Debian Edu Project
Summary
Chemistry
Debian Edu 化学関連アプリケーション群

本メタパッケージは、化学の指導に利用できる各種アプリケーションに依存してい ます。

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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
分子可視化およびモデリングシステム
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Avogadro は、分子および生体分子をターゲットとする分子グラフィックスおよ び分子モデリングシステムです。分子軌道や静電ポテンシャルなどの分子の物 性を可視化でき、直感的な分子ビルダーを備えています。

次のような機能があります:

  • 力場に基づいた配座の自動最適化機能を備える分子モデリングツール
  • 拘束や配座異性体探索を含む分子力学法ツール
  • 分子軌道その他のな同値面の可視化
  • 振動の可視化、振動スペクトルのプロット
  • 結晶単位格子の編集
  • Gaussian, GAMESS および MOLPRO 量子化学パッケージ用の 入力データの生成

  • 拡張可能なプラグインアーキテクチャ、Python でのスクリプティング

Avogadro は、PDB, XYZ, CML, CIF, Molden ファイルのほか、Gaussian, GAMESS, MOLPRO などの出力ファイルも読み込むことができます。

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
高品質な分子構造や二次元化学公式を表示
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EasyChem は、高品質の分子図および PDF、PS、LaTeX および fig にエクスポート 可能な二次元化学公式の作成を補助するプログラムです。

EasyChem は、元々は化学書籍中の図式を作成するために開発され、現在商用および 非商用の化学関連書籍の出版に頻繁に利用されています。

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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
GNOME2 デスクトップ向け二次元化学構造エディタ
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GChemPaint は複数の文書インターフェイスによる二次元化学構造用エディタ です。描画した分子は NIST ウェブブックおよび PubChem で検索できます。

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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
元素周期表アプリケーション
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GPeriodic は X/GTK+ ベースの小さなプログラムで、元素の周期表を閲覧した り、各元素の詳しいデータを見たりできるようになっています。現在 118 の 元素が表示されます。

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Kalzium
periodic table and chemistry tools
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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.

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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