#1446 Dearomatization does not work with query features

api/tests/integration/ref/arom/query_dearom.py.out

@@ -0,0 +1,22 @@
+**** Dearomatize query molecules
+Aromatic: c1ccccc1
+Dearomatized: [#6]1-[#6]=[#6]-[#6]=[#6]-[#6]=1
+
+Aromatic: c1cccc[c;h0]1
+Dearomatized: [#6]1-[#6]=[#6]-[#6]=[#6]-[#6;h0]=1
+
+Aromatic: c1cccc[c;X4]1
+Dearomatized: [#6]1-[#6]=[#6]-[#6]=[#6]-[#6;X4]=1
+
+Aromatic: [#6]12:[#6]:[#6]:[#6]:[#6]:[#6]:1:[#6]:[#7]:[#7;h1]:2
+Dearomatized: [#6]12-[#6]=[#6]-[#6]=[#6]-[#6]-1=[#6]-[#7]-[#7;h1]=2
+
+Aromatic: [#6]12:[#6]:[#6]:[#6]:[#6]:[#6]:1:[#6]:[#7]:[#7;h0]:2
+Dearomatized: [#6]12-[#6]=[#6]-[#6]=[#6]-[#6]-1=[#6]-[#7]-[#7;h0]=2
+
+Aromatic: [#6]12:[#6]:[#6]:[#6]:[#6]:[#6]:1:[#6]:[#7;h0]:[#7]:2
+Dearomatized: [#6]12-[#6]=[#6]-[#6]=[#6]-[#6]=1-[#6]=[#7;h0]-[#7]-2
+
+Aromatic: [#6]12:[#6]:[#6]:[#6]:[#6]:[#6]:1:[#6]:[#7;h0]:[#7;h0]:2
+Cannot be dearomatized: [#6]12:[#6]:[#6]:[#6]:[#6]:[#6]:1:[#6]:[#7;h0]:[#7;h0]:2
+

api/tests/integration/tests/arom/query_dearom.py

@@ -0,0 +1,50 @@
+import os
+import sys
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+from env_indigo import *
+
+print("**** Dearomatize query molecules")
+
+indigo = Indigo()
+
+m = indigo.loadSmarts("c1ccccc1")
+print("Aromatic: %s" % m.smarts())
+m.dearomatize()
+print("Dearomatized: %s\n" % m.smarts())
+
+m = indigo.loadSmarts("c1[ch0]cccc1")
+print("Aromatic: %s" % m.smarts())
+m.dearomatize()
+print("Dearomatized: %s\n" % m.smarts())
+
+m = indigo.loadSmarts("c1[cX4]cccc1")
+print("Aromatic: %s" % m.smarts())
+m.dearomatize()
+print("Dearomatized: %s\n" % m.smarts())
+
+m = indigo.loadSmarts("[#6]12:[#7;h1]:[#7]:[#6]:[#6]:1:[#6]:[#6]:[#6]:[#6]:2")
+print("Aromatic: %s" % m.smarts())
+m.dearomatize()
+print("Dearomatized: %s\n" % m.smarts())
+
+m = indigo.loadSmarts("[#6]12:[#7;h0]:[#7]:[#6]:[#6]:1:[#6]:[#6]:[#6]:[#6]:2")
+print("Aromatic: %s" % m.smarts())
+m.dearomatize()
+print("Dearomatized: %s\n" % m.smarts())
+
+m = indigo.loadSmarts("[#6]12:[#7]:[#7;h0]:[#6]:[#6]:1:[#6]:[#6]:[#6]:[#6]:2")
+print("Aromatic: %s" % m.smarts())
+m.dearomatize()
+print("Dearomatized: %s\n" % m.smarts())
+
+m = indigo.loadSmarts(
+    "[#6]12:[#7;h0]:[#7;h0]:[#6]:[#6]:1:[#6]:[#6]:[#6]:[#6]:2"
+)
+print("Aromatic: %s" % m.smarts())
+m.dearomatize()
+print("Cannot be dearomatized: %s\n" % m.smarts())

