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[Fix] Compound Grouping, Identity prediction of enviFormer, Setting params (#337)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#337
This commit is contained in:
jebus
2026-02-20 10:14:28 +13:00
parent 0ff046363c
commit d2c2e643cb
8 changed files with 43 additions and 20 deletions
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21
epdb/models.py
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@ -769,7 +769,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
num_structs = self.structures.count()
stand_smiles = set()
for structure in self.structures.all():
stand_smiles.add(FormatConverter.standardize(structure.smiles))
stand_smiles.add(FormatConverter.standardize(structure.smiles, remove_stereo=True))
if len(stand_smiles) != 1:
logger.debug(
@ -838,7 +838,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
if parsed is None:
raise ValueError("Given SMILES is invalid")
standardized_smiles = FormatConverter.standardize(smiles)
standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
# Check if we find a direct match for a given SMILES
if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
@ -911,7 +911,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
if parsed is None:
raise ValueError("Given SMILES is invalid")
standardized_smiles = FormatConverter.standardize(smiles)
standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
is_standardized = standardized_smiles == smiles
@ -2011,19 +2011,23 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
# Clean for potential XSS
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
is_generic_name = False
if name is None or name == "":
name = f"Pathway {Pathway.objects.filter(package=package).count() + 1}"
is_generic_name = True
pw.name = name
if description is not None and description.strip() != "":
pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
pw.predicted = predicted
pw.save()
try:
# create root node
Node.create(pw, smiles, 0)
Node.create(pw, smiles, 0, name=name if not is_generic_name else None)
except ValueError as e:
# Node creation failed, most likely due to an invalid smiles
# delete this pathway...
@ -3445,10 +3449,17 @@ class EnviFormer(PackageBasedModel):
for smile in smi.split(".")
]
)
if smi in canon_smiles:
logger.debug(f"Found input SMILES={smi} in prediction results. Skipping...")
continue
except ValueError: # This occurs when the predicted string is an invalid SMILES
logging.info(f"EnviFormer predicted an invalid SMILES: {smi}")
continue
res.append(PredictionResult([ProductSet([smi])], prob, None))
results.append(res)
return results
@ -3587,7 +3598,7 @@ class EnviFormer(PackageBasedModel):
)
root_node = ".".join(
[
FormatConverter.standardize(smile)
FormatConverter.standardize(smile, remove_stereo=True)
for smile in root_node[0].default_node_label.smiles.split(".")
]
)