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

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.

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,

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

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

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

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

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 =

[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)

Re: [Rdkit-discuss] GetSubstructMatches() as smiles

On Aug 7, 2019, at 13:08, Paolo Tosco wrote: > You can use > > Chem.MolFragmentToSmiles(mol, match) > > where match is a tuple of atom indices returned by GetSubstructMatch(). Note however that if only the atom indices are given then Chem.MolFragmentToSmiles() will include all bonds which

Re: [Rdkit-discuss] GetSubstructMatches() as smiles

Hi Mel, You can use Chem.MolFragmentToSmiles(mol, match) where match is a tuple of atom indices returned by GetSubstructMatch(). Cheers, p. > On 7 Aug 2019, at 11:36, Melissa Adasme wrote: > > Dear rdkitters, > > I'm trying to find substructures (query molecules built from SMARTS) matching

[Rdkit-discuss] GetSubstructMatches() as smiles

Dear rdkitters, I'm trying to find substructures (query molecules built from SMARTS) matching my molecules (SMILES). I found the GetSubstructMatches() method which works pretty well returning the indices of matching atoms in my molecule. I wonder if there is a way to directly obtain the SMILES

Re: [Rdkit-discuss] GetSubstructMatches

Hi Jean-Marc, The answer is in the error message, once you know how to read it, which isn't really trivial: On Wed, Dec 14, 2016 at 5:35 PM, Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > > Traceback (most recent call last): >File "glmap.py", line 11, in > matches =

Re: [Rdkit-discuss] GetSubstructMatches

Sure, it works! Thanks, Greg. Jean-Marc Le 14/12/2016 à 17:43, Greg Landrum a écrit : Hi Jean-Marc, The answer is in the error message, once you know how to read it, which isn't really trivial: On Wed, Dec 14, 2016 at 5:35 PM, Jean-Marc Nuzillard

[Rdkit-discuss] GetSubstructMatches

Hi all, I have encountered the following problem : Traceback (most recent call last): File "glmap.py", line 11, in matches = mol.GetSubstructMatches(skel) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, str) did not match C++ signature:

Re: [Rdkit-discuss] GetSubstructMatches() and resonance structures

: [Rdkit-discuss] GetSubstructMatches() and resonance structures Dear all, The following code snippet compares two resonance structures of formate anion: import rdkit from rdkit import Chem mol1=Chem.MolFromSmiles('C([O-])=O') mol2=Chem.MolFromSmiles('C(=O)[O-]') mol1

[Rdkit-discuss] GetSubstructMatches() and resonance structures

Dear all, The following code snippet compares two resonance structures of formate anion: import rdkit from rdkit import Chem mol1=Chem.MolFromSmiles('C([O-])=O') mol2=Chem.MolFromSmiles('C(=O)[O-]') mol1.GetSubstructMatches(mol2, uniquify = False) ((0, 2, 1),) mol1.GetSubstructMatches(mol1,

Re: [Rdkit-discuss] GetSubstructMatches()

Subject: Re: [Rdkit-discuss] GetSubstructMatches() Dear Ling, On Thu, Aug 22, 2013 at 11:49 PM, S.L. Chan slch...@yahoo.com wrote: Good afternoon folks, I would imagine that if you remove the hydrogens, the resulting molecule would be a substructure of the original molecule. However, when I

[Rdkit-discuss] GetSubstructMatches()

Good afternoon folks, I would imagine that if you remove the hydrogens, the resulting molecule would be a substructure of the original molecule. However, when I do the following to the attached MDL mol file, there is no matches. from rdkit import Chem mol = Chem.MolFromMolFile('temp.mol',

Re: [Rdkit-discuss] GetSubstructMatches()

Dear Ling, On Thu, Aug 22, 2013 at 11:49 PM, S.L. Chan slch...@yahoo.com wrote: Good afternoon folks, I would imagine that if you remove the hydrogens, the resulting molecule would be a substructure of the original molecule. However, when I do the following to the attached MDL mol file,