If I make a file foo.smi with just this in it: [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1ccccc1c2=O
And then make and use an index file: ~/openbabel/bin/obabel foo.smi -ofs ~/openbabel/bin/obabel foo.fs -ocan -sfoo.smi -at5 -aa --title "" I find that the structure is only 0.7 similar to itself. I thought the explicit double bond between the two aromatic carbons "c2=c1" was the problem, and tried removing it, but the canonicalization process just adds it back in. The molecule was originally drawn in Kekule form in an sdf and converted to the above SMILES by obabel. Open Babel Version 2.3.1 Is this a bug, or just the kind of ambiguity one has to live with when working with weird molecules? Thanks, Jeff ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
