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
Re: [Rdkit-discuss] GetSubstructMatches and unique match
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
Re: [Rdkit-discuss] GetSubstructMatches and unique match
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
Re: [Rdkit-discuss] GetSubstructMatches and unique match
Dear Paolo, this answers my question as well, but in an unexpected way. Best, Jean-Marc 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. On 05/05/2020 11:52, Quoc-Tuan DO wrote: Dear Paolo, Thank you for your reply. I understand now... I did not use uniquify option first then only uniquify=True. I thought the default would be uniquify=False. Actually my problem is to find 2 distinct units of isoprene (pattern) in the borneol (smiles) as the latter is a monoterpene. Do you have any idea I can do this ? Thanks in advance for your time. Best regards, QT Le 04/05/2020 à 19:53, Paolo Tosco a écrit : Dear Quoc-Tuan, On 04/05/2020 09:10, Greenpharma S.A.S. wrote: 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. GetSubstructMatches() will report all matches of the pattern against your molecule. In your case, there are 35 matches which are all constituted by different atom indices. Furthermore, with or without uniquify, I have the same answers. If you set uniquify=False, you actually get 70 matches, so twice as many answers. This time, matches can be constitued by the same indices, provided they are in a different permutation. I have uploaded a gist here: https://gist.github.com/ptosco/6d70cec235361fbaddc7cbc2cf9c3b5d that hopefully will make this clearer. Cheers, p. 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Jean-Marc Nuzillard Directeur de Recherches au CNRS Institut de Chimie Moléculaire de Reims CNRS UMR 7312 Moulin de la Housse CPCBAI, Bâtiment 18 BP 1039 51687 REIMS Cedex 2 France Tel : 03 26 91 82 10 Fax : 03 26 91 31 66 http://www.univ-reims.fr/icmr http://eos.univ-reims.fr/LSD/CSNteam.html http://www.univ-reims.fr/LSD/ http://www.univ-reims.fr/LSD/JmnSoft/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] GetSubstructMatches and unique match
Dear Quoc-Tuan, this should do what you need: https://gist.github.com/ptosco/dc4d27153e6e8e45aed654761e4d7409 Cheers, p. On 05/05/2020 11:52, Quoc-Tuan DO wrote: Dear Paolo, Thank you for your reply. I understand now... I did not use uniquify option first then only uniquify=True. I thought the default would be uniquify=False. Actually my problem is to find 2 distinct units of isoprene (pattern) in the borneol (smiles) as the latter is a monoterpene. Do you have any idea I can do this ? Thanks in advance for your time. Best regards, QT Le 04/05/2020 à 19:53, Paolo Tosco a écrit : Dear Quoc-Tuan, On 04/05/2020 09:10, Greenpharma S.A.S. wrote: 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. GetSubstructMatches() will report all matches of the pattern against your molecule. In your case, there are 35 matches which are all constituted by different atom indices. Furthermore, with or without uniquify, I have the same answers. If you set uniquify=False, you actually get 70 matches, so twice as many answers. This time, matches can be constitued by the same indices, provided they are in a different permutation. I have uploaded a gist here: https://gist.github.com/ptosco/6d70cec235361fbaddc7cbc2cf9c3b5d that hopefully will make this clearer. Cheers, p. 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] GetSubstructMatches and unique match
Dear Paolo, Thank you for your reply. I understand now... I did not use uniquify option first then only uniquify=True. I thought the default would be uniquify=False. Actually my problem is to find 2 distinct units of isoprene (pattern) in the borneol (smiles) as the latter is a monoterpene. Do you have any idea I can do this ? Thanks in advance for your time. Best regards, QT Le 04/05/2020 à 19:53, Paolo Tosco a écrit : Dear Quoc-Tuan, On 04/05/2020 09:10, Greenpharma S.A.S. wrote: 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. GetSubstructMatches() will report all matches of the pattern against your molecule. In your case, there are 35 matches which are all constituted by different atom indices. Furthermore, with or without uniquify, I have the same answers. If you set uniquify=False, you actually get 70 matches, so twice as many answers. This time, matches can be constitued by the same indices, provided they are in a different permutation. I have uploaded a gist here: https://gist.github.com/ptosco/6d70cec235361fbaddc7cbc2cf9c3b5d that hopefully will make this clearer. Cheers, p. 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] GetSubstructMatches and unique match
Dear Quoc-Tuan, GetSubstructMatches() tries to find isoprene at all positions where this is possible. You may want to test your SMARTS and its matching with structures at this great place: https://smartsview.zbh.uni-hamburg.de/ Maybe you would prefer to known whether borneol follows the isoprene rule or not by trying to cover its structure with two, unbound, isoprene units. I really would like to know how to write that with SMARTS. Jean-Marc Le 04/05/2020 à 10:10, Greenpharma S.A.S. a écrit : 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 -- Jean-Marc Nuzillard Directeur de Recherches au CNRS Institut de Chimie Moléculaire de Reims CNRS UMR 7312 Moulin de la Housse CPCBAI, Bâtiment 18 BP 1039 51687 REIMS Cedex 2 France Tel : 03 26 91 82 10 Fax : 03 26 91 31 66 http://www.univ-reims.fr/icmr http://eos.univ-reims.fr/LSD/CSNteam.html http://www.univ-reims.fr/LSD/ http://www.univ-reims.fr/LSD/JmnSoft/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] GetSubstructMatches and unique match
Dear Quoc-Tuan, On 04/05/2020 09:10, Greenpharma S.A.S. wrote: 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. GetSubstructMatches() will report all matches of the pattern against your molecule. In your case, there are 35 matches which are all constituted by different atom indices. Furthermore, with or without uniquify, I have the same answers. If you set uniquify=False, you actually get 70 matches, so twice as many answers. This time, matches can be constitued by the same indices, provided they are in a different permutation. I have uploaded a gist here: https://gist.github.com/ptosco/6d70cec235361fbaddc7cbc2cf9c3b5d that hopefully will make this clearer. Cheers, p. 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
