Comments (3)
NADH looks like this
original_smiles = 'NC(=O)C1=CN([C@@H]2O[C@H](COP(=O)(O)OP(=O)(O)OC[C@H]3O[C@@H](N4C=NC5=C4N=CN=C5N)[C@H](O)[C@@H]3O)[C@@H](O)[C@H]2O)C=CC1'
original_mol = Chem.MolFromSmiles(original_smiles)
tautomerized_mol = TautomerCanonicalizer().canonicalize(original_mol)
Draw.MolsToGridImage([original_mol,tautomerized_mol],
molsPerRow=1,subImgSize=(600,300),
legends=['original','tautomer'])
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I think this is caused by the phosphonic acid rules: https://github.com/mcs07/MolVS/blob/master/molvs/tautomer.py#L130
It can probably be fixed by making the SMARTS pattern more strict to match only the intended target:
https://en.wikipedia.org/wiki/Phosphorous_acid
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You are correct, removing that rule stops that moiety from being modified. When you say, "more strict", you think specify an explicit number of bonds on the Phosphorous in the SMARTS pattern?
Why does rdkit allow 7 bonds on the phosphorous? Rdkit is a vast package, but looking at the definition of Phosphorous, it has max bonds of 5.
If I do SantizeMol, the hydrogen stays put. When I paste the structure into ChemDraw, its not valid.
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Related Issues (20)
- Triazole tautomers not normalized
- Tautomer patterns should be referenced to their original research paper.
- Molecule did not standardise overnight HOT 4
- error standardizing ionization HOT 1
- Is there salt removal implemented in there? HOT 3
- molvs hugs on some molecules HOT 2
- MolVS 0.1.0 Standardization fails on Python 3 HOT 6
- Fluorine considered metal HOT 1
- stdout=False - output is still printed
- Propagate the warning 'Tautomer enumeration stopped at maximum... '
- test_tautomer.py extended results in C++ implementation HOT 1
- Only one molecule from the input SMILES file is processed... HOT 7
- Tautomer canonicalization bug
- standardize should unsalt
- standardize script of mol file without rdkit or openbabel HOT 2
- RDKit Integration HOT 6
- tautomer.TautomerEnumerator() function HOT 6
- Unable to standardize some PubChem molecules HOT 1
- Missing preferred citation format in the documentation.
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