def validate_inchikey_computable(molfile: str) -> None:
"""Validates that an InChIKey can be computed from the provided molfile.
Args:
molfile: The molfile string
Raises:
ValidationError: If the InChIKey cannot be computed.
"""
try:
get_inchikey(molfile)
except IndigoException:
raise ValidationError(
"InChIKey not computable for provided structure.")
def to_internal_value(self, data):
matched_fields = set(self.alt_structures) & set(
self.initial_data.keys())
formatted_fields = [
format_value(f) for f in sorted(self.alt_structures)
]
formatted_matched_fields = [
format_value(f) for f in sorted(matched_fields)
]
if not matched_fields:
raise ValidationError({
"non_field_errors":
f"One of {sorted(formatted_fields)} required."
})
if len(matched_fields) > 1:
raise ValidationError({
"non_field_errors":
(f"Only one of {formatted_fields} allowed. "
f"Recieved {formatted_matched_fields}.")
})
data = super().to_internal_value(data) # calls field validators
structure = next(k for k in self.alt_structures if k in data)
data["molfile_v3000"] = get_molfile_v3000(data.pop(structure))
if "inchikey" not in data:
data["inchikey"] = get_inchikey(data["molfile_v3000"])
return data
def filter_smiles(self, queryset, name, value):
validate_smiles(value)
validate_inchikey_computable(value)
# There is an inconsistency w/ inchikey conversion, discussion below
# https://github.com/Chemical-Curation/chemcurator_django/pull/224#issuecomment-675129692
value = get_molfile_v3000(value)
inchikey = get_inchikey(value)
return queryset.filter(inchikey=inchikey)
def filter_molfile_v2000(self, queryset, name, value):
validate_molfile_v2000(value)
validate_inchikey_computable(value)
inchikey = get_inchikey(value)
return queryset.filter(inchikey=inchikey)
def get_calculated_inchikey(self, obj):
return get_inchikey(obj.molfile_v3000)
def _inchikey(self):
"""Computes the inchikey from the molfile."""
try:
return get_inchikey(self.molfile_v3000)
except IndigoException:
return None