Hi Greg Thanks for your quick answer. What I am doing is essentially the following:
from rdkit.Chem import MolStandardize my_standardizer = MolStandardize.standardize.Standardizer() standard_tautomer = my_standardizer.tautomer_parent(input_mol) I assume that at the stage I construct my_standardizer there would be some opportunity slip in an alternative configuration info By the way, I think also that one of the two cases of vanishing stereo-chemistry reported in https://github.com/rdkit/rdkit/issues/2363 is caused by an overly eager keto/enol tautomerizer. Best regards Ansgar Ansgar Schuffenhauer Senior Investigator I T +41 79 608 9063 ansgar.schuffenha...@novartis.com<mailto:ansgar.schuffenha...@novartis.com> Novartis Pharma AG NIBR From: Greg Landrum <greg.land...@gmail.com> Sent: Montag, 22. Juli 2019 17:42 To: Schuffenhauer, Ansgar <ansgar.schuffenha...@novartis.com> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 141, Issue 16 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<mailto: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<mailto:ansgar.schuffenha...@novartis.com> Novartis Pharma AG NIBR _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_rdkit-2Ddiscuss&d=DwMFaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I&m=uiXOLxD_7MgeeA9MyeUBlDB3ufzf53oBws3smVh4cc8&s=L4Bzk6_VPaAqyj_iM8_9rz9diujKH9rSgsNrvBa5958&e=>
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