fix: Adds lhs_pdb to ComputedMolecule (also move to Python 3.11.7)

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.11.6-slim-bullseye
+FROM python:3.11.7-slim-bullseye
 
 # We rely on the presence of a requirements.txt file in project root.
 # This is achieved prior to a container build using poetry

viewer/cset_upload.py

@@ -306,12 +306,10 @@ def set_mol(
             long_inchi = inchi
             inchi = inchi[:254]
 
-        ref_cpd: Compound = self.create_mol(
+        compound: Compound = self.create_mol(
             inchi, name=molecule_name, long_inchi=long_inchi
         )
 
-        mol_block = Chem.MolToMolBlock(mol)
-
         insp = mol.GetProp('ref_mols')
         insp = insp.split(',')
         insp = [i.strip() for i in insp]
@@ -345,8 +343,6 @@ def set_mol(
 
             insp_frags.append(ref)
 
-        _ = mol.GetProp('original SMILES')
-
         # Try to get the SiteObservation.
         # This may fail.
         prot = self.get_site_observation(
@@ -377,10 +373,17 @@ def set_mol(
             logger.info('Creating new ComputedMolecule')
             computed_molecule = ComputedMolecule()
 
+        lhs_pdb = None
+        if mol.HasProp('lhs_pdb'):
+            lhs_pdb = mol.GetProp('lhs_pdb')
+        elif mol.HasProp('ref_pdb'):
+            lhs_pdb = mol.GetProp('ref_pdb')
+
         assert computed_molecule
-        computed_molecule.compound = ref_cpd
+        computed_molecule.compound = compound
         computed_molecule.computed_set = compound_set
-        computed_molecule.sdf_info = mol_block
+        computed_molecule.sdf_info = Chem.MolToMolBlock(mol)
+        computed_molecule.lhs_pdb = lhs_pdb
         computed_molecule.molecule_name = molecule_name
         computed_molecule.name = f"{target}-{computed_molecule.identifier}"
         computed_molecule.smiles = smiles

viewer/migrations/0026_add_lhs_pdb_to_computedmolecule.py

@@ -0,0 +1,22 @@
+# Generated by Django 3.2.23 on 2023-12-21 14:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('viewer', '0025_increase_length_of_computedset_method'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='computedmolecule',
+            name='lhs_pdb',
+            field=models.TextField(
+                blank=True,
+                help_text='Set from the lhs_pdb or ref_pdb property of the underlying Molecule',
+                max_length=50,
+                null=True,
+            ),
+        ),
+    ]

viewer/models.py

@@ -876,6 +876,12 @@ class ComputedMolecule(models.Model):
 
     compound = models.ForeignKey(Compound, on_delete=models.CASCADE)
     sdf_info = models.TextField(help_text="The 3D coordinates for the molecule")
+    lhs_pdb = models.TextField(
+        max_length=MOLECULE_NAME_LENGTH,
+        help_text="Set from the lhs_pdb or ref_pdb property of the underlying Molecule",
+        null=True,
+        blank=True,
+    )
     computed_set = models.ForeignKey(ComputedSet, on_delete=models.CASCADE)
     name = models.CharField(
         max_length=50, help_text="A combination of Target and Identifier"
@@ -911,11 +917,12 @@ def __str__(self) -> str:
         return f"{self.smiles}"
 
     def __repr__(self) -> str:
-        return "<ComputedMolecule %r %r %r %r>" % (
+        return "<ComputedMolecule %r %r %r %r %r>" % (
             self.id,
             self.smiles,
             self.name,
             self.compound,
+            self.lhs_pdb,
         )