Re: [Rdkit-discuss] SMARTS/SMARTS and SMILES/SMARTS substructure matching

2014-03-07 Thread Toby Wright
Thanks Greg, The final strange behaviour I've noticed that could trip fellow users up is with matching kekule verses aromatic representations of the same molecule in SMARTS against SMILES. Most surprisingly C1=CC=CC=C1 is not a substructure of itself but has c1c1 as a substructure (if the

Re: [Rdkit-discuss] SMARTS/SMARTS and SMILES/SMARTS substructure matching

2014-03-07 Thread Greg Landrum
Hi Toby, On Fri, Mar 7, 2014 at 11:57 AM, Toby Wright toby.wri...@inhibox.comwrote: Thanks Greg, The final strange behaviour I've noticed that could trip fellow users up is with matching kekule verses aromatic representations of the same molecule in SMARTS against SMILES. Most surprisingly

Re: [Rdkit-discuss] SMARTS/SMARTS and SMILES/SMARTS substructure matching

2014-03-05 Thread Christos Kannas
Hi Greg, Thanks a lot for the explanation. It makes things clearer now. Well the reason I'm doing SMARTS-SMARTS match is because I would like to match functional groups with the reactants in reactions. Regards, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob

Re: [Rdkit-discuss] SMARTS/SMARTS and SMILES/SMARTS substructure matching

2014-03-05 Thread Toby Wright
Hi, This is probably related to the above so I thought I'd post it on this thread. I am noticing inconsistent behaviour when a molecule created via SMARTS that contains an 'or' statement has HasSubstructMatch called on it, as opposed to it being the argument to HasSubstructMatch. A simple example