from django.conf import settings as s from django.test import TestCase, override_settings from epdb.exceptions import InvalidSMILESException, InvalidMolfileException from epdb.logic import PackageManager from epdb.models import Compound, User, CompoundStructure @override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True) class CompoundTest(TestCase): fixtures = ["test_fixtures_incl_model.jsonl.gz"] def setUp(self): pass @classmethod def setUpClass(cls): super(CompoundTest, cls).setUpClass() cls.user = User.objects.get(username="anonymous") cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc") # A valid V2000 molfile for 4-Nitrobenzoic acid (O=C(O)C1=CC=C([N+](=O)[O-])C=C1) cls.VALID_MOLFILE = """\n Mrv2211 01012500002D\n\n 12 12 0 0 0 0 999 V2000\n 1.4289 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.4289 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 1.2375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.4289 0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 -2.8875 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0\n 0.0000 -3.3000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n 1.4289 -3.3000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 2 0 0 0 0\n 4 5 1 0 0 0 0\n 5 6 2 0 0 0 0\n 6 1 1 0 0 0 0\n 2 7 1 0 0 0 0\n 7 8 2 0 0 0 0\n 7 9 1 0 0 0 0\n 5 10 1 0 0 0 0\n 10 11 1 0 0 0 0\n 10 12 2 0 0 0 0\nM CHG 2 10 1 11 -1\nM END\n""" cls.INVALID_MOLFILE = "this is not a valid molfile" def test_smoke(self): c = Compound.create( self.package, smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", name="Afoxolaner", description="No Desc", ) self.assertEqual( c.default_structure.smiles, "C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", ) self.assertEqual(c.name, "Afoxolaner") self.assertEqual(c.description, "No Desc") def test_missing_smiles(self): with self.assertRaises(InvalidSMILESException): _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc") with self.assertRaises(InvalidSMILESException): _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc") with self.assertRaises(InvalidSMILESException): _ = Compound.create(self.package, smiles=" ", name="Afoxolaner", description="No Desc") def test_smiles_are_trimmed(self): c = Compound.create( self.package, smiles=" C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F ", name="Afoxolaner", description="No Desc", ) self.assertEqual( c.default_structure.smiles, "C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", ) def test_name_and_description_optional(self): c = Compound.create( self.package, smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", ) self.assertEqual(c.name, "Compound 1") self.assertEqual(c.description, "no description") def test_empty_name_and_description_are_ignored(self): c = Compound.create( self.package, smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", name="", description="", ) self.assertEqual(c.name, "Compound 1") self.assertEqual(c.description, "no description") def test_deduplication(self): c1 = Compound.create( self.package, smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", name="Afoxolaner", description="No Desc", ) c2 = Compound.create( self.package, smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", name="Afoxolaner", description="No Desc", ) # Check if create detects that this Compound already exist # In this case the existing object should be returned self.assertEqual(c1.pk, c2.pk) self.assertEqual(len(self.package.compounds), 1) def test_wrong_smiles(self): with self.assertRaises(InvalidSMILESException): _ = Compound.create( self.package, smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", name="Afoxolaner", description="No Desc", ) def test_create_with_standardized_smiles(self): c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Standardized SMILES", description="No Desc", ) self.assertEqual(len(c.structures.all()), 1) cs = c.structures.all()[0] self.assertEqual(cs.normalized_structure, True) self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1") def test_create_with_non_standardized_smiles(self): c = Compound.create( self.package, smiles="[O-][N+](=O)c1ccc(C(=O)[O-])cc1", name="Non Standardized SMILES", description="No Desc", ) self.assertEqual(len(c.structures.all()), 2) for cs in c.structures.all(): if cs.normalized_structure: self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1") break else: # Loop finished without break, lets fail... self.assertEqual(1, 2) def test_add_structure_smoke(self): c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Standardized SMILES", description="No Desc", ) c.add_structure("[O-][N+](=O)c1ccc(C(=O)[O-])cc1", "Non Standardized