Debian Edu Project
Summary
Chemistry
Aplikace Debian Edu se vztahem k chemii

Tento metabalíček závisí na různých aplikacích, které lze využít při výuce chemie.

Description

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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

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Debian Edu Chemistry packages

Official Debian packages with high relevance

Avogadro
Molecular Graphics and Modelling System
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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.

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  OMICtools 
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0.8.1-5https://screenshots.debian.net/screenshots/000/001/732/large.png
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Chemtool
chemical structures drawing program
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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.

Please cite: Matthias Brüstle: Chemtool - Moleküle zeichnen mit dem Pinguin. (eprint) Nachr. Chem. 49(11):1310-1313 (2001)
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Easychem
Vykreslí molekuly a chemické vzorce
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EasyChem je program, který vám pomůže s vytvářením vysoce kvalitních diagramů molekul a chemických vzorců (2D), které je možno exportovat do formátu PDF, PS, LaTeX a fig.

EasyChem byl původně vytvořen pro vytváření diagramů do chemických knih a nyní se často používá pro komerční i nekomerční účely vytváření těchto publikací.

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Education-menus
Debian Edu menu reorganization
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A package to reorganize menu branches in order to get a structure easy to use for teachers and students.

Gchempaint
Editor 2D chemické struktury pro desktop GNOME2
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GChemPaint je editor 2D chemických struktur s rozhraním podporujícím otevření více dokumentů. Hotové molekuly je možno hledat na NIST Webbook a PubChem.

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Gdis
Prohlížeč molekul a krystalových modelů
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GTK program pro zobrazení a úpravu izolovaných molekul, periodických systémů a krystalických uspořádání. Program je ve fázi vývoje, ale funguje docela dobře. Má následující vlastnosti:

  • Podpora různých typů souborů ((CIF, BIOSYM, XYZ, XTL, MARVIN, a GULP)
  • Jednoduché vytváření a manipulace s molekulami
  • Dialogové vytváření počátečních konfigurací pro simulace dynamiky molekul
  • Rozmanité vizualizační nástroje (geometrické informace, zvýraznění určité oblasti, atd.)
  • Animace souborů BIOSYM (také vykreslení animací, uvidíte dále)

GDIS také umožňuje provádět následující funkce dostupné v jiných balíčcích:

  • Vykreslení modelu (díky POVRay)
  • Minimalizace energie (díky GULP)
  • Výpočet morfologie (díky cdd)
  • Zpracování prostoru (díky SgInfo)
  • Pohlížení periodické tabulky (díky GPeriodic)
  • Načítání dalších typů souborů, jako je PDB (díky Babel)
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Gperiodic
Periodická tabulka prvků
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Gperiodic je malý program založený na X/GTK+, umožňující procházení periodickou tabulkou prvků a prohlížení některých detailních informací o každém prvku. V současnosti zahrnuje 118 prvků.

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Kalzium
periodic table and chemistry tools
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Newer upstream!
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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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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  OMICtools 
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Viewmol
graphical front end for computational chemistry programs
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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  OMICtools 
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Official Debian packages with lower relevance

Rasmol
visualization of biological macromolecules
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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
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)
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