Backmerge: #1431 Crash during parsing query mol-file

api/tests/integration/ref/formats/mol_features.py.out

@@ -13075,3 +13075,5 @@ M  V30 END SGROUP
 M  V30 END CTAB
 M  END
 
+*** 1431 Query explicit valency crash ***
+[#6;+2;v;D0;$([*,#1]=,#,:[*,#1]);x0]1=[#6]-[#6]=[#6]-[#6]=[#6]-1.[#6]-[#6]-[#6@@](-[#6])-[#6]-[#6]

api/tests/integration/tests/formats/mol_features.py

@@ -176,3 +176,10 @@ def printGroupsInfo(m):
 print(smiles)
 indigo.setOption("molfile-saving-mode", "3000")
 print(mol.molfile())
+
+print("*** 1431 Query explicit valency crash ***")
+qmol = indigo.loadQueryMoleculeFromFile(
+    joinPathPy("molecules/query_crash_1431.mol", __file__)
+)
+
+print(qmol.smarts())

api/tests/integration/tests/formats/molecules/query_crash_1431.mol

@@ -0,0 +1,38 @@
+
+  SMMXDraw07231311392D
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 12 11 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 12.4156 -5.7104 0 0 CHG=2 VAL=1 INVRET=2 SUBST=-1 UNSAT=1 RBCNT=-2 
+M  V30 2 C 13.7493 -6.4805 0 0 
+M  V30 3 C 13.7493 -8.0205 0 0 
+M  V30 4 C 12.4156 -8.7905 0 0 
+M  V30 5 C 11.082 -8.0205 0 0 
+M  V30 6 C 11.082 -6.4805 0 0 
+M  V30 7 C 3.8438 -5.3438 0 0 
+M  V30 8 C 4.703 -5.8398 0 0 
+M  V30 9 C 5.5622 -5.3438 0 0 CFG=2 
+M  V30 10 C 6.4214 -5.8398 0 0 
+M  V30 11 C 7.2806 -5.3438 0 0 
+M  V30 12 C 5.5622 -4.3516 0 0 
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2 
+M  V30 2 2 2 3 
+M  V30 3 1 3 4 
+M  V30 4 2 4 5 
+M  V30 5 1 5 6 
+M  V30 6 2 6 1 
+M  V30 7 1 7 8 
+M  V30 8 1 8 9 
+M  V30 9 1 9 10 
+M  V30 10 1 10 11 
+M  V30 11 1 9 12 CFG=1 
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEREL1 ATOMS=(1 9)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END

core/indigo-core/molecule/src/query_molecule.cpp

@@ -1855,7 +1855,8 @@ QueryMolecule::Atom* QueryMolecule::releaseAtom(int idx)
 
 void QueryMolecule::resetAtom(int idx, QueryMolecule::Atom* atom)
 {
-    _atoms.reset(idx);
+    if (atom != _atoms[idx])
+        _atoms.reset(idx);
     _atoms[idx] = atom;
     updateEditRevision();
 }