Hi Jose, There isn’t currently anything in the cartridge that allows you to retrieve the matching atom ids for a substructure query. I think it should be possible to add the functionality, but I need to take a look.
-greg On Mon, 10 Dec 2018 at 13:41, Jose Manuel Gally <[email protected]> wrote: > Hi all, > > I am using the RDKit postgresql cartridge to perform some substructure > searches on a large number of molecules, as described here: > > https://www.rdkit.org/docs/Cartridge.html > > However, in addition to which row matched the query, I would also like > to know what are the atom indices for each match. > > For now I am doing this in 2 consecutive steps, as shown below. > > Is there a way to achieve this in a single step from the postgresql query? > > Thanks! > > Best regards, > > Jose Manuel > > > # 0/ initialization > query_smiles = "c1ccccc1" > query_mol = Chem.MolFromSmiles(query_smiles) > > # 1/ get substructure matches > cur.execute(f"select mol_send(m) from rdk.mols where m@>'{query_smiles}' > LIMIT 1") > results = cur.fetchall() > mols = [ Chem.Mol(m[0].tobytes()) for m in results ] > > # 2/ get substructure atom indexes: > for m in mols: > print(m.GetSubstructMatches(query_mol)) > > > And for instance I get as results the substructures atom indices: > ((5, 6, 7, 8, 16, 21), (9, 10, 11, 12, 14, 15), (22, 23, 24, 25, 33, 34)) > > > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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