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Features

• Supported input file types are
  • MDL/Symyx/Accelrys SD file format, versions V2000 and V3000.
  • SMILES string representation. SMILES can be input from the command-line, in a configuration file ('input-file=<smiles>'), or in a text file with one SMILES (followed by an optional molecule name) per line.
  • MOL2 file format.
  • Visipoint binary file format (VBF). This is an experimental format being currently developed. An informal specification is in preparation, please ask if you are interested in the details.
  • XMol XYZ file format. The parser expects hydrogen atoms to be present and guesses bond orders based on geometry. Formal atomic charges are assigned to atoms for which no charge is listed in the XYZ file.
  • A very crude implementation of the PDB and Gaussian output log formats. These may be useful for the extraction of ligand structures from PDB files (dump the protein before attempting this!) and quantum mechanically optimized structures from Gaussian logs. Bonding and hybridisation states of atoms are guessed based on their local geometry.
• Supported output file types are MDL/Symyx/Accelrys SD file format, versions V2000 and V3000 (latter used when the size of the structure so requires or if forced using option 'output-format=sdf:v3'), MOL2, and VBF formats.
• Assigns partial charges to atoms (MOL2 output format). Available charges are MMFF94-type non-polarizable charges and polarizable (conformation-dependent) electronegativity equalization charges (SFKEEM and EEM). The polarizable models are not intended to be used while performing geometry optimization, only when assigning partial charges - see options 'onlycharge' and 'chargemodel'.
• Molecular superposition using a Gaussian shape-density and partial charge weighted shape-density representation of the structures. (New in version 0.6.0). This is an experimental feature that, unfortunately, doesn't seem to work very well.