[Feature] Generate Compounds by Molfile (#423)

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

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: