[Feature] Generate Compounds by Molfile (#423)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#423

epapi/tests/v1/test_api_permissions.py

@@ -117,25 +117,28 @@ class APIPermissionTestBase(TestCase):
 
         # Create test compounds in each package
         cls.reviewed_compound = Compound.create(
-            cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
+            cls.reviewed_package, "C", name="Reviewed Compound", description="Test compound"
         )
         cls.owned_compound = Compound.create(
-            cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
+            cls.unreviewed_package_owned, "CC", name="Owned Compound", description="Test compound"
         )
         cls.read_compound = Compound.create(
-            cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
+            cls.unreviewed_package_read, "CCC", name="Read Compound", description="Test compound"
         )
         cls.write_compound = Compound.create(
-            cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
+            cls.unreviewed_package_write, "CCCC", name="Write Compound", description="Test compound"
         )
         cls.all_compound = Compound.create(
-            cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
+            cls.unreviewed_package_all, "CCCCC", name="All Compound", description="Test compound"
         )
         cls.no_access_compound = Compound.create(
-            cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
+            cls.unreviewed_package_no_access,
+            "CCCCCC",
+            name="No Access Compound",
+            description="Test compound",
         )
         cls.group_compound = Compound.create(
-            cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
+            cls.group_package, "CCCCCCC", name="Group Compound", description="Test compound"
         )
 
 

epapi/tests/v1/test_contract_get_entities.py

@@ -294,8 +294,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Reviewed Compound {idx:03d}",
+            name=f"Reviewed Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
     @classmethod
@@ -305,8 +305,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Draft Compound {idx:03d}",
+            name=f"Draft Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
 

epdb/exceptions.py

@@ -1,2 +1,6 @@
 class InvalidSMILESException(Exception):
     pass
+
+
+class InvalidMolfileException(Exception):
+    pass

epdb/legacy_api.py

@@ -791,6 +791,7 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
 
 class CreateCompound(Schema):
     compoundSmiles: str
+    compoundMolFile: str | None = None
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
@@ -804,9 +805,13 @@ def create_package_compound(
 ):
     try:
         p = get_package_for_write(request.user, package_uuid)
-        # inchi is not used atm
         c = Compound.create(
-            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
+            p,
+            c.compoundSmiles,
+            molfile=c.compoundMolFile,
+            name=c.compoundName,
+            description=c.compoundDescription,
+            inchi=c.inchi,
         )
         return redirect(c.url)
     except ValueError as e:
@@ -1899,6 +1904,7 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 class CreateNode(Schema):
     nodeAsSmiles: str
+    nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
@@ -1918,7 +1924,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         else:
             node_depth = -1
 
-        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+        n = Node.create(
+            pw,
+            n.nodeAsSmiles,
+            node_depth,
+            molfile=n.nodeAsMolFile,
+            name=n.nodeName,
+            description=n.nodeReason,
+        )
 
         return redirect(n.url)
     except ValueError:

epdb/models.py

@@ -31,7 +31,10 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import InvalidSMILESException
+from epdb.exceptions import (
+    InvalidMolfileException,
+    InvalidSMILESException,
+)
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -789,6 +792,13 @@ class Compound(
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
+    def get_structure_by_smiles(self, smiles: str) -> "CompoundStructure":
+        for struct in self.structures.all():
+            if struct.smiles == smiles:
+                return struct
+
+        raise ValueError(f"No structure with SMILES {smiles} found for {self.get_name()}")
+
     @property
     def structures(self) -> QuerySet:
         return CompoundStructure.objects.filter(compound=self)
@@ -857,8 +867,24 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: "Package",
+        smiles: str,
+        molfile: str | None = None,
+        name: str | None = None,
+        description: str | None = None,
+        *args,
+        **kwargs,
     ) -> "Compound":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles.strip() == "":
             raise InvalidSMILESException("SMILES is required")
 
@@ -878,11 +904,16 @@ class Compound(
         if CompoundStructure.objects.filter(
             smiles=standardized_smiles, compound__package=package
         ).exists():
-            # TODO should we add a structure?
+            found_c = CompoundStructure.objects.get(
-            return CompoundStructure.objects.get(
                 smiles=standardized_smiles, compound__package=package
             ).compound
 
+            # As a direct match wasn't found add a new structure
+            # TODO return newly created structure
+            _ = found_c.add_structure(smiles, molfile=molfile, name=name, description=description)
+
+            return found_c
+
         # Generate Compound
         c = Compound()
         c.package = package
@@ -914,7 +945,12 @@ class Compound(
             )
 
         cs = CompoundStructure.create(
-            c, smiles, name=name, description=description, normalized_structure=is_standardized
+            c,
+            smiles,
+            molfile=molfile,
+            name=name,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         c.default_structure = cs
@@ -927,11 +963,22 @@ class Compound(
         self,
         smiles: str,
         name: str = None,
+        molfile: str = None,
         description: str = None,
         default_structure: bool = False,
         *args,
         **kwargs,
     ) -> "CompoundStructure":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles == "":
             raise ValueError("SMILES is required")
 
@@ -951,16 +998,28 @@ class Compound(
             )
 
         if is_standardized:
-            CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
 
         # Check if we find a direct match for a given SMILES and/or its standardized SMILES
-        if CompoundStructure.objects.filter(
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=self.package).exists():
-            smiles__in=smiles, compound__package=self.package
+            found_cs = CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
-        ).exists():
+
-            return CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
+
+            return found_cs
 
         cs = CompoundStructure.create(
-            self, smiles, name=name, description=description, normalized_structure=is_standardized
+            self,
+            smiles,
+            name=name,
+            molfile=molfile,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         if default_structure:
@@ -1141,10 +1200,35 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
+        compound: Compound,
+        smiles: str,
+        molfile: str = None,
+        name: str = None,
+        description: str = None,
+        *args,
+        **kwargs,
     ):
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            found_cs = CompoundStructure.objects.get(smiles=smiles, compound=compound)
+
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
+
+            return found_cs
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
@@ -2174,11 +2258,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def add_node(
         self,
         smiles: str,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
-        depth: Optional[int] = -1,
+        description: str | None = None,
+        depth: int = -1,
     ):
-        return Node.create(self, smiles, depth, name=name, description=description)
+        return Node.create(self, smiles, depth, molfile=molfile, name=name, description=description)
 
     @transaction.atomic
     def add_edge(
@@ -2336,28 +2421,43 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         pathway: "Pathway",
         smiles: str,
         depth: int,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
+        description: str | None = None,
     ):
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         stereo_removed = False
         if pathway.predicted and FormatConverter.has_stereo(smiles):
             smiles = FormatConverter.standardize(smiles, remove_stereo=True)
             stereo_removed = True
 
-        c = Compound.create(pathway.package, smiles, name=name, description=description)
+        c = Compound.create(
+            pathway.package, smiles, molfile=molfile, name=name, description=description
+        )
 
-        if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
+        structure = c.get_structure_by_smiles(smiles)
-            return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
+
+        if Node.objects.filter(pathway=pathway, default_node_label=structure).exists():
+            return Node.objects.get(pathway=pathway, default_node_label=structure)
 
         n = Node()
         n.stereo_removed = stereo_removed
         n.pathway = pathway
         n.depth = depth
 
-        n.default_node_label = c.default_structure
+        n.default_node_label = structure
         n.save()
 
-        n.node_labels.add(c.default_structure)
+        n.node_labels.add(structure)
         n.save()
 
         return n

epdb/views.py

@@ -19,7 +19,7 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .exceptions import InvalidSMILESException
+from .exceptions import InvalidMolfileException, InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -1386,12 +1386,18 @@ def package_compounds(request, package_uuid):
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
         compound_smiles = request.POST.get("compound-smiles")
+        compound_molfile = request.POST.get("compound-molfile")
         compound_description = request.POST.get("compound-description")
+
         try:
             c = Compound.create(
-                current_package, compound_smiles, compound_name, compound_description
+                current_package,
+                compound_smiles,
+                molfile=compound_molfile,
+                name=compound_name,
+                description=compound_description,
             )
-        except ValueError as e:
+        except (InvalidSMILESException, InvalidMolfileException) as e:
             raise BadRequest(str(e))
 
