms
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/erkale/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/susilehtola/erkale]]
 +
|-
 +
|fleur
 +
|FLAPW code for atomic computations in quantum chemistry and physics
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/fleur/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.flapw.de/pm/index.php]]
 +
|-
 +
|gabedit
 +
|Graphical user interface for several chemistry software packages
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/gabedit/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://sourceforge.net/projects/gabedit/]]
 +
|-
 +
|gamess-us
 +
|General Atomic and Molecular Electronic Structure System (US)
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/gamess-us/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.msg.chem.iastate.edu/gamess/]]
 +
|-
 +
|gchemutils
 +
|C++ classes and Gtk3 widgets related to chemistry
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/gchemutils/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.nongnu.org/gchemutils/]]
 +
|-
 +
|gdma
 +
|Anthony Stone's Gaussian Distributed Multipole Analysis
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/gdma/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/psi4/gdma]]
 +
|-
 +
|ghemical
 +
|Computational chemistry software package
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/ghemical/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.bioinformatics.org/ghemical/ghemical/index.html]]
 +
|-
 +
|gpaw-setups
 +
|Setups (data files) for py-gpaw, the DFT quantum chemistry software
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/gpaw-setups/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://wiki.fysik.dtu.dk/gpaw/setups/setups.html]]
 +
|-
 +
|gromacs
 +
|Compute molecular dynamics
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/gromacs/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.gromacs.org]]
 +
|-
 +
|iboview
 +
|Program for analyzing molecular electronic structure
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/iboview/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.iboview.org/]]
 +
|-
 +
|jdftx
 +
|Software for joint density functional theory in chemistry
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/jdftx/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://jdftx.org/]]
 +
|-
 +
|kalzium
 +
|Periodic table of elements for KDE 4
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/kalzium/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.kde.org/applications/education/kalzium]]
 +
|-
 +
|kim-api
 +
|Framework for reliable, reproducible, portable molecular simulations
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/kim-api/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://openkim.org/]]
 +
|-
 +
|lammps
 +
|Classical molecular dynamics code with a focus on materials modeling
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/lammps/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://lammps.sandia.gov/]]
 +
|-
 +
|latte
 +
|Quantum chemistry: Density functional tight binding molecular dynamics
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/latte/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/lanl/LATTE]]
 +
|-
 +
|libccp4
 +
|Protein X-ray crystallography toolkit
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libccp4/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.ccp4.ac.uk/]]
 +
|-
 +
|libcint
 +
|General GTO integrals for quantum chemistry
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libcint/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/sunqm/libcint]]
 +
|-
 +
|libefp
 +
|Effective fragment potential method in quantum chemistry
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libefp/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://libefp.github.io]]
 +
|-
 +
|libgridxc
 +
|Library to compute the exchange and correlation energy and potentials
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libgridxc/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://launchpad.net/libgridxc]]
 +
|-
 +
|libint
 +
|Evaluate the integrals in modern atomic and molecular theory
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libint/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/evaleev/libint]]
 +
|-
 +
|liboglappth
 +
|Support libraries of science/ghemical port
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/liboglappth/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.uku.fi/~thassine/projects/ghemical/]]
 +
|-
 +
|libssm
 +
|C++ toolkit for superposition of macromolecules
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libssm/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://launchpad.net/ssm]]
 +
|-
 +
|lm-uiuc
 +
|Software for sampling trajectories of the reaction-diffusion equations
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/lm/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.scs.illinois.edu/schulten/lm/]]
 +
|-
 +
|luscus
 +
|Molecular editor and viewer
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/luscus/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://sourceforge.net/projects/luscus/]]
