Hi Greg Very useful. Thank you. I’ll be able to deal with the SMARTS part myself
But your answer has left me with another series of questions: You are saying that I am still using the old MolVS code for tautomer processing. That explains why the performance in terms of execution speed is not yet fully at the level I am used to expect from rdkit (no complaint meant, you just have set the bar quite high with rdkit in general). Are you saying, that actually with respect to tautomer standardization there is no C++ port from Google Summer of Code? Or is there something, which is not quite ready? Or is there a tautomer code in the C++ and I am just not using it? In this case, what would be the right function to use? What is your recommendation when it comes to tautomer standardization? . For the sake of clarity I am looking for a tautomer standardizer, that does produce a uniform, canonical tautomer, I am not asking for the pyhsical.-chemical right, that is lowest energy energy one, as this is a task I assume no simple rule based tautomer standardizer can perform. Is the C++ port everything that is in rdkit.Chem.MolStandardize.rdMolStandardize? 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: Dienstag, 23. Juli 2019 14:43 To: Schuffenhauer, Ansgar <ansgar.schuffenha...@novartis.com> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: rdkit.MolStandardize tautomer Hi Ansgar, This is still using the MolVS tautomer-handling code since we didn't finish the canonicalization part during last year's Google Summer of Code.[1] That means it's not using the parameter file that you found. The rules that are used are here: https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/MolStandardize/tautomer.py<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rdkit_rdkit_blob_master_rdkit_Chem_MolStandardize_tautomer.py&d=DwMFaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I&m=BnaAWSqyTt4tDiaikrUZmNMgOhNeWPi73bwdA9j4-T8&s=d5ldgC12XWgrCnPLSa9hZ9_B2zYRiw8riuv93BTPsz0&e=> You can change those at runtime, but it you need to be careful to properly re-import modules after doing so. Here's an example showing how to do that: https://gist.github.com/greglandrum/4ac2b4e7f8c61e25836e106467aef150<https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com_greglandrum_4ac2b4e7f8c61e25836e106467aef150&d=DwMFaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I&m=BnaAWSqyTt4tDiaikrUZmNMgOhNeWPi73bwdA9j4-T8&s=Q-EeeeZdfD5bjCY_U7PrtfL5iHexxeP7faW30BsozuM&e=> I'm not going to claim that the SMARTS which I constructed to change the 1,3 (thio)ketol/enol is the right one, but it does at least show how to make the changes and reload the standardize module so that it takes effect. I hope this helps, -greg [1] and I haven't made it a priority because I dread the "no, that's not the right canonical tautomer" arguments that will ensue On Tue, Jul 23, 2019 at 8:54 AM Schuffenhauer, Ansgar <ansgar.schuffenha...@novartis.com<mailto:ansgar.schuffenha...@novartis.com>> wrote: 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rdkit_rdkit_issues_2363&d=DwMFaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I&m=BnaAWSqyTt4tDiaikrUZmNMgOhNeWPi73bwdA9j4-T8&s=bALfjkh7w44Zp0A885uv77DRWnreozm-_FML9XdeW60&e=> 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<mailto:greg.land...@gmail.com>> Sent: Montag, 22. Juli 2019 17:42 To: Schuffenhauer, Ansgar <ansgar.schuffenha...@novartis.com<mailto:ansgar.schuffenha...@novartis.com>> Cc: rdkit-discuss@lists.sourceforge.net<mailto: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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