SMILES") self.assertEqual(len(c.structures.all()), 2) def test_add_structure_with_different_normalized_smiles(self): c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Standardized SMILES", description="No Desc", ) with self.assertRaises(ValueError): c.add_structure( "C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", "Different Standardized SMILES", ) def test_delete(self): c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Standardization Test", description="No Desc", ) c.delete() self.assertEqual(Compound.objects.filter(package=self.package).count(), 0) self.assertEqual( CompoundStructure.objects.filter(compound__package=self.package).count(), 0 ) def test_set_as_default_structure(self): c1 = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Standardized SMILES", description="No Desc", ) default_structure = c1.default_structure c2 = c1.add_structure("[O-][N+](=O)c1ccc(C(=O)[O-])cc1", "Non Standardized SMILES") c1.set_default_structure(c2) self.assertNotEqual(default_structure, c2) def test_create_structure_from_molfile(self): c = Compound.create( self.package, smiles="PLACEHOLDER", molfile=self.VALID_MOLFILE, name="Molfile Compound", description="Created from molfile", ) cs = CompoundStructure.create( compound=c, smiles="PLACEHOLDER", molfile=self.VALID_MOLFILE, name="Molfile Structure", description="Structure from molfile", ) # The SMILES must have been derived from the molfile, not the placeholder self.assertNotEqual(cs.smiles, "PLACEHOLDER") self.assertIsNotNone(cs.smiles) self.assertTrue(len(cs.smiles) > 0) def test_create_structure_from_molfile_stores_molfile(self): c = Compound.create( self.package, smiles="c1c(C(=O)O)ccc([N+]([O-])=O)c1", name="Molfile Store Test", description="No Desc", ) cs = c.default_structure # O=C(O)C1=CC=C([N+](=O)[O-])C=C1 will be overwritten with # c1c(C(=O)O)ccc([N+]([O-])=O)c1 and molfile will be set # on the existing structure _ = CompoundStructure.create( compound=c, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", molfile=self.VALID_MOLFILE, name="Structure with Molfile", description="No Desc", ) # Fetch fresh from DB to confirm persistence cs_db = CompoundStructure.objects.get(pk=cs.pk) self.assertIsNotNone(cs_db.molfile) self.assertNotEqual(cs_db.molfile.strip(), "") def test_create_structure_from_invalid_molfile_raises(self): c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Invalid Molfile Test", description="No Desc", ) with self.assertRaises(InvalidMolfileException): CompoundStructure.create( compound=c, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", molfile=self.INVALID_MOLFILE, name="Bad Structure", description="No Desc", ) def test_molfile_takes_precedence_over_smiles(self): """When both molfile and smiles are supplied, molfile must win.""" c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Precedence Test", description="No Desc", ) cs = CompoundStructure.create( compound=c, smiles="C", # intentionally wrong / different SMILES molfile=self.VALID_MOLFILE, name="Molfile Wins", description="No Desc", ) # SMILES should be derived from molfile, not the supplied "C" self.assertNotEqual(cs.smiles, "C") def test_empty_molfile_falls_back_to_smiles(self): """An empty or whitespace-only molfile should be ignored and SMILES used instead.""" c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Empty Molfile Test", description="No Desc", ) cs = CompoundStructure.create( compound=c, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", molfile=" ", # whitespace only – should be ignored name="Fallback to SMILES", description="No Desc", ) self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1") def test_none_molfile_falls_back_to_smiles(self): """None as molfile should be ignored and SMILES used instead.""" c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="None Molfile Test", description="No Desc", ) cs = CompoundStructure.create( compound=c, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", molfile=None, name="Fallback None Molfile", description="No Desc", ) self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1") def test_molfile_deduplication(self): """Creating a structure twice from the same molfile should return the existing object.""" c = Compound.create( self.package, smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1", name="Molfile Dedup Test", description="No Desc", ) cs1 = CompoundStructure.create( compound=c, smiles="PLACEHOLDER", molfile=self.VALID_MOLFILE, name="Molfile Structure", description="No Desc", ) cs2 = CompoundStructure.create( compound=c, smiles="PLACEHOLDER", molfile=self.VALID_MOLFILE, name="Molfile Structure", description="No Desc", ) self.assertEqual(cs1.pk, cs2.pk)