 +
|-
 +
|madness
 +
|Multiresolution adaptive numeric environment for scientific simulation
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/madness/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/m-a-d-n-e-s-s/madness]]
 +
|-
 +
|massxpert
 +
|massXpert software for (bio)chemists
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/massxpert/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://salsa.debian.org/debichem-team/massxpert]]
 +
|-
 +
|mdynamix
 +
|General purpose molecular dynamics code
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/mdynamix/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.fos.su.se/~sasha/mdynamix/]]
 +
|-
 +
|mmdb2
 +
|C++ toolkit for working with macromolecular coordinate files
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/mmdb2/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://launchpad.net/mmdb]]
 +
|-
 +
|mmtf-cpp
 +
|C++ MMTF format API, decoder and encoder, for molecular structures
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/mmtf-cpp/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://mmtf.rcsb.org/]]
 +
|-
 +
|mol2ps
 +
|Read molecular structure files and generate Postscript output
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/mol2ps/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2ps.html]]
 +
|-
 +
|molgif
 +
|Tool to create GIF animations of molecules
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/molgif/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/ilyak/molgif]]
 +
|-
 +
|molsketch
 +
|2D molecule editor
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/molsketch/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://molsketch.sourceforge.net/]]
 +
|-
 +
|mpqc
 +
|Massively Parallel Quantum Chemistry Program
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/mpqc/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|linkhttps://mpqc.org/]]
 +
|-
 +
|msms
 +
|Program to efficiently compute molecular surfaces
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/msms/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|linkhttp://mgltools.scripps.edu/downloads#msms]]
 +
|-
 +
|multiwfn
 +
|Multifunctional wavefunction analysis for quantum chemistry
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/multiwfn/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|linkhttp://sobereva.com/multiwfn/index.html]]
 +
|-
 +
|namd
 +
|Computer software for molecular dynamics simulation
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/namd/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.ks.uiuc.edu/Research/namd/]]
 +
|-
 +
|nwchem
 +
|High-performance computational chemistry software
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/nwchem/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.nwchem-sw.org/index.php/Main_Page]]
 +
|-
 +
|nwchem-data
 +
|Data for NWChem, the computational chemistry software
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/nwchem-data/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.nwchem-sw.org/index.php/Main_Page]]
 +
|-
 +
|openbabel
 +
|Chemical toolbox designed to speak the many languages of chemical data
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/openbabel/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://openbabel.org/wiki/Main_Page]]
 +
|-
 +
|openkim
 +
|Knowledgebase of Interatomic Models
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/openkim/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://openkim.org/]]
 +
|-
 +
|openkim-models
 +
|Open Knowledgebase of Interatomic Models
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/openkim-models/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://openkim.org/]]
 +
|-
 +
|opsin
 +
|Open Parser for Systematic IUPAC Nomenclature of chemical names
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/opsin/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://bitbucket.org/dan2097/opsin/src/default/]]
 +
|-
 +
|p5-Chemistry-3DBuilder
 +
|Generate 3D coordinates from a connection table
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-3DBuilder/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-3DBuilder]]
 +
|-
 +
|p5-Chemistry-Bond-Find
 +
|Detect bonds in a molecule and assign formal bond orders
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-Bond-Find/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Bond-Find]]
 +
|-
 +
|p5-Chemistry-Canonicalize
 +
|Number the atoms in a molecule in a unique way
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-Canonicalize/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Canonicalize]]
 +
|-
 +
|p5-Chemistry-Elements
 +
|Perl extension for working with Chemical Elements
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-Elements/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Elements]]
 +
|-
 +
|p5-Chemistry-File-MDLMol
 +
|MDL molfile reader/write
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-File-MDLMol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-SMARTS]]
 +
|-
 +
|p5-Chemistry-File-Mopac
 +
