similarity + substructure + smarts search endpoints created

Author: brokesm

src/genui/apps.py

@@ -18,6 +18,7 @@
     'genui.qsar',
     'genui.generators',
     'genui.maps',
+    'genui.search',
 ]
 
 def extensions():

src/genui/compounds/initializers/base.py

@@ -8,6 +8,9 @@
 
 from django.db import transaction, IntegrityError
 from rdkit import Chem
+from rdkit.Chem import AllChem
+from rdkit.Chem import MACCSkeys
+
 
 from genui.compounds.initializers.exceptions import SMILESParsingError, StandardizationError, \
     InconsistentIdentifiersException
@@ -102,6 +105,8 @@ def createChemicalEntity(self, smiles):
         canon_smiles = Chem.MolToSmiles(rdmol_std, isomericSmiles=True, canonical=True, allHsExplicit=False)
         inchi = Chem.MolToInchi(rdmol_std)
         inchi_key = Chem.InchiToInchiKey(inchi)
+        morganFP = AllChem.GetMorganFingerprintAsBitVect(rdmol_std)
+        maccsFP = MACCSkeys.GenMACCSKeys(rdmol_std)
         if ChemicalEntity.objects.filter(inchiKey=inchi_key).exists():
             ret = ChemicalEntity.objects.get(
                 inchiKey=inchi_key
@@ -117,7 +122,9 @@ def createChemicalEntity(self, smiles):
                     canonicalSMILES=canon_smiles,
                     inchi=inchi,
                     inchiKey=inchi_key,
-                    rdMol=canon_smiles
+                    rdMol=canon_smiles,
+                    morganFP=morganFP,
+                    maccsFP=maccsFP
                 )
             except IntegrityError as exp:
                 attempted = {

src/genui/compounds/migrations/0003_add_compound_fingerprints.py

@@ -0,0 +1,19 @@
+# Generated by Django 5.1.3 on 2026-01-14 13:41
+
+import django_rdkit.models.fields
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('compounds', '0002_initial'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='chemicalentity',
+            name='maccsFP',
+            field=django_rdkit.models.fields.BfpField(null=True),
+        ),
+    ]

src/genui/compounds/migrations/0004_index_fingerprints.py

@@ -0,0 +1,26 @@
+# Generated by Django 5.1.3 on 2026-01-14 14:26
+
+import django.contrib.postgres.indexes
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('compounds', '0003_add_compound_fingerprints'),
+    ]
+
+    operations = [
+        migrations.AddIndex(
+            model_name='chemicalentity',
+            index=django.contrib.postgres.indexes.GistIndex(fields=['rdMol'], name='compounds_c_rdMol_19154a_gist'),
+        ),
+        migrations.AddIndex(
+            model_name='chemicalentity',
+            index=django.contrib.postgres.indexes.GistIndex(fields=['morganFP'], name='compounds_c_morganF_b5466a_gist'),
+        ),
+        migrations.AddIndex(
+            model_name='chemicalentity',
+            index=django.contrib.postgres.indexes.GistIndex(fields=['maccsFP'], name='compounds_c_maccsFP_9a9ce4_gist'),
+        ),
+    ]

src/genui/compounds/models.py

@@ -1,5 +1,6 @@
 from django.db.models import Count
 from django_rdkit import models
+from django.contrib.postgres.indexes import GistIndex
 from djcelery_model.models import TaskMixin
 from polymorphic.models import PolymorphicModel
 from rdkit import Chem
@@ -93,9 +94,15 @@ class ChemicalEntity(models.Model):
     # from django-rdkit
     rdMol = models.MolField()
     morganFP = models.BfpField(null=True)
+    maccsFP = models.BfpField(null=True)
 
     class Meta:
         unique_together = ('canonicalSMILES', 'inchiKey')
+        indexes = [
+            GistIndex(fields=['rdMol']),
+            GistIndex(fields=['morganFP']),
+            GistIndex(fields=['maccsFP']),
+        ]
 
     def __str__(self):
         return '%s object <%s>' % (self.__class__.__name__, self.inchiKey)

src/genui/search/__init__.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

src/genui/search/admin.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class SearchConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'genui.search'

src/genui/search/apps.py

@@ -0,0 +1,17 @@
+"""
+genuisetup.py in src/genui/search/
+
+"""
+
+PARENT = 'genui'
+
+def setup(*args, **kwargs):
+    from . import models
+    from genui.utils.init import createGroup
+    createGroup(
+        "GenUI_Users",
+        [
+            models.SearchMolecule,
+            models.SearchMolSet
+        ]
+    )

src/genui/search/genuisetup.py

@@ -0,0 +1,10 @@
+"""
+initializer.py in src/genui/search/
+
+"""
+from genui.search.models import SearchMolecule
+from genui.compounds.models import ActivitySet, Activity, ActivityTypes, ActivityUnits
+
+
+class SearchSetInitializer():
+    pass