I've edited the SMILES writer so that it doesn't add hydrogens to chiral centers (and fixed the resulting problems)...but tautomer test is still failing.
- Noel On 30 May 2012 16:29, Craig James <cja...@emolecules.com> wrote: > Hi Tim, > > When I reverted the SMILES canonicalizer (that is, > SMIBaseFormat::WriteMolecule()) back so that it doesn't copy the molecule, I > solved the performance problem, but it causes the Tautomer Test to fail. > I've looked through your tautomer code briefly, but before I spend a great > deal of time figuring it all out, I wonder if you can spot the problem > quickly since you wrote the tautomer code. > > My guess is that the SMILES canonicalizer screws up your tautomer code > because it adds explicit hydrogens to chiral centers (mostly for convenience > so that there would always be four bonds to every tetrahedral center), which > understandably would alter the nature of what the tautomer generator is > doing. > > So the first question: Does the SMILES canonicalizer still need to add > explicit hydrogens to the chiral atoms? You rewrote all of the stereo code, > and I wonder if the extra hydrogens are even necessary. I looked through > the graphsym.cpp can canon.cpp files and couldn't see any need for the > explicit hydrogens. I might try disabling the add-explicit-hydrogens > feature and see if the tests still pass, but I prefer a more analytical > approach. > > Second question: Is there some reason why the tautomer code gets screwed up > by the added explicit hydrogens? Is it something that could be fixed > easily? > > I'm going to dig around an older version of smilesformat.cpp and canon.cpp > to refresh my memory about where the explicit hydrogens were needed. > > Thanks, > Craig > > ------------------------------------------------------------------------------ > 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 > ------------------------------------------------------------------------------ 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
