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…)