Debian Edu Chemistry packages

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.

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.

EasyChem 是一个帮助您创建高质量分子图形及二维化学式的软件，能够将其导出为 PDF，PS，LaTex 及 fig 格式。

EasyChem 原初的开发目的是为化学图书创建图表，而现在则经常在商业和非商业的化 学相关图书中使用该用途。

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

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

一个基于 GTK+ 的程序，用于显示和操作孤立分子、周期系统和晶体环境。目前仍在 开发中，但已经有相当的功能了。主要功能有：

• 支持多种文件格式(CIF、BIOSYM、XYZ、XTL、MARVIN 和 GULP)
• 带有简单的分子创建、操作工具
• 有对话框用于启动分子动力学模拟
• 各种可视化工具(几何信息、区域高亮等)
• BIOSYM 文件的动画演示

GDIS 还能通过安装其它一些软件包实现下列额外功能：

• 模型渲染(courtesy of POVRay)
• 能量最小化(courtesy of GULP)
• 表型计算(courtesy of cdd)
• Space group processing (courtesy of SgInfo)
• 查看元素周期表 (courtesy of GPeriodic)
• 导入其它文件格式，如 PDB (courtesy of Babel)

GPeriodic 是一个小型的基于 X/GTK+ 的元素周期表程序，用于浏览化学 元素周期表，并且可以查看每种元素的详细信息。 目前表里列了 118 种元素。

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 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.

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.