Debian Edu Project
Summary
Chemistry
Debian Edu chemistry related applications

This metapackage depends on various applications that can be used to teach chemistry.

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 Debian Edu to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Edu mailing list

Links to other tasks

Debian Edu Chemistry packages

Official Debian packages with high relevance

avogadro
Molecular Graphics and Modelling System
Versions of package avogadro
ReleaseVersionArchitectures
jessie1.0.3-10.1amd64,armel,armhf,i386
buster1.2.0-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.99.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.93.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.97.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.99.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
stretch1.2.0-1+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
Popcon: 63 users (47 upd.)*
Versions and Archs
License: DFSG free
Git

Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

  • Molecular modeller with automatic force-field based geometry optimization
  • Molecular Mechanics including constraints and conformer searches
  • Visualization of molecular orbitals and general isosurfaces
  • Visualization of vibrations and plotting of vibrational spectra
  • Support for crystallographic unit cells
  • Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
  • Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

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 
chemtool
chemical structures drawing program
Versions of package chemtool
ReleaseVersionArchitectures
sid1.6.14-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie1.6.14-1amd64,armel,armhf,i386
stretch1.6.14-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.6.14-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.6.14-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm1.6.14-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.6.14-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
Debtags of package chemtool:
fieldchemistry
interfacex11
roleprogram
scopeapplication
uitoolkitgtk
useediting, learning
works-withimage, image:vector
works-with-formatsvg
x11application
Popcon: 27 users (19 upd.)*
Versions and Archs
License: DFSG free
Git

Chemtool is a GTK+ based 2D chemical structure editor for X11. It supports many bond styles, most forms of text needed for chemical typesetting and splines/arcs/curved arrows.

Drawings can be exported to MOL and PDB format, SVG or XFig format for further annotation, as a PiCTeX drawing, as a bitmap or as Postscript files (several of these through XFig's companion program fig2dev).

The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file. Cht can either be called directly by Chemtool or on the console.

Please cite: Matthias Brüstle: Chemtool - Moleküle zeichnen mit dem Pinguin. (eprint) Nachr. Chem. 49(11):1310-1313 (2001)
Screenshots of package chemtool
easychem
Draw high-quality molecules and 2D chemical formulas
Versions of package easychem
ReleaseVersionArchitectures
stretch0.6-8amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.6-8amd64,armel,armhf,i386
buster0.6-8amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.6-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm0.6-9amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie0.6-9amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
sid0.6-9amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package easychem:
fieldchemistry
interfacex11
roleprogram
uitoolkitgtk
useediting, learning, viewing
x11application
Popcon: 23 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

EasyChem is a program that helps you creating high quality diagrams of molecules and 2D chemical formulas that can be exported to PDF, PS, LaTeX and fig.

EasyChem was originally developed to create diagrams for chemistry books and is now frequently used for this purpose in commercial and non-commercial chemistry-related books.

Screenshots of package easychem
education-menus
Debian Edu menu reorganization
Versions of package education-menus
ReleaseVersionArchitectures
sid2.12.15all
bookworm2.12.15all
bullseye2.11.37all
buster2.10.47amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.924amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.812+deb8u1amd64,armel,armhf,i386
trixie2.12.15all
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

A package to reorganize menu branches in order to get a structure easy to use for teachers and students.

gchempaint
2D chemical structures editor for the GNOME2 desktop
Versions of package gchempaint
ReleaseVersionArchitectures
stretch0.14.15-1+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.14.9-1amd64,armel,armhf,i386
buster0.14.17-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.14.17-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm0.14.17-6.1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.14.17-6.2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
Debtags of package gchempaint:
fieldchemistry
interfacex11
roleprogram
suitegnome
uitoolkitgtk
useediting, learning
x11application
Popcon: 26 users (19 upd.)*
Versions and Archs
License: DFSG free
Git

GChemPaint is an editor for 2D chemical structures with a multiple document interface. Drawn molecules can be searched at NIST Webbook and PubChem.

gdis
molecular and crystal model viewer
Versions of package gdis
ReleaseVersionArchitectures
bookworm0.90-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.90-6amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie0.90-5amd64,armel,armhf,i386
stretch0.90-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.90-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.90-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package gdis:
fieldchemistry
interface3d, x11
roleprogram
uitoolkitgtk
useediting, learning, viewing
works-with3dmodel
x11application
Popcon: 18 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

A GTK+ based program for the display and manipulation of isolated molecules, periodic systems and crystalline habits. It is in development, but is nonetheless fairly functional. It has the following features:

  • Support for several file types (CIF, BIOSYM, XYZ, XTL, MARVIN, and GULP)
  • A simple molecular creation and manipulation tool
  • A dialogue for creating starting configurations for molecular dynamics simulations
  • Assorted tools for visualization (geometry information, region highlighting, etc.)
  • Animation of BIOSYM files (also rendered animations, see below)