|MOPAC 6 input file reader/writer
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-Mopac]]
 +
|- 
 +
|p5-Chemistry-File-PDB
 +
|Perl module to read and write PDB files
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-File-PDB/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-PDB]]
 +
|-
 +
|p5-Chemistry-File-SLN
 +
|SLN linear notation parser/writer
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-SLN]]
 +
|-
 +
|p5-Chemistry-File-SMARTS
 +
|SMARTS chemical substructure pattern linear notation parser
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-File-SMARTS/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-SMARTS]]
 +
|-
 +
|p5-Chemistry-File-SMILES
 +
|SMILES linear notation parser/writer
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-SMILES]]
 +
|-
 +
|p5-Chemistry-File-VRML
 +
|Generate VRML models for molecules
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-VRML]]
 +
|-
 +
|p5-Chemistry-File-XYZ
 +
|XYZ molecule format reader/writer
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-File-XYZ]]
 +
|-
 +
|p5-Chemistry-FormulaPattern
 +
|Match molecule by formula
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-FormulaPattern]]
 +
|-
 +
|p5-Chemistry-InternalCoords
 +
|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
 +
|Table of the isotopes exact mass data
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Isotope]]
 +
|-
 +
|p5-Chemistry-MacroMol
 +
|Perl toolkit to describe macromolecules
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-MacroMol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-MacroMol]]
 +
|-
 +
|p5-Chemistry-MidasPattern
 +
|Select atoms in macromolecules
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-MidasPattern]]
 +
|-
 +
|p5-Chemistry-Mok
 +
|Molecular awk interpreter
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Mok]]
 +
|-
 +
|p5-Chemistry-Mol
 +
|Perl toolkit to describe molecules
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/p5-Chemistry-Mol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Mol]]
 +
|-
 +
|p5-Chemistry-Pattern
 +
|Chemical substructure pattern matching
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Pattern]]
 +
|-
 +
|p5-Chemistry-Reaction
 +
|Represent a ring as a substructure of a molecule
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Reaction]]
 +
|-
 +
|p5-Chemistry-Ring
 +
|Represent a ring as a substructure of a molecule
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Chemistry-Ring]]
 +
|-
 +
|p5-PerlMol
 +
|Perl modules for molecular chemistry
 +
|[[File:1329059652.png|35px|link=https://metacpan.org/release/PerlMol]]
 +
|-
 +
|packmol
 +
|Pack molecules in defined regions of space
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/packmol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://m3g.iqm.unicamp.br/packmol/home.shtml]]
 +
|-
 +
|pcmsolver
 +
|API for the Polarizable Continuum Model
 +
|[[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
 +
|Python library to analyze molecular dynamics trajectories
 +
|[[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
 +
|Test code and the trajectory data for test cases of MDAnalysis
 +
|[[File:1329059652.png|35px|link=https://www.mdanalysis.org]]
 +
|-
 +
|py27-PyQuante
 +
|Quantum chemistry in Python
 +
|[[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
 +
|OpenGL-based molecular visualization system
 +
|[[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
 +
|Python library to analyze molecular dynamics trajectories
 +
|[[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
 +
|Test code and the trajectory data for test cases of MDAnalysis
 +
|[[File:1329059652.png|35px|link=https://www.mdanalysis.org]]
 +
|-
 +
|py37-avogadrolibs
 +
|Python bindings for Avogadro2 chemistry libraries
 +
|[[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
 +
|Library for deep learning in biology and 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
 +
|Package useful for solving problems in chemistry
 +
|[[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
 +
|DFT and beyond within the projector-augmented wave method in chemistry
 +
|[[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
 +
|Collection of molecular modelling tools for python
 +
|[[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
 +
|Essentials for quantum chemistry
 +
|[[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
 +
|Quantum chemistry program executor and IO standardizer (QCSchema)
 +
|[[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
 +
|Learn quantum spin and entanglement
 +
|[[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
 +
|Library to support reading and writing of Rich Molecular Format files
 +
|[[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
 +
|Lightweight molecule manipulation codebase
 +
|[[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
 +
|First-principles molecular dynamics code
 +
|[[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
 +
|Many-body ab initio Quantum Monte Carlo code for quantum chemstry
 +
|[[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/]]
 
