Hi Ansgar, It is possible to specify the tautomer parameter file that is used, but in order for me to explain how, I need to know how you are currently using the code to enumerate tautomers (i.e. which function you are calling).
As for the format: it's tab-delimited and the first entry is the name. The "r/f" flag is an indicator of which direction the transform is going that is just there to make the name unique. In the SMARTS the first atom is the one with the mobile H and the last atom is where it should be moved to. -greg On Mon, Jul 22, 2019 at 3:08 PM Schuffenhauer, Ansgar < ansgar.schuffenha...@novartis.com> wrote: > Dear all > > For the standardizer module (Chem.MolStandardize), what is the best way to > change some of the tautomerizer rules? > There is a data file in > share/RDKit/Data/Molstandardize/tautomerTransforms.in which I assume to > define the default. > > // Name SMARTS Bonds Charges > 1,3 (thio)keto/enol f [CX4!H0]-[C]=[O,S,Se,Te;X1] > 1,3 (thio)keto/enol r [O,S,Se,Te;X2!H0]-[C]=[C] > 1,5 (thio)keto/enol f [CX4,NX3;!H0]-[C]=[C][CH0]=[O,S,Se,Te;X1] > 1,5 (thio)keto/enol r [O,S,Se,Te;X2!H0]-[CH0]=[C]-[C]=[C,N] > ... > > Now my questions are > 1. What is the Syntax of this file? What does the "f" and the "r" stand > for? Do the smarts have to start with the atom carrying the mobile H? > 2. How can I instruct rdkit not to use this default file, but the one > supplied by the user. > > The background for this question that the smarts for keto/enol seems to be > a bit too generic, as it catches also the alpha C-atoms of carboxylic acids > and amides. Generation of tautomers here leads to a epimerization of > stereo-centers in alpha positions of carboxylic acids and amides. That > appears odd to me, as such stereo-centers are quite stable (in contrast to > those of "real" ketones and aldehydes). > > > Best regards > > Ansgar > > Ansgar Schuffenhauer > Senior Investigator I > T +41 79 608 9063 > ansgar.schuffenha...@novartis.com > > Novartis Pharma AG > NIBR > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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