Hi Susan, You are correct, #4787 should have fixed the problem in the PostgreSQL cartridge. I usually build my own cartridge and I am not involved in the conda builds, so unfortunately I cannot give an answer to your question
For the second question, in Python query molecules generated from SMARTS strings are by default not sanitized, as in the cartridge. However, Chem.MolFromMolBlock by default sanitizes molecules; if you wish to keep query molblock features intact you need to explicitly pass sanitize=False as in my previous example, and only do partial sanitization if needed passing appropriate flags to Chem.SanitizeMol to avoid altering atom/bond queries. Cheers, p. > On 27 Jul 2022, at 15:49, Susan Leung <susanhle...@gmail.com> wrote: > > > Hi Paolo, > > Great thanks for this, that's very helpful. > > I am actually using this query in the postgres cartridge and am seeing > similar behaviour using version 2021.09.2 but I think this might be fixed in > 2021.09.3 with #4787 . However, I think the conda package ( > https://anaconda.org/rdkit/rdkit-postgresql ) is still on version 2021.09.2, > would it be possible to update this? > > But I also wanted to ask about the concept of a qmol in the cartridge that > doesn't undergo sanitization versus the corresponding behaviour in Python? > Please correct me if I'm wrong, but there is no concept of a qmol in Python? > > Many thanks! > > Susan > >> On Tue, Jul 26, 2022 at 9:04 PM Paolo Tosco <paolo.tosco.m...@gmail.com> >> wrote: >> Hi Susan, >> >> I see why that happens, and I'll let Greg comment if this is a bug or the >> intended behavior. >> In the meantime, I can propose a workaround. >> >> The reason why it happens is that aromatization, which is part of the >> sanitization operations, converts your aromatic query bond into a single >> bond, probably in the assumption that it was labelled as aromatic by mistake >> (it is indeed an exocyclic bond and it is not part of a ring in the >> q_aromatic molecule). You can clearly see that if you carry out sanitization >> as a separate step: >> >> q_aromatic = Chem.MolFromMolBlock(qb_aromatic, sanitize=False) >> q_aromatic >> >> for b in q_aromatic.GetBonds(): >> print(b.GetIdx(), b.GetBondType(), b.DescribeQuery()) >> 0 DOUBLE >> 1 SINGLE >> 2 DOUBLE >> 3 SINGLE >> 4 SINGLE >> 5 DOUBLE >> 6 AROMATIC >> >> Bond 6 is AROMATIC, but bears no query. >> Let's store an array of the currently aromatic bonds: >> >> are_aromatic = [b.GetIdx() for b in q_aromatic.GetBonds() if >> b.GetIsAromatic()] >> are_aromatic >> [6] >> >> After sanitization, the aromatic bond turns into a single bond: >> >> Chem.SanitizeMol(q_aromatic) >> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE >> for b in q_aromatic.GetBonds(): >> print(b.GetIdx(), b.GetBondType(), b.DescribeQuery()) >> 0 AROMATIC >> 1 AROMATIC >> 2 AROMATIC >> 3 AROMATIC >> 4 AROMATIC >> 5 AROMATIC >> 6 SINGLE >> >> We know that it was aromatic before sanitization, so let's make it an >> aromatic query bond: >> >> aromatic_query_bond = Chem.MolFromSmarts("*:*").GetBondWithIdx(0) >> aromatic_query_bond.GetBondType(), aromatic_query_bond.DescribeQuery() >> (rdkit.Chem.rdchem.BondType.AROMATIC, 'BondOrder 12 = val\n') >> >> q_aromatic = Chem.RWMol(q_aromatic) >> for b_idx in are_aromatic: >> q_aromatic.ReplaceBond(b_idx, aromatic_query_bond) >> >> Now q_aromatic matches as expected: >> >> print(m.HasSubstructMatch(q_aromatic)) >> True >> >> Cheers, >> p. >> >> >>> On Tue, Jul 26, 2022 at 6:17 PM Susan Leung <susanhle...@gmail.com> wrote: >>> Hi all, >>> >>> Sorry it's me with another substructure query question... >>> >>> Please can anyone explain the following behaviour to me? I have 4 queries >>> that differ by just one query bond. To me, it should match an aromatic bond >>> type (4) but it doesn't. However, it matches single_or_aromatic and >>> double_or_aromatic query bond types but not single_or_double…. >>> >>> Best wishes, >>> >>> Susan >>> >>> import rdkit >>> print(rdkit.