|-
 
|-
 
!colspan="3"|
 
!colspan="3"|
 
|-
 
|-
−
!colspan="3"|'''If you don't find a package you are looking for yet, it is recommended to search the ''' [[File:Icon FreeBSD.png|50px|link=https://www.freebsd.org/ports/categories-grouped.html]]'''Ports Collection.'''
+
!colspan="3"|'''If you don't find a package, you are looking for, <br/>we recommend to search the ''' [[File:Icon FreeBSD.png|50px|link=https://www.freebsd.org/ports/categories-grouped.html]]'''Ports Collection.'''
 
|-
 
|-
 
!colspan="3"|
 
!colspan="3"|
 
|-
 
|-
−
!colspan="3"|'''Back to the''' [[image:Icon Disti GhostBSD.png|50px|link=Applications]]'''Applications'''
+
!colspan="3"|'''Back to ''' [[image:Icon Disti GhostBSD.png|50px|link=Science and Engineering]] '''Science and Engineering'''
−
 
+
 
|}
 
|}
  
  
 
[[Category:Station]]
 
[[Category:Station]]

Latest revision as of 14:20, 20 January 2020

Welcome to theIcon Disti GhostBSD.png Chemistry
App/Package Abstract Addition or Link
CheMPS2 Spin-adapted implementation of DMRG for ab initio quantum chemistry Icon FreeBSD.png 1329059652.png
Jmol Java 3D viewer for chemical structures Icon FreeBSD.png 1329059652.png
MolScript Display 3D molecules in schematic and detailed representations Icon FreeBSD.png 1329059652.png
atom-chemistry Program for DFT calculations in atoms Icon FreeBSD.png 1329059652.png
avogadro2 Chemical editor and visualization application Icon FreeBSD.png 1329059652.png
avogadrolibs Avogadro2 libraries for chemical editor and visualization applications Icon FreeBSD.png 1329059652.png
bagel Brilliantly Advanced General Electronic-structure Library Icon FreeBSD.png 1329059652.png
bodr Chemistry data like element and isotope properties, atomic radii, etc Icon FreeBSD.png 1329059652.png
cdk-chemistry Chemistry Development Kit Icon FreeBSD.png 1329059652.png
checkmol Analyze molecules for the presence of functional groups Icon FreeBSD.png 1329059652.png
chemical-mime-data Collection of chemical MIME types for UNIX desktops Icon FreeBSD.png 1329059652.png
chemtool Draw organic molecules easily and store them Icon FreeBSD.png 1329059652.png
cp2k Quantum chemistry and solid state physics software package Icon FreeBSD.png 1329059652.png
dalton Powerful molecular electronic structure program for quantum chemistry Icon FreeBSD.png 1329059652.png
datawarrior Chemistry-aware multi-purpose data visualization and analysis program Icon FreeBSD.png 1329059652.png
dkh Wolf, Reiher, and Hess's Douglas-Kroll-Hess relativistic correction Icon FreeBSD.png 1329059652.png
dlpolyclassic Molecular dynamics simulation package Icon FreeBSD.png 1329059652.png
elk-chemistry- All-electron full-potential linearised augmented-planewave code Icon FreeBSD.png 1329059652.png
epte Electronic Periodic Table of the Elements Icon FreeBSD.png 1329059652.png
erd AcesIII electron repulsion integrals Icon FreeBSD.png 1329059652.png
erkale Quantum chemistry program to solve the electronic structure of atoms Icon FreeBSD.png 1329059652.png
erkale-pseudopotentials Pseudopotentials for Erkale, the quantum chemistry program Icon FreeBSD.png 1329059652.png
erkale-serial Quantum chemistry program to solve the electronic structure of atoms Icon FreeBSD.png 1329059652.png
fleur FLAPW code for atomic computations in quantum chemistry and physics Icon FreeBSD.png 1329059652.png
gabedit Graphical user interface for several chemistry software packages Icon FreeBSD.png 1329059652.png
gamess-us General Atomic and Molecular Electronic Structure System (US) Icon FreeBSD.png 1329059652.png
gchemutils C++ classes and Gtk3 widgets related to chemistry Icon FreeBSD.png 1329059652.png
gdma Anthony Stone's Gaussian Distributed Multipole Analysis Icon FreeBSD.png 1329059652.png
