On Tue, Oct 4, 2011 at 2:36 PM, Egon Willighagen <[email protected]> wrote: > On Tue, Oct 4, 2011 at 2:07 PM, gilleain torrance >> parser.setPreservingAromaticity(true); >> mol = parser.parseSmiles(structure); >> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); > > Ah, a recent patch (well, about a year ago: > ae21ee2e39c61ae6d1c6aaf7f8919c0fb40170b3) caused atom typing to be not > perceived when aromaticity is not perceived. I puzzled why I was happy > with that change... I'll cook up a patch to ensure that atom types are > again perceived, even when aromaticity is taking literally from the > SMILES string.
I have dropped patches here: https://sourceforge.net/tracker/?func=detail&aid=3418458&group_id=20024&atid=320024# These will make the AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms() after the SMILES parsing redundant. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
