On 24/05/2012 23:56, Craig James wrote: > If I'm not mistaken, these two SMILES should represent the same > molecule, but OB thinks they're different: > > c1ncccc1 > c1[n]cccc1 > > According to the SMILES spec, putting the nitrogen in brackets only says > that its charge is zero and H-count is zero, which are the defaults when > the nitrogen is written as "n". > > But OpenBabel thinks they're different. Note the "M RAD" line in the > second one. > > $ echo "c1ncccc1" | babel -i smi -o sdf > > OpenBabel05241215472D > > 6 6 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 6 1 0 0 0 0 > 1 2 2 0 0 0 0 > 2 3 1 0 0 0 0 > 3 4 2 0 0 0 0 > 4 5 1 0 0 0 0 > 5 6 2 0 0 0 0 > M END > $$$$ > > [carbon:cj] ~/tmp $ echo "c1[n]cccc1" | babel -i smi -o sdf > > OpenBabel05241215472D > > 6 6 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 6 1 0 0 0 0 > 1 2 2 0 0 0 0 > 2 3 1 0 0 0 0 > 3 4 2 0 0 0 0 > 4 5 1 0 0 0 0 > 5 6 2 0 0 0 0 > M RAD 1 2 2 > M END > $$$$ > > This causes the SMILES writer to generate two different SMILES for this > molecule, one with [n] and one with a bare "n". > > Is my analysis correct? Any idea where to begin looking to fix this?
This is caused by OBAtomTyper::CorrectAromaticNitrogens() which was present in prehistory but its purpose has never been apparent. It is deprecated, said to be "currently unused for anything significant" and "currently sets OBMol::SetAromaticCorrected and returns". This wasn't so, but is now, and the example above now works properly. I expect the dashboard will throw up any unexpected side effects. Chris ------------------------------------------------------------------------------ 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-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