         return redirect(c.url)
@@ -1517,11 +1523,15 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
         structure_smiles = request.POST.get("structure-smiles")
+        structure_molfile = request.POST.get("structure-molfile")
         structure_description = request.POST.get("structure-description")
 
         try:
             cs = current_compound.add_structure(
-                structure_smiles, structure_name, structure_description
+                structure_smiles,
+                molfile=structure_molfile,
+                name=structure_name,
+                description=structure_description,
             )
         except ValueError:
             return error(
@@ -2339,9 +2349,12 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
+        node_molfile = request.POST.get("node-molfile").strip()
 
         try:
-            current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+            current_pathway.add_node(
+                node_smiles, molfile=node_molfile, name=node_name, description=node_description
+            )
         except InvalidSMILESException:
             return error(
                 request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"

tests/test_compound_model.py

@@ -1,7 +1,7 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
-from epdb.exceptions import InvalidSMILESException
+from epdb.exceptions import InvalidSMILESException, InvalidMolfileException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
@@ -19,6 +19,10 @@ class CompoundTest(TestCase):
         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,
@@ -190,3 +194,153 @@ class CompoundTest(TestCase):
 
         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)

tests/views/test_compound_views.py

@@ -11,6 +11,9 @@ from epdb.models import Compound, Scenario, ExternalDatabase
 class CompoundViewTest(TestCase):
     fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
+    # A valid V2000 molfile for 4-Nitrobenzoic acid (O=C(O)C1=CC=C([N+](=O)[O-])C=C1)
+    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"""
+
     @classmethod
     def setUpClass(cls):
         super(CompoundViewTest, cls).setUpClass()
@@ -396,3 +399,108 @@ class CompoundViewTest(TestCase):
 
         c = Compound.objects.get(url=compound_url)
         self.assertEqual(len(c.aliases), 0)
+
+    def test_create_compound_via_molfile(self):
+        """POSTing a valid molfile without a SMILES should create a compound successfully."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Created from molfile",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        self.assertEqual(c.name, "4-Nitrobenzoic acid")
+        self.assertEqual(c.description, "Created from molfile")
+        # SMILES should have been extracted from molfile, so it must be non-empty
+        self.assertIsNotNone(c.default_structure.smiles)
+        self.assertNotEqual(c.default_structure.smiles.strip(), "")
+
+    def test_create_compound_molfile_takes_precedence_over_smiles(self):
+        """When both molfile and SMILES are submitted, the molfile should win."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile precedence test",
+                "compound-smiles": "C",  # intentionally wrong/different
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        # The resulting SMILES must NOT be the dummy "C" supplied via compound-smiles
+        self.assertNotEqual(c.default_structure.smiles, "C")
+
+    def test_create_compound_via_invalid_molfile_returns_error(self):
+        """POSTing an invalid molfile should not create a compound and should return an error response."""
+        initial_count = self.user1_default_package.compounds.count()
+
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "Bad Molfile Compound",
+                "compound-description": "Should fail",
+                "compound-molfile": "this is not a molfile at all",
+            },
+        )
+
+        # The view should signal an error (non-2xx or a redirect to an error page, not 302 to a new compound)
+        self.assertNotEqual(response.status_code, 302)
+        # No new compound should have been created
+        self.assertEqual(self.user1_default_package.compounds.count(), initial_count)
+
+    def test_create_compound_via_empty_molfile_falls_back_to_smiles(self):
+        """Submitting an empty molfile with a valid SMILES should fall back to SMILES."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "Fallback SMILES Compound",
+                "compound-description": "Empty molfile fallback",
+                "compound-smiles": "C(CCl)Cl",
+                "compound-molfile": "   ",  # whitespace only
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
+
+    def test_create_compound_via_molfile_deduplication(self):
+        """Submitting the same molfile twice should return the existing compound."""
+        response1 = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile dedup test",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response1.status_code, 302)
+        compound_url_1 = response1.url
+
+        response2 = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile dedup test",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response2.status_code, 302)
+        self.assertEqual(response2.url, compound_url_1)
+        self.assertEqual(self.user1_default_package.compounds.count(), 1)