Hi, I made a start on some tautomer enumeration and canonicalization code using RDKit in python a few months ago but got distracted before it was fully complete.
Here's what I have: https://gist.github.com/mcs07/9956421 It's a bit of a mess, but seems to work and might be useful if someone wants to build on it. One thing to note: I started by implementing the transforms using the RDKit reaction tools, but ran into problem with it incorrectly breaking open rings in certain cases (http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg03791.html). So I switched to just matching SMARTS and then adjusting the relevant bond orders and charges as needed. This seems to work alright in my limited testing. Also I just used the first canonical SMILES alphabetically to break a tie for the canonical tautomer, whereas as I believe the original implementation uses CACTVS hashcodes. Matt On 3 Apr 2014, at 15:55, Markus Sitzmann <[email protected]> wrote: > Hello, > > I was about to ask the same (I am one of the authors of the mentioned > paper) - I had seen this post (gosh, a year ago) but had no time back > then to answer (job search and a move from the US to Europe). > > I was digging into this last week a bit, however, I can not say much > yet - very initial work. If something comes out of it, I would > contribute it to RDKit. Well, if somebody has already done, I am > happy, too. Or we join forces (however, for me it is only some private > hacking with not so much time). > > Markus > > On Wed, Apr 2, 2014 at 11:32 AM, Dave W <[email protected]> wrote: >> Hi Markus and all, >> >> Did you or anyone else end up coding this up? I am looking into doing it >> myself, but if it's already been done... >> >> Many thanks, >> Dave >> >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
