Debian Edu Project
Summary
Chemistry
Aplikacje Debiana Edu powiązane z chemią

Metapakiet zależny od różnych aplikacji, które można wykorzystać do nauki chemii.

Description

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Debian Edu Chemistry packages

Official Debian packages with high relevance

Avogadro
System do molekularnego modelowania i wizualizacji
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Avogadro jest systemem do molekularnego modelowania oraz wizualizacji cząsteczek i biocząsteczek. Może wizualizować właściwości cząsteczek, takie jak orbitale lub potencjały elektrostatyczne, a ponadto udostępnia intuicyjne narzędzie do budowania cząsteczek.

Podstawowe możliwości:

  • molekularne modelowanie z automatyczną optymalizacją opartą na geometrii pól siłowych;
  • mechanika molekularna obejmująca wyszukiwanie według ograniczeń i konformacji;
  • wizualizacja orbitali molekularnych oraz ogólnych izopowierzchni;
  • wizualizacja drgań i kreślenie widm oscylacyjnych;
  • obsługa krystalograficznych komórek elementarnych;
  • generowanie wejścia dla pakietów chemii kwantowej Gaussian, GAMESS i MOLPRO;
  • elastyczna architektura wtyczek i skryptów Pythona.

Avogadro odczytuje formaty plików takie jak: PDB, XYZ, CML, CIF, Molden oraz dane wyjściowe: Gaussian, GAMESS i MOLPRO.

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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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
Wyświetlanie wysokiej jakości cząsteczek i dwuwymiarowych formuł chemicznych
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EasyChem to program, który pomaga tworzyć wysokiej jakości diagramy molekularne i dwuwymiarowe formuły chemiczne, które można eksportować do formatów PDF, PS, LaTeX i FIG.

EasyChem został pierwotnie zaprojektowany w celu tworzenia diagramów do książek związanych z chemią i jest obecnie często wykorzystywany pod tym względem w komercyjnych i niekomercyjnych książkach tego rodzaju.

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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
2D chemical structures editor for the GNOME2 desktop
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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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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
tablica okresowa pierwiastków
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GPeriodic jest małym programem X napisanym w GTK+, który pozwala na przeszukiwanie tablicy okresowej pierwiastków oraz wyświetlanie szczegółowych informacji o każdym jej elemencie. Obecnie jest obsługiwanych 118 pierwiastków.

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Kalzium
Układ okresowy pierwiastków i narzędzia chemiczne
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Kalzium jest w pełni funkcjonalną aplikacją chemiczną, obejmującą układ okresowy pierwiastków, opis zagadnień z zakresu chemii, rozwiązywanie równań chemicznych oraz podgląd cząsteczek w 3D.

Pakiet jest częścią modułu edukacyjnego KDE.

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Pymol
Molekularny system graficzny
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PyMOL jest systemem grafiki molekularnej, ukierunkowanym na średnie i duże biocząsteczki takie jak białka. Potrafi tworzyć wysokiej jakości, gotowe do opublikowania, molekularne grafiki i animacje.

Wśród możliwości:

  • wizualizowanie molekuł, trajektorii molekularnych i powierzchnii danych krystalograficznych lub orbitalnych;
  • budowanie i rzeźbienie molekularne;
  • kreślenie wewnętrznej grafiki i generowanie filmów;
  • pełna rozszerzalność i obsługa skryptów za pośrednictwem interfejsu Pythona.

PyMOL umożliwia odczytywanie następujących formatów plików: PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps i 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.

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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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