23.4 PDB File Format

23.4.1 OEReadPDBFile

def MyReadPDBMolecule(ifs, mol):
    mol.Clear()
    if OEReadPDBFile(ifs,mol):
        OEDetermineConnectivity(mol)
        OEFindRingAtomsAndBonds(mol)
        OEPerceiveBondOrders(mol)
        OEAssignImplicitHydrogens(mol)
        OEAssignFormalCharges(mol)
        OEAssignAromaticFlags(mol)
        return 1
    mol.Clear()
    return 0

23.4.2 OEWritePDBFile

def MyWritePDBMolecule(ofs, mol):
    if OEHasResidues(mol):
        OEPDBOrderAtoms(mol)
    else:
        OEPerceiveResidues(mol)

    if mol.GetDimension() < 3:
        # If no co-ordinates, write out bonds and bond orders.
        flags = OEPDBOFlag_ORDERS | OEPDBOFlag_BONDS;
    else:
        flags = OEPDBOFlag_DEFAULT;

    OEWritePDBFile(ofs, mol, flags)

				OEChem - Python Theory Manual

				OEChem - Python Theory Manual