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- Gabedit is a graphical interface to Gaussian, Molcas and Molpro computational chemistry packages running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported and graphics can be exported in many formats.
- Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
- PerlMol -- Perl Modules for Molecular Chemistry
- PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging".
- Babel is a program designed to interconvert a number of file formats currently used in molecular modeling.
- The Chemistry Development Kit (CDK)
- e CDK classes are Java utitility classes for ChemoInformatics and Computational chemistry, written in Java. They are developed constantly developed parallel to other projects that make use of them. They are a complete re-write of the CompChem classes that were the basis of JChemPaint, a Java Editor for 2D chemical structures, and of JMDraw, a Java package for the graphical layout of 2D chemical structures.
- A molecular mass calculator for Unix/X11
- A Perl module for calculating molecular mass of chemical compounds.
- KDE-inspired molecular weight calculator
- KMol is a KDE-inspired molecular weight and elemental composition calculator.
- LabJ (a.k.a Electronic Laboratory Notebook, ELN, Laboratory Journal) assists in planning chemical reactions and stores chemical information. Open Source, but it requires ISIS Desktop package from MSI.
- A set of WordPerfect macros for including chemical formatting in WP docs.
- ChemCalc is intended to be a calculator oriented towards chemistry.
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