Using Graphsim Domain OperatorsΒΆ

To perform Tanimoto search on the default fingerprint in the index use the graphsim(<column_name>, <query>, <min_similarity>, <max_hits>) operator. For example:

select id from nci_open
where c$arnachm1.graphsim(smiles,
      'ClC1CCC2(C3CCC4(C(CCC4C3CC(C2(C1)Br)Br)C(C)CCCC(C)C)C)C',
      0.50, -1) = 1;

In order to extract similarity scores for the graphsim operators, the ancillary operator graphsim_score is available: graphsim(<column_name>, <fingerprint>, <search_method>, <query>, <min_similarity>, <max_hits>, <arg1>, <arg2>). Fingerprint is one of the fingerprint types in the index, <search_method> can be either Tanimoto or Tversky and arg1 and arg2 are used to set the alpha and beta parameters for Tversky search (where beta can be null).

select id, smiles from nci_open
 where c$arnachm1.graphsim(smiles, 'maccs166', 'tversky',
       'ClC1CCC2(C3CCC4(C(CCC4C3CC(C2(C1)Br)Br)C(C)CCCC(C)C)C)C',
       0.7, -1, 0.95, null) = 1;

In order to extract similarity scores for the graphsim operators two ancillary operators are available:

select id, c$arnachm1.graphsim_score(1) from nci_open
 where c$arnachm1.graphsim(smiles,
       'ClC1CCC2(C3CCC4(C(CCC4C3CC(C2(C1)Br)Br)C(C)CCCC(C)C)C)C',
       0.50, -1, 1) = 1;

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Graphsim Implementation Notes