__version__) >>> from rdkit import Chem >>> >>> qb_double_or_aromatic = """ >>> ACCLDraw07262216372D >>> >>> 0 0 0 0 0 999 V3000 >>> M V30 BEGIN CTAB >>> M V30 COUNTS 7 7 0 0 0 >>> M V30 BEGIN ATOM >>> M V30 1 C 45.7538 -37.6779 0 0 >>> M V30 2 C 44.7323 -37.0872 0 0 >>> M V30 3 C 44.7323 -35.9099 0 0 >>> M V30 4 C 45.7553 -35.3193 0 0 >>> M V30 5 C 46.7807 -35.9049 0 0 >>> M V30 6 C 46.7807 -37.085 0 0 >>> M V30 7 O 45.7553 -34.1382 0 0 >>> M V30 END ATOM >>> M V30 BEGIN BOND >>> M V30 1 2 2 1 >>> M V30 2 1 3 2 >>> M V30 3 2 4 3 >>> M V30 4 1 5 4 >>> M V30 5 1 1 6 >>> M V30 6 2 6 5 >>> M V30 7 7 4 7 >>> M V30 END BOND >>> M V30 END CTAB >>> M END >>> """ >>> qb_single_or_aromatic = """ >>> ACCLDraw07262216372D >>> >>> 0 0 0 0 0 999 V3000 >>> M V30 BEGIN CTAB >>> M V30 COUNTS 7 7 0 0 0 >>> M V30 BEGIN ATOM >>> M V30 1 C 45.7538 -37.6779 0 0 >>> M V30 2 C 44.7323 -37.0872 0 0 >>> M V30 3 C 44.7323 -35.9099 0 0 >>> M V30 4 C 45.7553 -35.3193 0 0 >>> M V30 5 C 46.7807 -35.9049 0 0 >>> M V30 6 C 46.7807 -37.085 0 0 >>> M V30 7 O 45.7553 -34.1382 0 0 >>> M V30 END ATOM >>> M V30 BEGIN BOND >>> M V30 1 2 2 1 >>> M V30 2 1 3 2 >>> M V30 3 2 4 3 >>> M V30 4 1 5 4 >>> M V30 5 1 1 6 >>> M V30 6 2 6 5 >>> M V30 7 6 4 7 >>> M V30 END BOND >>> M V30 END CTAB >>> M END >>> """ >>> qb_aromatic = """ >>> ACCLDraw07262216372D >>> >>> 0 0 0 0 0 999 V3000 >>> M V30 BEGIN CTAB >>> M V30 COUNTS 7 7 0 0 0 >>> M V30 BEGIN ATOM >>> M V30 1 C 45.7538 -37.6779 0 0 >>> M V30 2 C 44.7323 -37.0872 0 0 >>> M V30 3 C 44.7323 -35.9099 0 0 >>> M V30 4 C 45.7553 -35.3193 0 0 >>> M V30 5 C 46.7807 -35.9049 0 0 >>> M V30 6 C 46.7807 -37.085 0 0 >>> M V30 7 O 45.7553 -34.1382 0 0 >>> M V30 END ATOM >>> M V30 BEGIN BOND >>> M V30 1 2 2 1 >>> M V30 2 1 3 2 >>> M V30 3 2 4 3 >>> M V30 4 1 5 4 >>> M V30 5 1 1 6 >>> M V30 6 2 6 5 >>> M V30 7 4 4 7 >>> M V30 END BOND >>> M V30 END CTAB >>> M END >>> """ >>> qb_single_or_double = """ >>> ACCLDraw07262216372D >>> >>> 0 0 0 0 0 999 V3000 >>> M V30 BEGIN CTAB >>> M V30 COUNTS 7 7 0 0 0 >>> M V30 BEGIN ATOM >>> M V30 1 C 45.7538 -37.6779 0 0 >>> M V30 2 C 44.7323 -37.0872 0 0 >>> M V30 3 C 44.7323 -35.9099 0 0 >>> M V30 4 C 45.7553 -35.3193 0 0 >>> M V30 5 C 46.7807 -35.9049 0 0 >>> M V30 6 C 46.7807 -37.085 0 0 >>> M V30 7 O 45.7553 -34.1382 0 0 >>> M V30 END ATOM >>> M V30 BEGIN BOND >>> M V30 1 2 2 1 >>> M V30 2 1 3 2 >>> M V30 3 2 4 3 >>> M V30 4 1 5 4 >>> M V30 5 1 1 6 >>> M V30 6 2 6 5 >>> M V30 7 5 4 7 >>> M V30 END BOND >>> M V30 END CTAB >>> M END >>> """ >>> mb = """ >>> ACCLDraw07262216212D >>> >>> 0 0 0 0 0 999 V3000 >>> M V30 BEGIN CTAB >>> M V30 COUNTS 10 11 0 0 0 >>> M V30 BEGIN ATOM >>> M V30 1 O 4.9598 -34.3327 0 0 >>> M V30 2 O 3.4666 -32.8272 0 0 >>> M V30 3 C 6.9426 -35.2057 0 0 >>> M V30 4 C 4.5926 -33.1985 0 0 >>> M V30 5 C 6.143 -34.3327 0 0 >>> M V30 6 C 8.0972 -34.9529 0 0 >>> M V30 7 C 6.5101 -33.1985 0 0 >>> M V30 8 C 8.4562 -33.8227 0 0 >>> M V30 9 N 5.5514 -32.509 0 0 CFG=3 >>> M V30 10 C 7.6606 -32.9537 0 0 >>> M V30 END ATOM >>> M V30 BEGIN BOND >>> M V30 1 1 1 4 >>> M V30 2 2 4 2 >>> M V30 3 1 5 3 >>> M V30 4 1 5 1 >>> M V30 5 2 3 6 >>> M V30 6 2 5 7 >>> M V30 7 1 6 8 >>> M V30 8 1 7 9 >>> M V30 9 1 9 4 >>> M V30 10 1 7 10 >>> M V30 11 2 10 8 >>> M V30 END BOND >>> M V30 END CTAB >>> M END >>> """ >>> m = Chem.MolFromMolBlock(mb) >>> >>> q_double_or_aromatic = Chem.MolFromMolBlock(qb_double_or_aromatic) >>> print(m.HasSubstructMatch(q_double_or_aromatic)) >>> >>> q_single_or_aromatic = Chem.MolFromMolBlock(qb_single_or_aromatic) >>> print(m.HasSubstructMatch(q_single_or_aromatic)) >>> >>> q_aromatic = Chem.MolFromMolBlock(qb_aromatic) >>> print(m.HasSubstructMatch(q_aromatic)) >>> >>> q_single_or_double = Chem.MolFromMolBlock(qb_single_or_double) >>> print(m.HasSubstructMatch(q_single_or_double)) >>> >>> >>> 2022.03.2 >>> >>> True >>> >>> True >>> >>> False >>> >>> False >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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