DebiChem Project
Summary
Input Preparation and Output Processing
DebiChem input preparation and output processing

This metapackage will install graphical frontends and input generators/output processors for computational chemistry packages which might be useful for chemists.

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Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

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DebiChem Input Preparation and Output Processing packages

Official Debian packages with high relevance

ase
??? missing short description for package ase :-(
Versions of package ase
ReleaseVersionArchitectures
sid3.26.0-3all
forky3.26.0-3all
bullseye3.21.1-2all
bookworm3.22.1-3all
trixie3.24.0-1all
upstream3.28.0
Popcon: 19 users (5 upd.)*
Newer upstream!
 License: DFSG free
Git
avogadro
??? missing short description for package avogadro :-(
Versions of package avogadro
ReleaseVersionArchitectures
trixie1.100.0-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bookworm1.97.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.101.0-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
forky1.101.0-1amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
bullseye1.93.0-2amd64,arm64,armhf,i386
upstream2.0.0
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
Popcon: 55 users (77 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
Registry entries: Bio.tools  SciCrunch 
Other screenshots of package avogadro
VersionURL
1.0.1-3+b1https://screenshots.debian.net/screenshot/avogadro/8025
 Screenshots of package avogadro
ballview
??? missing short description for package ballview :-(
Versions of package ballview
ReleaseVersionArchitectures
bookworm1.5.0+git20180813.37fc53c-11amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.5.0+git20180813.37fc53c-6amd64,arm64,i386
sid1.5.0+git20220524.d85d2dd-2amd64,arm64,i386,loong64,ppc64el,riscv64,s390x
Debtags of package ballview:
interfacex11
roleprogram
uitoolkitqt
x11application
Popcon: 4 users (4 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof and Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. (PubMed,eprint) Bioinformatics 22(3):365-366 (2006)
Registry entries: SciCrunch 
Screenshots of package ballview
c2x
??? missing short description for package c2x :-(
Versions of package c2x
ReleaseVersionArchitectures
forky2.42.a+ds-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid2.42.a+ds-2amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye2.35a+ds-1amd64,arm64,armhf,i386
bookworm2.40.e+ds-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.42+ds-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Popcon: 4 users (3 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Rutter, M.J.: C2x: A tool for visualisation and input preparation for Castep and other electronic structure codes. Computer Physics Communications 225:174–179 (2018)
cclib
??? missing short description for package cclib :-(
Versions of package cclib
ReleaseVersionArchitectures
bookworm1.6.2-2all
bullseye1.6.2-2all
sid1.8.1-3all
forky1.8.1-3all
trixie1.8-1all
upstream2.0a1
Popcon: 97 users (108 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. (eprint) J. Comp. Chem. 29(5):839-845 (2008)
gabedit
??? missing short description for package gabedit :-(
Versions of package gabedit
ReleaseVersionArchitectures
bookworm2.5.1+ds-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye2.5.1~20200828-1amd64,arm64,armhf,i386
Debtags of package gabedit:
fieldchemistry
roleprogram
uitoolkitgtk
Popcon: 8 users (3 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Abdul-Rahman Allouche: Gabedit - A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
gausssum
??? missing short description for package gausssum :-(
Versions of package gausssum
ReleaseVersionArchitectures
trixie3.0.2-2all
forky3.0.2-3all
bullseye3.0.2-2all
sid3.0.2-3all
bookworm3.0.2-2all
Debtags of package gausssum:
fieldchemistry
roleprogram
Popcon: 12 users (1 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. J. Comp. Chem. 29(5):839-845 (2008)
jmol
??? missing short description for package jmol :-(
Versions of package jmol
ReleaseVersionArchitectures
sid16.3.55+dfsg-1all
forky16.3.55+dfsg-1all
trixie-backports16.3.55+dfsg-1~bpo13+1all
trixie16.2.33+dfsg-1all
bookworm14.32.83+dfsg-2all
bullseye14.6.4+2016.11.05+dfsg1-4all
Debtags of package jmol:
fieldchemistry
roleprogram
scopeutility
useviewing
Popcon: 43 users (54 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: A. Herráez: Biomolecules in the computer: Jmol to the rescue. (PubMed,eprint) Biochem Mol Biol Educ. 34(4):255-261 (2006)
Registry entries: SciCrunch 
Screenshots of package jmol
python3-pycifrw
??? missing short description for package python3-pycifrw :-(
Versions of package python3-pycifrw
ReleaseVersionArchitectures
forky5.0.1+~3.0.13.427.g9e493fc-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye4.4-2amd64,arm64,armhf,i386
bookworm4.4.4-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie4.4.6-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
sid5.0.1+~3.0.13.427.g9e493fc-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream5.0.1+~v3.0.13.467.g68733c4
Popcon: 15 users (2 upd.)*
Newer upstream!
 License: DFSG free
Git
travis
??? missing short description for package travis :-(
Versions of package travis
ReleaseVersionArchitectures
sid220729-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye200504+hf2-1amd64,arm64,armhf,i386
bookworm220729-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie220729-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky220729-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
Popcon: 5 users (0 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Martin Brehm and Barbara Kirchner: TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories. (eprint) J. Chem. Inf. Model. 51(8):2007-2023 (2011)
xcrysden
??? missing short description for package xcrysden :-(
Versions of package xcrysden
ReleaseVersionArchitectures
bullseye1.6.2-4amd64,arm64,armhf,i386
bookworm1.6.2-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.6.2-4amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky1.6.2-5amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
sid1.6.2-5amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream1.6.3-rc2
Popcon: 18 users (3 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Anton Kokalj: Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale. (eprint) Comp. Mater. Sci. 28(2):155-168 (2003)
Screenshots of package xcrysden

Packaging has started and developers might try the packaging code in VCS

viewmol
graphical front end for computational chemistry programs
Responsible: Debichem Team (Drew Parsons)
Versions of package viewmol
ReleaseVersionArchitectures
VCS2.4.1-26all
Versions and Archs
 License: GPL-2.0+
Debian package not available
Git
Version: 2.4.1-26

Viewmol is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

At present Viewmol includes input filters for Discover, DMol3, Gamess, Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as for PDB files. Structures can be saved as Accelrys' car-files, MDL files, and Turbomole coordinate files. Viewmol can generate input files for Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that OpenBabel can serve as an input as well as an output filter for coordinates.
Registry entries: SciCrunch 
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 284384