Hello,
I've been trying around with OBIsomorphismMapper and Stereochemistry. (See
python code below)
I've been using the stereochemically unspecified Smiles as well as Smiles with
explicit stereocenter definition.
When you look at the scripts output you see that CC(Cl)CCC and CCC[C@@H](Cl)C
are no match, however,
CCC[C@@H](Cl)C and CC(Cl)CCC as well as CCC[C@H](Cl)C and CCC[C@@H](Cl)C
are found to be isomorphs. Can I make my code respect different stereochemistry?
Many thanks,
Susan
No OBBuilder: CC(Cl)CCC CC(Cl)CCC 6
No OBBuilder: CC(Cl)CCC CCC[C@@H](Cl)C 0
No OBBuilder: CC(Cl)CCC CCC[C@H](Cl)C 0
No OBBuilder: CCC[C@@H](Cl)C CC(Cl)CCC 6
No OBBuilder: CCC[C@@H](Cl)C CCC[C@@H](Cl)C 7
No OBBuilder: CCC[C@@H](Cl)C CCC[C@H](Cl)C 7
No OBBuilder: CCC[C@H](Cl)C CC(Cl)CCC 6
No OBBuilder: CCC[C@H](Cl)C CCC[C@@H](Cl)C 7
No OBBuilder: CCC[C@H](Cl)C CCC[C@H](Cl)C 7
OBuilder: CC(Cl)CCC CC(Cl)CCC smiles: 6 OBMol: 17
OBuilder: CC(Cl)CCC CCC[C@@H](Cl)C smiles: 7 OBMol: 17
OBuilder: CC(Cl)CCC CCC[C@H](Cl)C smiles: 7 OBMol: 17
OBuilder: CCC[C@@H](Cl)C CC(Cl)CCC smiles: 6 OBMol: 17
OBuilder: CCC[C@@H](Cl)C CCC[C@@H](Cl)C smiles: 7 OBMol: 17
OBuilder: CCC[C@@H](Cl)C CCC[C@H](Cl)C smiles: 7 OBMol: 17
OBuilder: CCC[C@H](Cl)C CC(Cl)CCC smiles: 6 OBMol: 17
OBuilder: CCC[C@H](Cl)C CCC[C@@H](Cl)C smiles: 7 OBMol: 17
OBuilder: CCC[C@H](Cl)C CCC[C@H](Cl)C smiles: 7 OBMol: 17
#### Python code ####
def getQuery(mol):
if isinstance(mol, ob.OBMol):
query = ob.CompileMoleculeQuery(mol)
elif isinstance(mol, str):
query = ob.CompileSmilesQuery(mol)
else:
raise TypeError("Unsupported type in input molecule: "+type(mol))
return query
def simpleSearch(probe,ref):
query = getQuery(ref)
isomapper = ob.OBIsomorphismMapper.GetInstance(query)
isomorph = ob.vpairUIntUInt()
isomapper.MapFirst(probe, isomorph)
return isomorph
if __name__=="__main__":
builder = ob.OBBuilder()
conv = ob.OBConversion()
conv.SetInFormat("smi")
smiles = ["CC(Cl)CCC", "CCC[C@@H](Cl)C", "CCC[C@H](Cl)C" ]
mols = []
for smi in smiles:
mol = None
mol = ob.OBMol()
smilesOK = conv.ReadString(mol, smi)
for mis in smiles:
print("No OBBuilder:", smi, mis, len(simpleSearch(mol, mis)))
if smilesOK:
builder.Build(mol)
mol.AddHydrogens()
mols.append(mol)
for m,mol in enumerate(mols):
for s,smi in enumerate(smiles):
print("OBuilder:", smiles[m], smi, "smiles:", len(simpleSearch(mol,
smi)), "OBMol:", len(simpleSearch(mol, mols[s])))
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