jebus/enviPy-bayer
1
0
Fork 0
forked from enviPath/enviPy
Code Issues Pull Requests Actions Releases Activity

pyproject.toml update and merge from develop

Browse Source
This commit is contained in:
Liam Brydon
2025-11-07 08:09:06 +13:00
parent 8282855975
commit 6a5413b492
7 changed files with 242 additions and 41 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
epdb/models.py
View File

@ -311,7 +311,7 @@ class ExternalDatabase(TimeStampedModel):
},
{
"database": ExternalDatabase.objects.get(name="ChEBI"),
"placeholder": "ChEBI ID without prefix e.g. 12345",
"placeholder": "ChEBI ID without prefix e.g. 10576",
},
],
"structure": [
@ -329,7 +329,7 @@ class ExternalDatabase(TimeStampedModel):
},
{
"database": ExternalDatabase.objects.get(name="ChEBI"),
"placeholder": "ChEBI ID without prefix e.g. 12345",
"placeholder": "ChEBI ID without prefix e.g. 10576",
},
],
"reaction": [
@ -343,7 +343,7 @@ class ExternalDatabase(TimeStampedModel):
},
{
"database": ExternalDatabase.objects.get(name="UniProt"),
"placeholder": "Query ID for UniPro e.g. rhea:12345",
"placeholder": "Query ID for UniProt e.g. rhea:12345",
},
],
}
@ -478,7 +478,7 @@ class ChemicalIdentifierMixin(ExternalIdentifierMixin):
return self.add_external_identifier("CAS", cas_number)
def get_pubchem_identifiers(self):
return self.get_external_identifier("PubChem Compound") or self.get_external_identifier(
return self.get_external_identifier("PubChem Compound") | self.get_external_identifier(
"PubChem Substance"
)
@ -3001,6 +3001,7 @@ class EnviFormer(PackageBasedModel):
@cached_property
def model(self):
from enviformer import load
ckpt = os.path.join(s.MODEL_DIR, "enviformer", str(self.uuid), f"{self.uuid}.ckpt")
mod = load(device=s.ENVIFORMER_DEVICE, ckpt_path=ckpt)
return mod
@ -3020,7 +3021,9 @@ class EnviFormer(PackageBasedModel):
start = datetime.now()
products_list = self.model.predict_batch(canon_smiles)
end = datetime.now()
logger.info(f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}")
logger.info(
f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}"
)
results = []
for products in products_list: