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[Fix] Canonicalize SMILES when checking overlaps in smiles_covered_by (#443)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#443
This commit is contained in:
jebus
2026-08-12 21:01:41 +12:00
parent 093daa5ecf
commit ada270aa3c
2 changed files with 36 additions and 20 deletions
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26
utilities/chem.py
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@ -68,6 +68,8 @@ class PredictionResult(object):
class FormatConverter(object):
tautomer_enumerator = rdMolStandardize.TautomerEnumerator()
@staticmethod
def mass(smiles):
return Descriptors.MolWt(FormatConverter.from_smiles(smiles))
@ -240,8 +242,9 @@ class FormatConverter(object):
Chem.RemoveStereochemistry(res_mol)
if canonicalize_tautomers:
te = rdMolStandardize.TautomerEnumerator() # idem
res_mol = te.Canonicalize(res_mol)
tautomers = FormatConverter.tautomer_enumerator.Enumerate(res_mol)
if len(tautomers) >= 1:
res_mol = FormatConverter.tautomer_enumerator.PickCanonical(tautomers)
return Chem.MolToSmiles(res_mol, kekuleSmiles=True)
@ -389,7 +392,7 @@ class FormatConverter(object):
prods.append(p)
except ValueError as e:
logger.error(f"Sanitizing and converting failed:\n{e}")
logger.debug(f"Sanitizing and converting failed:\n{e}")
continue
if len(prods):
@ -397,7 +400,8 @@ class FormatConverter(object):
pss.add(ps)
except Exception as e:
logger.error(f"Applying {smirks} on {smiles} failed:\n{e}")
logger.debug(f"Applying {smirks} on {smiles} failed:\n{e}")
pass
return list(pss)
@ -482,8 +486,10 @@ class FormatConverter(object):
if standardize:
for smi in l_smiles:
try:
smi = FormatConverter.standardize(
smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
smi = FormatConverter.canonicalize(
FormatConverter.standardize(
smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
)
)
except Exception:
# :shrug:
@ -497,8 +503,12 @@ class FormatConverter(object):
if standardize:
for smi in r_smiles:
try:
smi = FormatConverter.standardize(
smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
smi = FormatConverter.canonicalize(
FormatConverter.standardize(
smi,
remove_stereo=True,
canonicalize_tautomers=canonicalize_tautomers,
)
)
except Exception:
# :shrug: