Re: [Rdkit-discuss] GetSubstructMatches and unique match
Dear Paolo, Thank you very much. I'll test this and revert to you. Have a nice day. Best regards, Quoc-Tuan > Le 10 mai 2020 à 13:09, Paolo Tosco mailto:paolo.tosco.m...@gmail.com > a écrit : > > > Dear Quoc-Tuan, > > I think I have come with a reasonably fast algorithm that seems to be > more robust: > > https://gist.github.com/ptosco/dc4d27153e6e8e45aed654761e4d7409 > > Cheers, > p. > > On 06/05/2020 09:11, Quoc-Tuan DO wrote: > > > > Dear Paolo, > > > > > > > > Thank you again for your code. Sorry for bothering you again. It > works > > all fine for monoterpenes but not for diterpenes, sesquiterpenes nor > > triterpenes. > > > > > > > > pattern: C~C~C(~C)~C > > > > > > > > mol1: > CC(=O)O[C@H]1CC[C@]2([C@H](C1(C)C)CC=C([C@@H]2CC/C(=C/C(=O)O)/C)C)C > > > > > > > > => ((17, 18, 19, 20, 23), (16, 24, 13, 14, 15), (8, 9, 4, 12, 7)) > > > > > > > > It should find 4 distinct units. > > > > > > > > mol2: > OCC12CCC(C2C2C(CC1)(C)C1(C)CCC3C(C1CC2)(C)CCC(C3(C)C)O)C(=C)C > > > > > > > > => ((16, 25, 27, 17, 15), (18, 19, 12, 13, 14), (1, 2, 5, 6, 7)) > > > > > > > > It should find 6 distinct units. > > > > > > > > I tried with a smarts version of the pattern > > [#6]~[#6]~[#6](~[#6])~[#6], but got the same results as with smiles. > > > > > > > > What do you think? Is there something missing in the query? > > > > > > > > Thanks for your time, > > > > > > > > Best regards, > > > > > > > > QT > > > > > > > > > > > > Le 05/05/2020 à 14:52, Paolo Tosco a écrit : > > > > > > > > >> Dear Quoc-Tuan, > >> > >> this should do what you need: > >> > >> https://gist.github.com/ptosco/dc4d27153e6e8e45aed654761e4d7409 > >> > >> Cheers, > >> p. > >> > > > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] GetSubstructMatches and unique match
Dear All, Please could you help with the following problem (I could not find answers in discussion list) ? pattern='C~C~C(~C)~C' smiles='O[C@H]1C[C@H]2C([C@@]1(C)CC2)(C)C' pat = Chem.MolFromSmiles(pattern) mol = Chem.MolFromSmiles(smiles) res = mol.GetSubstructMatches(pat, uniquify=True) The results are: ((1, 2, 3, 4, 8), (1, 5, 4, 3, 9), (1, 5, 4, 3, 10), (1, 5, 4, 9, 10), (2, 1, 5, 4, 6), (2, 1, 5, 4, 7), (2, 1, 5, 6, 7), (2, 3, 4, 5, 9), (2, 3, 4, 5, 10), (2, 3, 4, 9, 10), (3, 4, 5, 1, 6), (3, 4, 5, 1, 7), (3, 4, 5, 6, 7), (5, 4, 3, 2, 8), (6, 5, 4, 3, 9), (6, 5, 4, 3, 10), (6, 5, 4, 9, 10), (7, 5, 4, 3, 9), (7, 5, 4, 3, 10), (7, 5, 4, 9, 10), (7, 8, 3, 2, 4), (8, 3, 4, 5, 9), (8, 3, 4, 5, 10), (8, 3, 4, 9, 10), (8, 7, 5, 1, 4), (8, 7, 5, 1, 6), (8, 7, 5, 4, 6), (9, 4, 3, 2, 8), (9, 4, 5, 1, 6), (9, 4, 5, 1, 7), (9, 4, 5, 6, 7), (10, 4, 3, 2, 8), (10, 4, 5, 1, 6), (10, 4, 5, 1, 7), (10, 4, 5, 6, 7)) I expect to have only 2 matches with uniquify=True as I only have 2 units of the pattern. Furthermore, with or without uniquify, I have the same answers. I also expected that there should be 2 "independent" lists but here, there is always at least one common atom between each list. Is there something misunderstood or misused? Thanks in advance for your help and explanations. Best regards, Quoc-Tuan ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
