Hi All, Thanks for the replies.
Matthew - I ran into the same problem as you with the reaction breaking ring bonds. My "hack" solutions was to check that the Murcko Generic Frameworks matched. This almost seems to work... almost. :) I shall take a look at your implementation. Cheers, Dave On Thu, Apr 3, 2014 at 4:26 PM, Matthew Swain <[email protected]> wrote: > 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 > > -- *Dr David Wood* *Molplex Pharmaceuticals* *The Biohub at Alderley Park* *Macclesfield* *Cheshire* *SK10 4TG* *01625 238702* *[email protected] <[email protected]>*
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