I didn't realize that triple bonds could be aromatic. Here is a benzyne from ChEBI, specifically CHEBI:33831 from
http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33831 >>> from rdkit import Chem >>> mol = Chem.MolFromSmiles("COC1=CC#CC=C1") >>> Chem.MolToSmiles(mol) 'COc1cc#ccc1' I point this out because I've been going on the assumption that if the two atoms are marked as aromatic and there's no explicit bond type stated then it must be aromatic. Otherwise, an explicit '-', '=', or '#' indicate non-aromatic bonds. With this assumption, it's possible to read a correctly perceived structure without needing your own perception. This is what RDKit does with the default sanitize=True option in MolFromSmiles. It appears that RDKit implements the above assumption, which means that sanitize=False doesn't handle the outputted aromatic triple bond. >>> mol = Chem.MolFromSmiles("COc1cc#ccc1") >>> for bond in mol.GetBonds(): ... print bond.GetBondType(), bond.GetIsAromatic() ... SINGLE False SINGLE False AROMATIC True AROMATIC True TRIPLE True AROMATIC True AROMATIC True AROMATIC True >>> mol = Chem.MolFromSmiles("COc1cc#ccc1", False) >>> for bond in mol.GetBonds(): ... print bond.GetBondType(), bond.GetIsAromatic() ... SINGLE False SINGLE False AROMATIC True AROMATIC True TRIPLE False AROMATIC True AROMATIC True AROMATIC True >>> I assume that RDKit is not suppose to have accepted the triple bond as aromatic. If that's correct, I'll file this as a bug under that topic. Andrew [email protected] ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
