Having to construct complex SMARTS queries. It is frequently useful to be able to exert a bit more control over substructure queries without This can be changed using the rdkit.do_chiral_sss configuration variable:Ĭhembl_25=# set rdkit.do_chiral_sss=true Ģ213985 | | | | | | | | | | rows) Note that by default stereochemistry is not taken into account when doing substructure queries:Ĭhembl_25=# select * from rdk.mols where limit 10 Ģ213985 | | | | | | CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC(=O)NC(C)(C)C(=O)NC(Cc1ccccc1)C(=O)NC(CC(C)C)C(=O)NC(Cc1ccccc1)C(=O)NC(CCCNC(=N)N)C(=O)N1CCCC1C(=O)NC(CCCNC(=N)N)C(=O)NC(CC(N)=O)C(N)=O This is slower than the pure SMILES query, this is generally true of SMARTS-based queries. One easy way to speed things up, particularly for queries that return a large number of results, is to only retrieve a limited number of results:Ĭhembl_25=# select * from rdk.mols where limit 500 Given we’re searching through 1.7 million compounds these search times aren’t incredibly slow, but it would be nice to have them quicker. Notice that the last two queries are starting to take a while to execute and count all the results.

Order by morganbv_fp(mol_from_smiles($1::cstring))mfp2 Įxample query molecules taken from the eMolecules home page:Ĭhembl_25=# select count(*) from rdk.mols where Where morganbv_fp(mol_from_smiles($1::cstring))%mfp2 Select molregno,m,tanimoto_sml(morganbv_fp(mol_from_smiles($1::cstring)),mfp2) as similarityįrom rdk.fps join rdk.mols using (molregno) Returns table(molregno bigint, m mol, similarity double precision) as Select molregno,torsionbv_fp(m) as torsionbv,morganbv_fp(m) as mfp2,featmorganbv_fp(m) as ffp2 into rdk.fps from rdk.mols Ĭreate index fps_ttbv_idx on rdk.fps using gist(torsionbv) Ĭreate index fps_mfp2_idx on rdk.fps using gist(mfp2) Ĭreate index fps_ffp2_idx on rdk.fps using gist(ffp2) Īlter table rdk.fps add primary key (molregno) Ĭreate or replace function get_mfp2_neighbors(smiles text) Select * into rdk.mols from (select molregno,mol_from_ctab(molfile::cstring) m from compound_structures) tmp where m is not null Ĭreate index molidx on rdk.mols using gist(m) Īlter table rdk.mols add primary key (molregno)

Smarts load