Thank you very much for the detective work, Wim! This is helpful. It looks like the _reverse_ transition is possible, though. If I start by generating tautomers of "mol2", then "mol1" is recovered, which indicates this is an allowed transform. Is it possible that one direction is allowed but not the reverse?
Failing a solution there, does anyone know if it is possible to add SMIRKS to the allowed tautomers through the python interface? Thanks, Lewis On Mon, Feb 5, 2024 at 9:52 PM Wim Dehaen <wimdeh...@gmail.com> wrote: > hi lewis, > if i am not mistaken this is because the tautomer transfor "1,3 aromatic > heteroatom H shift" does not account for other chalcogens than oxygen, so > no selenium, tellurium or sulfur. > you can find the list of transforms here: > https://github.com/rdkit/rdkit/blob/8dae48b7a17fd984c69d04549e6d9b53690f5c52/Code/GraphMol/MolStandardize/TautomerCatalog/tautomerTransforms.in#L46 > (poiting to the line with the relevant transform). > best wishes > wim > > On Mon, Feb 5, 2024 at 3:26 AM Lewis Martin <lewis.marti...@gmail.com> > wrote: > >> Hi all, >> I'm looking at scoring tautomers, and using the 'tautobase' dataset used >> by Weider et al* at: >> >> https://github.com/choderalab/neutromeratio/blob/master/data/b3lyp_tautobase_subset.txt >> >> This dataset has pairs of tautomers with experimental logK values to >> determine the preferred tautomer. >> >> In at least one case, depending on which tautomer you use as the 'entry' >> point, the enumerated tautomers by RDKit either do or don't include both of >> the pair of input molecules. *I'm hoping there's a way to uniquely >> recover the full set of possible tautomers from using any input tautomer. * >> >> Here's a code example: >> >> from rdkit import Chem >>> >> from rdkit.Chem import Draw >> >> from rdkit.Chem.Draw import IPythonConsole >>> IPythonConsole.drawOptions.addStereoAnnotation = True >>> from rdkit.Chem.MolStandardize import rdMolStandardize >>> >>> #same result if you don't do any of these params. >> >> tautomer_params = Chem.MolStandardize.rdMolStandardize.CleanupParameters() >>> tautomer_params.tautomerRemoveSp3Stereo = False >>> tautomer_params.tautomerRemoveBondStereo = False >>> tautomer_params.tautomerRemoveIsotopicHs = False >>> tautomer_params.tautomerReassignStereo = False >>> tautomer_params.doCanonical = True >>> >>> enumerator = rdMolStandardize.TautomerEnumerator(tautomer_params) >>> >>> smi1 = 'Sc1cc2ccccc2cn1' >>> smi2 = 'S=c1cc2ccccc2c[nH]1' >>> mol1 = Chem.MolFromSmiles(smi1) >>> mol2 = Chem.MolFromSmiles(smi2) >>> >>> #choose mol1 or mol2 to be source of tautomers: >>> #choose mol1, and look at the tautomers. Note that mol2 isn't present! >>> tauts = [Chem.MolFromSmiles(Chem.MolToSmiles(m)) for m in >>> enumerator.Enumerate(mol1)] >>> >>> Draw.MolsToGridImage([mol1, mol2]+tauts, legends=['mol1', 'mol2 (not >>> present in tauts!)'] + [f'taut{i}' for i in range(len(tauts))], >>> molsPerRow=4) >>> >> >> And a picture of this in a notebook for an at-a-glance view: >> https://gist.github.com/ljmartin/4a9d9eb684df3e11e59fc6502a4b7b03 >> >> Does anyone know a way to recover "mol2" within tautomers of "mol1"? >> >> Thank you! >> Lewis >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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