ghemical Computational chemistry software package Icon FreeBSD.png 1329059652.png
gpaw-setups Setups (data files) for py-gpaw, the DFT quantum chemistry software Icon FreeBSD.png 1329059652.png
gromacs Compute molecular dynamics Icon FreeBSD.png 1329059652.png
iboview Program for analyzing molecular electronic structure Icon FreeBSD.png 1329059652.png
jdftx Software for joint density functional theory in chemistry Icon FreeBSD.png 1329059652.png
kalzium Periodic table of elements for KDE 4 Icon FreeBSD.png 1329059652.png
kim-api Framework for reliable, reproducible, portable molecular simulations Icon FreeBSD.png 1329059652.png
lammps Classical molecular dynamics code with a focus on materials modeling Icon FreeBSD.png 1329059652.png
latte Quantum chemistry: Density functional tight binding molecular dynamics Icon FreeBSD.png 1329059652.png
libccp4 Protein X-ray crystallography toolkit Icon FreeBSD.png 1329059652.png
libcint General GTO integrals for quantum chemistry Icon FreeBSD.png 1329059652.png
libefp Effective fragment potential method in quantum chemistry Icon FreeBSD.png 1329059652.png
libgridxc Library to compute the exchange and correlation energy and potentials Icon FreeBSD.png 1329059652.png
libint Evaluate the integrals in modern atomic and molecular theory Icon FreeBSD.png 1329059652.png
liboglappth Support libraries of science/ghemical port Icon FreeBSD.png 1329059652.png
libssm C++ toolkit for superposition of macromolecules Icon FreeBSD.png 1329059652.png
lm-uiuc Software for sampling trajectories of the reaction-diffusion equations Icon FreeBSD.png 1329059652.png
luscus Molecular editor and viewer Icon FreeBSD.png 1329059652.png
madness Multiresolution adaptive numeric environment for scientific simulation Icon FreeBSD.png 1329059652.png
massxpert massXpert software for (bio)chemists Icon FreeBSD.png 1329059652.png
mdynamix General purpose molecular dynamics code Icon FreeBSD.png 1329059652.png
mmdb2 C++ toolkit for working with macromolecular coordinate files Icon FreeBSD.png 1329059652.png
mmtf-cpp C++ MMTF format API, decoder and encoder, for molecular structures Icon FreeBSD.png 1329059652.png
mol2ps Read molecular structure files and generate Postscript output Icon FreeBSD.png 1329059652.png
molgif Tool to create GIF animations of molecules Icon FreeBSD.png 1329059652.png
molsketch 2D molecule editor Icon FreeBSD.png 1329059652.png
mpqc Massively Parallel Quantum Chemistry Program Icon FreeBSD.png linkhttps://mpqc.org/
msms Program to efficiently compute molecular surfaces Icon FreeBSD.png linkhttp://mgltools.scripps.edu/downloads#msms
multiwfn Multifunctional wavefunction analysis for quantum chemistry Icon FreeBSD.png linkhttp://sobereva.com/multiwfn/index.html
namd Computer software for molecular dynamics simulation Icon FreeBSD.png 1329059652.png
nwchem High-performance computational chemistry software Icon FreeBSD.png 1329059652.png
nwchem-data Data for NWChem, the computational chemistry software Icon FreeBSD.png 1329059652.png
openbabel Chemical toolbox designed to speak the many languages of chemical data Icon FreeBSD.png 1329059652.png
openkim Knowledgebase of Interatomic Models Icon FreeBSD.png 1329059652.png
openkim-models Open Knowledgebase of Interatomic Models Icon FreeBSD.png 1329059652.png
opsin Open Parser for Systematic IUPAC Nomenclature of chemical names Icon FreeBSD.png 1329059652.png
p5-Chemistry-3DBuilder Generate 3D coordinates from a connection table Icon FreeBSD.png 1329059652.png
p5-Chemistry-Bond-Find Detect bonds in a molecule and assign formal bond orders Icon FreeBSD.png 1329059652.png
p5-Chemistry-Canonicalize Number the atoms in a molecule in a unique way Icon FreeBSD.png 1329059652.png
