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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, computational chemistry, and many related areas.

Features currently include:

  • A huge variety of common chemical file formats, including SDF/MOL, Mol2, PDB, SMILES, XYZ, CML... (details)
  • Recognition of file type based on filename extension
  • Chemical MIME support
  • Partial implementation of Daylight SMARTS molecular matching syntax
  • 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
  • 3D 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...)
  • More to come...

Currently does NOT (yet):

  • Generate coordinates for SMILES strings. (i.e., all coordinates will be zero when converting from a SMILES string or other "0D format".)
  • Handle 2D