Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

cases. Regards, Jim Metz -Original Message- From: Brian Cole To: James T. Metz Cc: RDKit Discuss Sent: Tue, Nov 7, 2017 7:23 pm Subject: Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match You can use Chem.CanonicalRankAtoms to de-duplicate the SMARTS matches

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

7:05 pm Subject: Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match I think you probably used a slightly different SMILES than the one you showed. The one you showed should have given ((0,1,3,4),(2,1,3,4)). The proper merge rule would then be to consider all matches equivalent i

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

Hi Jim, Would it not be easier to use a recursive SMARTS, so that you only count the carbon atoms? Something like [$([C,c]Cl)]-,=,:[$([C,c]Cl)], or, more compactly [$([#6]Cl)]~[$([#6]Cl)]. I haven't tested these, as I'm not close to a suitably equipped computer, but you should be able to get the g

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

Jim, I'm a bit confused by what you're trying to do. Maybe we can try simplifying. What would you like to have returned for each of these SMILES: 1) ClC=CCl 2) ClC(Cl)=CCl 3) ClC(Cl)=C(Cl)Cl If the answer is the same between 1) and 2), but different for 3), then the next question will be: "why?"

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

You can use Chem.CanonicalRankAtoms to de-duplicate the SMARTS matches based upon the atom symmetry like this: def count_unique_substructures(smiles, smarts): mol = Chem.MolFromSmiles(smiles) ranks = list(Chem.CanonicalRankAtoms(mol, breakTies=False)) pattern = Chem.MolFromSmarts(smart

Re: [Rdkit-discuss] Python code to merge tuples from a SMARTS match

I think you probably used a slightly different SMILES than the one you showed. The one you showed should have given ((0,1,3,4),(2,1,3,4)). The proper merge rule would then be to consider all matches equivalent if the 2nd and 3rd atom in the match agree, in any order; i.e, the two carbons, indices

[Rdkit-discuss] Python code to merge tuples from a SMARTS match

RDkit Discussion Group, I have written a SMARTS to detect vicinal chlorine groups using RDkit. There are 4 atoms involved in a vicinal chlorine group. SMARTS = '[Cl]-[C,c]-,=,:[C,c]-[Cl]' I am trying to count the number of ("unique") occurrences of this pattern. For some mo