p5-Chemistry-Elements Perl extension for working with Chemical Elements Icon FreeBSD.png 1329059652.png
p5-Chemistry-File-MDLMol MDL molfile reader/write Icon FreeBSD.png 1329059652.png
p5-Chemistry-File-Mopac MOPAC 6 input file reader/writer 1329059652.png
p5-Chemistry-File-PDB Perl module to read and write PDB files Icon FreeBSD.png 1329059652.png
p5-Chemistry-File-SLN SLN linear notation parser/writer 1329059652.png
p5-Chemistry-File-SMARTS SMARTS chemical substructure pattern linear notation parser Icon FreeBSD.png 1329059652.png
p5-Chemistry-File-SMILES SMILES linear notation parser/writer 1329059652.png
p5-Chemistry-File-VRML Generate VRML models for molecules 1329059652.png
p5-Chemistry-File-XYZ XYZ molecule format reader/writer 1329059652.png
p5-Chemistry-FormulaPattern Match molecule by formula 1329059652.png
p5-Chemistry-InternalCoords Represent the position of an atom using internal coordinates Icon FreeBSD.png 1329059652.png
p5-Chemistry-Isotope Table of the isotopes exact mass data 1329059652.png
p5-Chemistry-MacroMol Perl toolkit to describe macromolecules Icon FreeBSD.png 1329059652.png
p5-Chemistry-MidasPattern Select atoms in macromolecules 1329059652.png
p5-Chemistry-Mok Molecular awk interpreter 1329059652.png
p5-Chemistry-Mol Perl toolkit to describe molecules Icon FreeBSD.png 1329059652.png
p5-Chemistry-Pattern Chemical substructure pattern matching 1329059652.png
p5-Chemistry-Reaction Represent a ring as a substructure of a molecule 1329059652.png
p5-Chemistry-Ring Represent a ring as a substructure of a molecule 1329059652.png
p5-PerlMol Perl modules for molecular chemistry 1329059652.png
packmol Pack molecules in defined regions of space Icon FreeBSD.png 1329059652.png
pcmsolver API for the Polarizable Continuum Model Icon FreeBSD.png 1329059652.png
py27-MDAnalysis Python library to analyze molecular dynamics trajectories Icon FreeBSD.png 1329059652.png
py27-MDAnalysisTests Test code and the trajectory data for test cases of MDAnalysis 1329059652.png
py27-PyQuante Quantum chemistry in Python Icon FreeBSD.png 1329059652.png
py27-pymol OpenGL-based molecular visualization system Icon FreeBSD.png 1329059652.png
py37-MDAnalysis Python library to analyze molecular dynamics trajectories Icon FreeBSD.png 1329059652.png
py37-MDAnalysisTests Test code and the trajectory data for test cases of MDAnalysis 1329059652.png
py37-avogadrolibs Python bindings for Avogadro2 chemistry libraries Icon FreeBSD.png 1329059652.png
py37-chainer-chemistry Library for deep learning in biology and chemistry Icon FreeBSD.png 1329059652.png
py37-chempy Package useful for solving problems in chemistry Icon FreeBSD.png 1329059652.png
py37-gpaw DFT and beyond within the projector-augmented wave method in chemistry Icon FreeBSD.png 1329059652.png
py37-molmod Collection of molecular modelling tools for python Icon FreeBSD.png 1329059652.png
py37-qcelemental Essentials for quantum chemistry Icon FreeBSD.png 1329059652.png
py37-qcengine Quantum chemistry program executor and IO standardizer (QCSchema) Icon FreeBSD.png 1329059652.png
py37-qspin Learn quantum spin and entanglement Icon FreeBSD.png 1329059652.png
py37-rmf Library to support reading and writing of Rich Molecular Format files Icon FreeBSD.png 1329059652.png
py37-scoria Lightweight molecule manipulation codebase Icon FreeBSD.png 1329059652.png
qbox First-principles molecular dynamics code Icon FreeBSD.png 1329059652.png
qmcpack Many-body ab initio Quantum Monte Carlo code for quantum chemstry Icon FreeBSD.png 1329059652.png
If you don't find a package, you are looking for,
we recommend to search the Icon FreeBSD.pngPorts Collection.
Back to Icon Disti GhostBSD.png Science and Engineering
Retrieved from "http://wiki.ghostbsd.org/index.php?title=Chemistry&oldid=3835"