wip

bayer/models.py

@@ -15,6 +15,7 @@ from epdb.models import (
     SimpleAmbitRule,
     SimpleRDKitRule,
 )
+from utilities.chem import FormatConverter
 
 
 class Package(EnviPathModel):
@@ -114,7 +115,9 @@ class PESCompound(Compound):
 
         # Check if we find a direct match for a given pes_link
         if PESStructure.objects.filter(pes_link=pes_url, compound__package=package).exists():
-            return PESStructure.objects.get(pes_link=pes_url, compound__package=package).compound
+            # Due to normalization we might end up in having multiple structures
+            # All of them point to the same compound -> pick any
+            return PESStructure.objects.filter(pes_link=pes_url, compound__package=package).first().compound
 
         # Generate Compound
         c = PESCompound()
@@ -135,19 +138,37 @@ class PESCompound(Compound):
 
         c.save()
 
+        molfile = pes_data.get("representativeStructures", [{}])[0].get("ctab")
+
+        if molfile is None:
+            raise ValueError("PES data does not contain a valid mol file!")
+
+        smiles = FormatConverter.to_smiles(FormatConverter.from_molfile(molfile))
+
+        standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
+
         is_standardized = standardized_smiles == smiles
 
         if not is_standardized:
-            _ = CompoundStructure.create(
+            _ = PESStructure.create(
                 c,
+                pes_url,
+                molfile,
                 standardized_smiles,
                 name="Normalized structure of {}".format(name),
                 description="{} (in its normalized form)".format(description),
                 normalized_structure=True,
             )
 
-        cs = CompoundStructure.create(
-            c, smiles, name=name, description=description, normalized_structure=is_standardized
+
+        cs = PESStructure.create(
+            c,
+            pes_url,
+            molfile,
+            smiles,
+            name=name,
+            description=description,
+            normalized_structure=is_standardized
         )
 
         c.default_structure = cs
@@ -159,6 +180,53 @@ class PESCompound(Compound):
 class PESStructure(CompoundStructure):
     pes_link = models.URLField(blank=False, null=False, verbose_name="PES Link")
 
+    @staticmethod
+    @transaction.atomic
+    def create(
+            compound: Compound,
+            pes_link: str,
+            mol_file: str,
+            smiles: str,
+            name: str = None,
+            description: str = None,
+            *args,
+            **kwargs
+    ):
+        if compound.pk is None:
+            raise ValueError("Unpersisted Compound! Persist compound first!")
+
+        cs = PESStructure()
+        # Clean for potential XSS
+        if name is not None:
+            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        if description is not None:
+            cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        cs.smiles = smiles
+        cs.mol_file = mol_file
+        cs.pes_link = pes_link
+        cs.compound = compound
+
+        if "normalized_structure" in kwargs:
+            cs.normalized_structure = kwargs["normalized_structure"]
+
+        cs.save()
+
+        return cs
+
+    @transaction.atomic
+    def add_structure(
+        self,
+        smiles: str,
+        name: str = None,
+        description: str = None,
+        default_structure: bool = False,
+        *args,
+        **kwargs,
+    ) -> "CompoundStructure":
+        raise ValueError("Not supported!")
+
     def d3_json(self):
         return {
             "is_pes": True,