Re: [Rdkit-discuss] RDKit Reaction gives disconnected components

2017-03-30 Thread Greg Landrum
- > *From:* Brian Kelley [fustiga...@gmail.com] > *Sent:* 30 March 2017 17:59 > *To:* Stephen Roughley > *Cc:* RDKit Discuss (rdkit-discuss@lists.sourceforge.net) > *Subject:* Re: [Rdkit-discuss] RDKit Reaction gives disconnected > components > > Correction here, you are not maki

Re: [Rdkit-discuss] RDKit Reaction gives disconnected components

2017-03-30 Thread Stephen Roughley
Steve From: Brian Kelley [fustiga...@gmail.com] Sent: 30 March 2017 17:59 To: Stephen Roughley Cc: RDKit Discuss (rdkit-discuss@lists.sourceforge.net) Subject: Re: [Rdkit-discuss] RDKit Reaction gives disconnected components Correction here, you are not maki

Re: [Rdkit-discuss] RDKit Reaction gives disconnected components

2017-03-30 Thread Brian Kelley
Correction here, you are not making two products because you are grouping the results ala: >>> rxn = AllChem.ReactionFromSmarts("([C:1][*][N:2])>>([C:1].[N:2])") >>> prods = rxn.RunReactants([Chem.MolFromSmiles("FC1ON1I")]) >>> Chem.MolToSmiles(prods[0][0]) 'CF.NI' However, it appears that

Re: [Rdkit-discuss] RDKit Reaction gives disconnected components

2017-03-30 Thread Brian Kelley
I have a feeling you may need to make two reactions. Let's consider a dirt simple case: >>> rxn = AllChem.ReactionFromSmarts("[C:1][N:2]>>[C:1].[N:2]") >>> prods = rxn.RunReactants([Chem.MolFromSmiles("CN")]) >>> Chem.MolToSmiles(prods[0][0]) 'C' >>> Chem.MolToSmiles(prods[0][1]) 'N' >>>

[Rdkit-discuss] RDKit Reaction gives disconnected components

2017-03-30 Thread Stephen Roughley
Dear Greg/RDKitters, This may be user error, or misunderstanding of rSMARTS, so can anyone throw some light on the following behaviour? First example works as expected - there are 2× Ph in m4, so we end up with 2×2×2 copies of the expected product: