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
