On Tue, Oct 4, 2011 at 2:07 PM, gilleain torrance <[email protected]> wrote: > It seems like the problem is with the SMILESReader. Where your code has : > > SMILESReader sr = new SMILESReader(new StringReader(structure)); > MoleculeSet set = (MoleculeSet) sr.read(builder.newMoleculeSet()); > mol = set.getMolecule(0); > > you could use instead: > > SmilesParser parser = new SmilesParser(builder);
Agreed... if you are not working with File's or InputStream's, just use the SmilesParser. > 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. > which will preserve the double-bond structure in your smiles. That is weird, as I think that should be preserved anyway, because the CDK uses a flag to indicate that a IBond is aromatic, not the actual bond order... 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
