I want to evaluate the effectiveness of Open Babel's substructure screen
fingerprint.
More specifically, I have a query benchmark where the queries are SMILES
strings for molecules (not SMARTS patterns - they come from, for example,
Marvin or another structure editor), and for the target I have a set of SMILES
derived from the ChEMBL data set.
I want to use the molecule as a query, and find all matches, then generate the
fingerprint for the query and the targets and do a substructure screen. Then I
can compare the screen count to the actual count.
I'm stuck on the first part; using an input molecule as a substructure query.
My code is something like the following:
======
import pybel
ob = pybel.ob
target_pybmol = pybel.readstring("smi", "c1ccccc1C")
target_mol = target_pybmol.OBMol
query_pybmol = pybel.readstring("smi", "CC")
query_mol = query_pybmol.OBMol
compiled_query = ob.CompileMoleculeQuery(query_mol)
mapper = ob.OBIsomorphismMapper.GetInstance(compiled_query)
isomorph = ob.vpairUIntUInt()
mapper.MapFirst(target_mol, isomorph)
print list(isomorph)
======
The problem is, this doesn't report any matches. I think that's because the
"CC" in the query doesn't exactly match the "c-C" in the target - the ring
carbon aromaticity gets in the way.
Is there any way I can ask Open Babel to generate a query which only considers
the atom element number, and not the aromaticity? Better yet, if it considers
the atom element number, and if the query charge != 0 then also considers the
charge?
Or I am I going about this in the wrong way?
Cheers,
Andrew
da...@dalkescientific.com
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