GDIS also allows you to perform the following functions through other packages:

  • Model rendering (courtesy of POVRay)
  • Energy minimization (courtesy of GULP)
  • Morphology calculation (courtesy of cdd)
  • Space group processing (courtesy of SgInfo)
  • View the Periodic Table (courtesy of GPeriodic)
  • Load additional filetypes, such as PDB (courtesy of Babel)
Screenshots of package gdis
gperiodic
periodic table application
Versions of package gperiodic
ReleaseVersionArchitectures
bookworm3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
buster3.0.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.0.10-7amd64,armel,armhf,i386
stretch2.0.10-7amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
trixie3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
Debtags of package gperiodic:
fieldchemistry
interfacex11
roleprogram
scopeutility
uitoolkitgtk
uselearning, viewing
x11application
Popcon: 36 users (21 upd.)*
Versions and Archs
License: DFSG free
Git

GPeriodic is a small X/GTK+-based program which allows you to browse through a periodic table of chemical elements, and view somewhat detailed information on each of the elements. 118 elements are currently listed.

kalzium
periodic table and chemistry tools
Versions of package kalzium
ReleaseVersionArchitectures
sid22.12.3-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie4.14.2-1amd64,armel,armhf,i386
stretch16.08.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster17.08.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye20.12.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm22.12.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie22.12.3-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
upstream24.02.1
Debtags of package kalzium:
fieldchemistry
interface3d, x11
roleprogram
suitekde
uitoolkitqt
usebrowsing, learning, viewing
works-with3dmodel
x11application
Popcon: 182 users (151 upd.)*
Newer upstream!
License: DFSG free
Git

Kalzium is a full-featured chemistry application, including a Periodic Table of Elements, chemical reference, chemical equation solver, and 3D molecule viewer.

This package is part of the KDE education module.

Other screenshots of package kalzium
VersionURL
21.12.3https://screenshots.debian.net/shrine/screenshot/simage/large-7ac385be3f63bd95d07fa6b5ed246c93.png
21.12.3https://screenshots.debian.net/shrine/screenshot/simage/large-797c6653a678dee1d38a271cd31facd2.png
21.12.3https://screenshots.debian.net/shrine/screenshot/simage/large-b337656907b2f4c884df0e2fef25b617.png
22.12.3https://screenshots.debian.net/shrine/screenshot/24823/simage/large-b37a5de92bf3698c7145844e1ea4a4bd.png
4:20.04.0-1https://screenshots.debian.net/shrine/screenshot/19284/simage/large-c4639dd58a0b434a43f09b7bd601a95e.png
4:4.4.5-1https://screenshots.debian.net/shrine/screenshot/4862/simage/large-e344f66fe538f46bc890f8ed79d12678.png
4:3.5.9-2https://screenshots.debian.net/shrine/screenshot/1228/simage/large-6d015b0dadb288a0cc6f6e5d5d3331fa.png
Screenshots of package kalzium
pymol
Molecular Graphics System
Versions of package pymol
ReleaseVersionArchitectures
stretch1.8.4.0+dfsg-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.5.0+dfsg-1all
trixie2.5.0+dfsg-1all
bookworm2.5.0+dfsg-1all
bullseye2.4.0+dfsg-2all
buster2.2.0+dfsg-4all
jessie1.7.2.1-1amd64,armel,armhf,i386
Debtags of package pymol:
fieldbiology:structural, chemistry
interface3d, x11
roleprogram
scopeutility
uitoolkittk
uselearning, viewing
works-withimage
x11application
Popcon: 81 users (25 upd.)*
Versions and Archs
License: DFSG free
Git

PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

  • Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
  • Molecular builder and sculptor
  • Internal raytracer and movie generator
  • Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

Registry entries: Bio.tools  SciCrunch 

Official Debian packages with lower relevance

rasmol
visualization of biological macromolecules
Versions of package rasmol
ReleaseVersionArchitectures
stretch2.7.5.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,s390x
bookworm2.7.6.0-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie2.7.6.0-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x
sid2.7.6.0-3amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye2.7.6.0-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster2.7.6.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.7.5.2-2amd64,armel,armhf,i386
Debtags of package rasmol:
fieldchemistry
interfacex11
roleprogram
scopeutility
uitoolkitgtk
uselearning, viewing
x11application
Popcon: 20 users (11 upd.)*
Versions and Archs
License: DFSG free
Git

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files.

This package installs two versions of RasMol, rasmol-gtk has a modern GTK-based user interface and rasmol-classic is the version with the old Xlib GUI.

The package is enhanced by the following packages: rasmol-doc
Please cite: Roger A. Sayle and E. James Milner-White: RasMol: Biomolecular graphics for all. (PubMed) Trends in Biochemical Sciences (TIBS) 20(9):374 (1995)
Registry entries: Bio.tools 
Screenshots of package rasmol
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 236867