Appendix - Design and Use of Relational Databases in Chemistry - page 199

if obc.ReadString(mol, smi):
mol.SetTitle("")
mol.Kekulize()
return obc.WriteString(mol,1)
else:
raise ValueError("Error in input smiles")
return None
$EOPY$ Language plpythonu Immutable;
Create Or Replace Function openbabel.smiles_to_symbols(smi Text)
Returns Text[] As $EOPY$
import openbabel
obc = openbabel.OBConversion()
mol = openbabel.OBMol()
obc.SetInAndOutFormats("smi", "mol")
if obc.ReadString(mol, smi):
tbl = openbabel.OBElementTable()
return "{" + ",".join((tbl.GetSymbol(a.GetAtomicNum()) for a in
openbabel.OBMolAtomIter(mol))) + "}"
else:
raise ValueError("Error in input smiles")
return None
$EOPY$ Language plpythonu Immutable;
Create Or Replace Function openbabel.smiles_to_bonds(smi Text)
Returns Integer[] As $EOPY$
import openbabel
obc = openbabel.OBConversion()
mol = openbabel.OBMol()
obc.SetInAndOutFormats("smi", "mol")
if obc.ReadString(mol, smi):
bonds = []
for b in openbabel.OBMolBondIter(mol):
if b.IsAromatic():
bo = 4
else:
bo = b.GetBO()
bonds.append("{%d,%d,%d}" % (b.GetBeginAtomIdx(),
b.GetEndAtomIdx(), bo))
return "{" + ",".join(bonds) + "}"
else:
raise ValueError("Error in input smiles")
return None
$EOPY$ Language plpythonu Immutable;
Create Or Replace Function openbabel.smiles_to_molfile(smi Text)
Returns Text As $EOPY$
import openbabel
obc = openbabel.OBConversion()
mol = openbabel.OBMol()
obc.SetInAndOutFormats("smi", "mol")