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
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Debian Edu Chemistry packages
Official Debian packages with high relevance
avogadro
Molecular Graphics and Modelling System
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Versions of package avogadro |
Release | Version | Architectures |
jessie | 1.0.3-10.1 | amd64,armel,armhf,i386 |
buster | 1.2.0-4 | amd64,arm64,armhf,i386 |
sid | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.93.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.97.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2.0-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package avogadro: |
field | chemistry |
role | program |
uitoolkit | qt |
use | viewing |
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License: DFSG free
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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.
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chemtool
chemical structures drawing program
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Versions of package chemtool |
Release | Version | Architectures |
sid | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.6.14-1 | amd64,armel,armhf,i386 |
stretch | 1.6.14-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.6.14-3 | amd64,arm64,armhf,i386 |
bullseye | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.6.14-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package chemtool: |
field | chemistry |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | editing, learning |
works-with | image, image:vector |
works-with-format | svg |
x11 | application |
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License: DFSG free
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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.
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easychem
Draw high-quality molecules and 2D chemical formulas
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Versions of package easychem |
Release | Version | Architectures |
stretch | 0.6-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.6-8 | amd64,armel,armhf,i386 |
buster | 0.6-8 | amd64,arm64,armhf,i386 |
bullseye | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.6-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package easychem: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
use | editing, learning, viewing |
x11 | application |
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License: DFSG free
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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.
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education-menus
Debian Edu menu reorganization
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License: DFSG free
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A package to reorganize menu branches in order to get a structure
easy to use for teachers and students.
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gchempaint
2D chemical structures editor for the GNOME2 desktop
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Versions of package gchempaint |
Release | Version | Architectures |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gchempaint: |
field | chemistry |
interface | x11 |
role | program |
suite | gnome |
uitoolkit | gtk |
use | editing, learning |
x11 | application |
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License: DFSG free
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GChemPaint is an editor for 2D chemical structures with a multiple
document interface. Drawn molecules can be searched at NIST Webbook
and PubChem.
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gdis
molecular and crystal model viewer
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Versions of package gdis |
Release | Version | Architectures |
bookworm | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.90-5 | amd64,armel,armhf,i386 |
stretch | 0.90-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.90-5 | amd64,arm64,armhf,i386 |
bullseye | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gdis: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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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)
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gperiodic
periodic table application
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Versions of package gperiodic |
Release | Version | Architectures |
bookworm | 3.0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.0.3-1 | amd64,arm64,armhf,i386 |
jessie | 2.0.10-7 | amd64,armel,armhf,i386 |
stretch | 2.0.10-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 3.0.3-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gperiodic: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
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License: DFSG free
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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.
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kalzium
periodic table and chemistry tools
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Versions of package kalzium |
Release | Version | Architectures |
sid | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 4.14.2-1 | amd64,armel,armhf,i386 |
stretch | 16.08.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 17.08.3-1 | amd64,arm64,armhf,i386 |
bullseye | 20.12.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 24.08.1 |
Debtags of package kalzium: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | kde |
uitoolkit | qt |
use | browsing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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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.
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pymol
Molecular Graphics System
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Versions of package pymol |
Release | Version | Architectures |
trixie | 3.0.0+dfsg-1 | all |
sid | 3.0.0+dfsg-1 | all |
bookworm | 2.5.0+dfsg-1 | all |
bullseye | 2.4.0+dfsg-2 | all |
buster | 2.2.0+dfsg-4 | all |
jessie | 1.7.2.1-1 | amd64,armel,armhf,i386 |
stretch | 1.8.4.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package pymol: |
field | biology:structural, chemistry |
interface | 3d, x11 |
role | program |
scope | utility |
uitoolkit | tk |
use | learning, viewing |
works-with | image |
x11 | application |
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License: DFSG free
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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.
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Official Debian packages with lower relevance
rasmol
visualization of biological macromolecules
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Versions of package rasmol |
Release | Version | Architectures |
stretch | 2.7.5.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,s390x |
sid | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.7.5.2-2 | amd64,armel,armhf,i386 |
trixie | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.7.6.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.7.6.0-1 | amd64,arm64,armhf,i386 |
Debtags of package rasmol: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
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License: DFSG free
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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
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