Open Babel
http://openbabel.sourceforge.net/
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.
Features currently include:
- A huge variety of common chemical file formats, including SDF/MOL, Mol2, PDB, SMILES, XYZ, CML…
- Recognition of file type based on filename extension
- Chemical MIME support
- SMARTS matcher
- Flexible atom typer
- Flexible bond typer for perception of multiple bonds from atomic coordinates
- Gasteiger partial charge calculation
- Hydrogen addition and deletion
- Isotope support, calculation of average and exact masses
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Multiple conformer storage within molecules
- Command line conversion for multiple molecules in one file
- Command line interface
- Bitvector class
- Vector and matrix transformations
- Molecular test suite
- Open-source/Free Software under the GNU General Public License
- Cross platform (Windows, Linux, Mac OS X, SGI, Solaris, Dreamcast…)