api/wasm/indigo-ketcher/test/test.js

@@ -571,9 +571,8 @@ M  END
 
         test("dearomatize", "query_mol", () => {
             let options = new indigo.MapStringString();
-            assert.throws(() => {
-                indigo.dearomatize(qmol_smarts, "molfile", options);
-            });
+            const dearomatized_smiles = indigo.convert(indigo.dearomatize(mol_smiles_aromatized, "molfile", options), "smiles", options);
+            assert.equal(dearomatized_smiles, "C1C=CC=CC=1");
             options.delete();
         });
     }

core/indigo-core/molecule/molecule_dearom.h

@@ -150,6 +150,7 @@ namespace indigo
     protected:
         BaseMolecule& _molecule;
         int _aromaticGroups;
+        bool _isQueryMolecule;
 
         // Additional data stored here to prevent reallocatoins
         CP_DECL;
@@ -208,6 +209,7 @@ namespace indigo
         const AromaticityOptions& _options;
         int _connectivityGroups;
         int _activeGroup;
+        bool _isQueryMolecule;
 
         DearomatizationsGroups _aromaticGroups;
         DearomatizationsStorage* _dearomatizations;
@@ -222,10 +224,10 @@ namespace indigo
         void _initEdges(void);
         void _initVertices(void);
 
-        void _prepareGroup(int group, Molecule& submolecule);
+        void _prepareGroup(int group, BaseMolecule& submolecule);
 
         void _fixHeteratom(int atom_idx, bool toFix);
-        void _processMatching(Molecule& submolecule, int group, const byte* hetroAtomsState);
+        void _processMatching(BaseMolecule& submolecule, int group, const byte* hetroAtomsState);
         void _enumerateMatching(void);
         void _handleMatching(void);
     };
@@ -317,21 +319,22 @@ namespace indigo
     class MoleculeDearomatizer
     {
     public:
-        MoleculeDearomatizer(Molecule& mol, DearomatizationsStorage& dearomatizations);
+        MoleculeDearomatizer(BaseMolecule& mol, DearomatizationsStorage& dearomatizations);
 
         // Function dearomatizes as much as possible.
         // Returns true if all bonds were dearomatized, false overwise
-        static bool dearomatizeMolecule(Molecule& mol, const AromaticityOptions& options);
+        static bool dearomatizeMolecule(BaseMolecule& mol, const AromaticityOptions& options);
 
-        static bool restoreHydrogens(Molecule& mol, const AromaticityOptions& options);
-        static bool restoreHydrogens(Molecule& mol, bool unambiguous_only);
+        static bool restoreHydrogens(BaseMolecule& mol, const AromaticityOptions& options);
+        static bool restoreHydrogens(BaseMolecule& mol, bool unambiguous_only);
 
         void dearomatizeGroup(int group, int dearomatization_index);
         void restoreHydrogens(int group, int dearomatization_index);
 
     private:
         DearomatizationsStorage& _dearomatizations;
-        Molecule& _mol;
+        BaseMolecule& _mol;
+        bool _isQueryMolecule;
 
         int _countDoubleBonds(int group, int dearomatization_index);
         int _getBestDearomatization(int group);

core/indigo-core/molecule/query_molecule.h

@@ -342,6 +342,7 @@ namespace indigo
         void getBondDescription(int idx, Array<char>& description) override;
         bool possibleBondOrder(int idx, int order) override;
 
+        bool possibleAromaticBond(int idx);
         bool possibleNitrogenV5(int idx);
 
         static std::string getSmartsBondStr(QueryMolecule::Bond* bond);
@@ -378,6 +379,7 @@ namespace indigo
         static Bond* getBondOrderTerm(Bond& qb, bool& complex);
         static bool isOrBond(Bond& qb, int type1, int type2);
         static bool isSingleOrDouble(Bond& qb);
+        static bool isSmartsEmptyBond(Bond& qb);
         static int getQueryBondType(Bond& qb);
         static int getQueryBondType(Bond& qb, int& direction, bool& negative);
         static int getAtomType(const char* label);