Add secondary shell residues and their stabilising contacts

build/build.py

@@ -97,7 +97,7 @@ def main():
     print(f"{len(codes_to_check)} of these need to be checked")
 
     # Check
-    for code in tqdm(codes_to_check):
+    for code in tqdm(codes_to_check[:500]):
         with transaction.atomic():
             process_pdb_code(code)
 

build/factories.py

@@ -78,15 +78,31 @@ def create_site_record(site_dict, pdb_record, index, chains_dict):
     atoms_dict = {}
     for res in sorted(site_dict["residues"], key=lambda r: r.id):
         chain_record = chains_dict[res.chain.id] if isinstance(res, atomium.Residue) else None
-        create_residue_record(res, chain_record, site_record, atoms_dict)
+        create_residue_record(res, site_record, atoms_dict, chain_record)
+
+    # Add secondary residues
+    second_residues,  stabiliser_contacts = set(), set()
+    for residue in site_dict["residues"]:
+        for atom in residue.atoms():
+            nearby = atom.nearby_atoms(3)
+            for nearby_atom in nearby:
+                if isinstance(nearby_atom.het, atomium.Residue)\
+                 and nearby_atom.het not in site_dict["residues"]:
+                    second_residues.add(nearby_atom.het)
+                    stabiliser_contacts.add((atom, nearby_atom))
+    for res in second_residues:
+        create_residue_record(res, site_record, atoms_dict, primary=False)
 
     # Create bond records
     for metal, atoms in sorted(site_dict["metals"].items(), key=lambda a: a[0].id):
         for atom in sorted(atoms, key=lambda a: a.id):
             CoordinateBond.objects.create(
              metal=metals_dict[metal.id], atom=atoms_dict[atom]
             )
-
+    for primary, secondary in stabiliser_contacts:
+        StabilisingBond.objects.create(
+         primary_atom=atoms_dict[primary], secondary_atom=atoms_dict[secondary]
+        )
     return site_record
 
 
@@ -98,7 +114,7 @@ def create_chain_interaction_record(chain_record, site_record, sequence):
     )
 
 
-def create_residue_record(residue, chain_record, site_record, atoms_dict):
+def create_residue_record(residue, site_record, atoms_dict, chain_record=None, primary=True):
     """Creates a Residue record along with its atoms, from information given. A
     dictionary of atoms must be given to make coordinate bonds later."""
 
@@ -115,7 +131,7 @@ def create_residue_record(residue, chain_record, site_record, atoms_dict):
     signature = ".".join(signature)
     residue_record = Residue.objects.create(
      residue_number=numeric_id, chain_identifier=residue.chain.id,
-     insertion_code=insertion, chain_signature=signature,
+     insertion_code=insertion, chain_signature=signature, primary=primary,
      name=residue.name, chain=chain_record, site=site_record, atomium_id=residue.id
     )
     for atom in sorted(residue.atoms(), key=lambda a: a.id):

core/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 2.2 on 2019-06-16 17:53
+# Generated by Django 2.2 on 2019-09-25 13:27
 
 from django.db import migrations, models
 import django.db.models.deletion
@@ -94,6 +94,17 @@ class Migration(migrations.Migration):
                 'db_table': 'zinc_sites',
             },
         ),
+        migrations.CreateModel(
+            name='StabilisingBond',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('primary_atom', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='primary_atoms', to='core.Atom')),
+                ('secondary_atom', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='secondary_atoms', to='core.Atom')),
+            ],
+            options={
+                'db_table': 'stabilising_bonds',
+            },
+        ),
         migrations.CreateModel(
             name='Residue',
             fields=[
@@ -104,6 +115,7 @@ class Migration(migrations.Migration):
                 ('atomium_id', models.CharField(max_length=128)),
                 ('chain_identifier', models.CharField(max_length=128)),
                 ('chain_signature', models.CharField(blank=True, max_length=128)),
+                ('primary', models.BooleanField(default=True)),
                 ('chain', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.Chain')),
                 ('site', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.ZincSite')),
             ],
@@ -142,7 +154,7 @@ class Migration(migrations.Migration):
                 ('metal', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.Metal')),
             ],
             options={
-                'db_table': 'bonds',
+                'db_table': 'coordinate_bonds',
             },
         ),
         migrations.CreateModel(

core/models.py

@@ -170,7 +170,18 @@ class CoordinateBond(models.Model):
     """A bond between a metal atom and a liganding atom."""
 
     class Meta:
-        db_table = "bonds"
+        db_table = "coordinate_bonds"
 
     metal = models.ForeignKey(Metal, on_delete=models.CASCADE)
-    atom = models.ForeignKey(Atom, on_delete=models.CASCADE)
+    atom = models.ForeignKey(Atom, on_delete=models.CASCADE)
+
+
+
+class StabilisingBond(models.Model):
+    """A bond between a primary residie atom and a secondary residue atom."""
+
+    class Meta:
+        db_table = "stabilising_bonds"
+
+    primary_atom = models.ForeignKey(Atom, on_delete=models.CASCADE, related_name="primary_atoms")
+    secondary_atom = models.ForeignKey(Atom, on_delete=models.CASCADE, related_name="secondary_atoms")

tests/test_build.py

@@ -192,7 +192,7 @@ def test_can_work_properly(self):
         self.assertEqual(metal.z, 15.281)
         self.assertEqual(metal.omission_reason, None)
 
-        residues = site.residue_set.all()
+        residues = site.residue_set.filter(primary=True)
         self.assertEqual(residues.count(), 4)
         res1 = residues.get(atomium_id="A.94")
         self.assertEqual(res1.name, "HIS")