Input

Inputs formats include

SMILES string (Getting a SMILES for your ligand)

PDB (Protein Data Bank)

MolFiles (V2000, V3000 and SDFiles)

TRIPOS MOL2

XYZ

certain CIF files

GAMESS input and output files

simple python objects that are used by the PyQuante package

Output

Output formats include

PDB (Protein Data Bank)

XYZ

CIF

Notes

Since the PDB file format does not require that atomic connectivity be defined there is a auto connection feature that using quantum chemical bond length data the determine bond types. There are also some algorithmic solutions to determining the character of ring structures and automatic addition of hydrogen atoms if none are included in the input. A feature of the Python language allows this information to be store simply be serialising the appropriate object to disk. This object can be reloaded and retains all the topological information.