#1254 SMARTS with component-level grouping saved without '()'

Fix UTs
epam · Sep 13, 2023 · b95b6ab · b95b6ab
1 parent 51c0167
commit b95b6ab
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Showing 3 changed files with 7 additions and 15 deletions.
diff --git a/core/indigo-core/molecule/query_molecule.h b/core/indigo-core/molecule/query_molecule.h
@@ -372,7 +372,7 @@ namespace indigo
         // must belong to different connected components of the target molecule
         Array<int> components;
 
-        std::list<std::unordered_set<int>>& getComponentNeighbors();
+        void getComponentNeighbors(std::list<std::unordered_set<int>> &componentNeighbors);
 
         void invalidateAtom(int index, int mask) override;
 
@@ -399,9 +399,6 @@ namespace indigo
 
         PtrArray<Atom> _atoms;
         PtrArray<Bond> _bonds;
-
-        std::list<std::unordered_set<int>> _component_neighbors;
-        void _calculateComponentNeighbors();
     };
 
 } // namespace indigo

diff --git a/core/indigo-core/molecule/src/query_molecule.cpp b/core/indigo-core/molecule/src/query_molecule.cpp
@@ -2141,7 +2141,7 @@ void QueryMolecule::getQueryAtomLabel(int qa, Array<char>& result)
         result.readString(it->second.c_str(), true);
 }
 
-void QueryMolecule::_calculateComponentNeighbors()
+void QueryMolecule::getComponentNeighbors(std::list<std::unordered_set<int>> &componentNeighbors)
 {
     std::unordered_map<int, std::unordered_set<int>> componentAtoms;
     for (int i = 0; i < components.size(); ++i)
@@ -2152,16 +2152,11 @@ void QueryMolecule::_calculateComponentNeighbors()
             componentAtoms[componentId].insert(i);
         }
     }
+    componentNeighbors.clear();
     for (auto elem : componentAtoms)
     {
         auto atoms = elem.second;
         if (atoms.size() > 1)
-            _component_neighbors.emplace_back(atoms);
+            componentNeighbors.emplace_back(atoms);
     }
-}
-
-std::list<std::unordered_set<int>>& QueryMolecule::getComponentNeighbors()
-{
-    _calculateComponentNeighbors();
-    return _component_neighbors;
 }
diff --git a/core/indigo-core/reaction/src/rsmiles_loader.cpp b/core/indigo-core/reaction/src/rsmiles_loader.cpp
@@ -128,7 +128,7 @@ void RSmilesLoader::_loadReaction()
     {
         rcnt = std::make_unique<QueryMolecule>();
         r_loader.loadQueryMolecule(static_cast<QueryMolecule&>(*rcnt));
-        rcnt_extNeibs = static_cast<QueryMolecule&>(*rcnt).getComponentNeighbors();
+        static_cast<QueryMolecule&>(*rcnt).getComponentNeighbors(rcnt_extNeibs);
     }
     rcnt_aam.copy(rcnt->reaction_atom_mapping);
 
@@ -162,7 +162,7 @@ void RSmilesLoader::_loadReaction()
     {
         ctlt = std::make_unique<QueryMolecule>();
         c_loader.loadQueryMolecule(static_cast<QueryMolecule&>(*ctlt));
-        ctlt_extNeibs = static_cast<QueryMolecule&>(*ctlt).getComponentNeighbors();
+        static_cast<QueryMolecule&>(*ctlt).getComponentNeighbors(ctlt_extNeibs);
     }
     ctlt_aam.copy(ctlt->reaction_atom_mapping);
 
@@ -202,7 +202,7 @@ void RSmilesLoader::_loadReaction()
     {
         prod = std::make_unique<QueryMolecule>();
         p_loader.loadQueryMolecule(static_cast<QueryMolecule&>(*prod));
-        prod_extNeibs = static_cast<QueryMolecule&>(*prod).getComponentNeighbors();
+        static_cast<QueryMolecule&>(*prod).getComponentNeighbors(prod_extNeibs);
     }
     prod_aam.copy(prod->reaction_atom_mapping);