Re: [Rdkit-discuss] One tautomer not included in list of enumerated tautomers

[Wim D. <wim...@gm...>]

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 <lew...@gm...>
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
>
>
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