#3544 Indexing issues in Sgroups created as match to query molecule with unfolded hydrogens

api/c/indigo/src/indigo_molecule_operations.cpp

@@ -1627,7 +1627,8 @@ CEXPORT int indigoCreateSGroup(const char* type, int mapping, const char* name)
 
             for (auto i : temp.vertices())
             {
-                sgroup.atoms.push(m[i]);
+                if (m[i] >= 0)
+                    sgroup.atoms.push(m[i]);
             }
 
             for (auto i : mol.edges())

api/tests/integration/ref/basic/3544_sgroup_indexing.py.out

@@ -0,0 +1,11 @@
+****** Issue #3544: SGroup indexing with unfolded hydrogens ********
+Test 1: SUP sgroup from query with unfolded hydrogens
+SGroup atoms: C
+Test 2: SUP sgroup, both target and query with unfolded hydrogens
+SGroup atoms: C
+Test 3: DAT sgroup from query with unfolded hydrogens
+SGroup atoms: C
+Test 4: Control - SUP sgroup without unfolded hydrogens
+SGroup atoms: C
+Test 5: SUP sgroup from multi-atom query match with unfolded hydrogens
+SGroup atoms: C C

api/tests/integration/tests/basic/3544_sgroup_indexing.py

@@ -0,0 +1,116 @@
+import os
+import sys
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+from env_indigo import Indigo  # noqa
+
+indigo = Indigo()
+
+print("****** Issue #3544: SGroup indexing with unfolded hydrogens ********")
+
+# Test 1: Query with unfoldHydrogens, SUP sgroup
+print("Test 1: SUP sgroup from query with unfolded hydrogens")
+mol = indigo.createMolecule()
+mol.addAtom("C")
+
+query = indigo.createQueryMolecule()
+query.addAtom("C")
+query.unfoldHydrogens()
+
+matcher = indigo.substructureMatcher(mol)
+match = matcher.match(query)
+
+if match:
+    sgroup = mol.createSGroup("SUP", match, "TEST")
+    atoms = []
+    for atom in sgroup.iterateAtoms():
+        atoms.append(atom.symbol())
+    print("SGroup atoms: %s" % " ".join(atoms))
+else:
+    print("ERROR: match not found")
+
+# Test 2: Both target and query with unfoldHydrogens
+print("Test 2: SUP sgroup, both target and query with unfolded hydrogens")
+mol2 = indigo.createMolecule()
+mol2.addAtom("C")
+mol2.unfoldHydrogens()
+
+query2 = indigo.createQueryMolecule()
+query2.addAtom("C")
+query2.unfoldHydrogens()
+
+matcher2 = indigo.substructureMatcher(mol2)
+match2 = matcher2.match(query2)
+
+if match2:
+    sgroup2 = mol2.createSGroup("SUP", match2, "TEST2")
+    atoms2 = []
+    for atom in sgroup2.iterateAtoms():
+        atoms2.append(atom.symbol())
+    print("SGroup atoms: %s" % " ".join(sorted(atoms2)))
+else:
+    print("ERROR: match not found")
+
+# Test 3: DAT sgroup type with unfoldHydrogens
+print("Test 3: DAT sgroup from query with unfolded hydrogens")
+mol3 = indigo.createMolecule()
+mol3.addAtom("C")
+
+query3 = indigo.createQueryMolecule()
+query3.addAtom("C")
+query3.unfoldHydrogens()
+
+matcher3 = indigo.substructureMatcher(mol3)
+match3 = matcher3.match(query3)
+
+if match3:
+    sgroup3 = mol3.createSGroup("DAT", match3, "TEST3")
+    atoms3 = []
+    for atom in sgroup3.iterateAtoms():
+        atoms3.append(atom.symbol())
+    print("SGroup atoms: %s" % " ".join(atoms3))
+else:
+    print("ERROR: match not found")
+
+# Test 4: Control case - no unfoldHydrogens (should work regardless)
+print("Test 4: Control - SUP sgroup without unfolded hydrogens")
+mol4 = indigo.createMolecule()
+mol4.addAtom("C")
+
+query4 = indigo.createQueryMolecule()
+query4.addAtom("C")
+
+matcher4 = indigo.substructureMatcher(mol4)
+match4 = matcher4.match(query4)
+
+if match4:
+    sgroup4 = mol4.createSGroup("SUP", match4, "TEST4")
+    atoms4 = []
+    for atom in sgroup4.iterateAtoms():
+        atoms4.append(atom.symbol())
+    print("SGroup atoms: %s" % " ".join(atoms4))
+else:
+    print("ERROR: match not found")
+
+# Test 5: Multi-atom query with unfoldHydrogens in a larger molecule
+print("Test 5: SUP sgroup from multi-atom query match with unfolded hydrogens")
+mol5 = indigo.loadMolecule("CCCC")
+
+query5 = indigo.loadQueryMolecule("[#6][#6]")
+query5.unfoldHydrogens()
+
+matcher5 = indigo.substructureMatcher(mol5)
+match5 = matcher5.match(query5)
+
+if match5:
+    sgroup5 = mol5.createSGroup("SUP", match5, "TEST5")
+    atoms5 = []
+    for atom in sgroup5.iterateAtoms():
+        atoms5.append(atom.symbol())
+    print("SGroup atoms: %s" % " ".join(atoms5))
+else:
+    print("ERROR: match not found")