From 728bb8defea43f1dce3ab73db93be7fe1f04ea62 Mon Sep 17 00:00:00 2001
From: Brian Kelley <fustigator@gmail.com>
Date: Thu, 10 Sep 2020 02:11:47 -0400
Subject: [PATCH] Fixes #3403 (#3405)

* Fixes #3403

* Fix Typo

V is actually a set so we can clear it.

* Fix bug, use self.assertFalse
---
 Code/GraphMol/Substruct/SubstructMatch.cpp |  8 +++++---
 Code/GraphMol/Wrap/rough_test.py           | 13 +++++++++++++
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/Code/GraphMol/Substruct/SubstructMatch.cpp b/Code/GraphMol/Substruct/SubstructMatch.cpp
index e6d3e8547..7cfedec22 100644
--- a/Code/GraphMol/Substruct/SubstructMatch.cpp
+++ b/Code/GraphMol/Substruct/SubstructMatch.cpp
@@ -462,12 +462,14 @@ std::vector<MatchVectType> SubstructMatch(
     }
   }
 
-#ifdef RDK_THREADSAFE_SSS
   if (params.recursionPossible) {
-    BOOST_FOREACH (RecursiveStructureQuery *v, locked)
+    BOOST_FOREACH (RecursiveStructureQuery *v, locked) {
+      v->clear();
+#ifdef RDK_THREADSAFE_SSS
       v->d_mutex.unlock();
-  }
 #endif
+    }
+  }
   return matches;
 }
 
diff --git a/Code/GraphMol/Wrap/rough_test.py b/Code/GraphMol/Wrap/rough_test.py
index 1cd30e1a1..be0583d62 100644
--- a/Code/GraphMol/Wrap/rough_test.py
+++ b/Code/GraphMol/Wrap/rough_test.py
@@ -6142,7 +6142,20 @@ M  END
     for mol, refMol in zip(mols, refMols):
       self.assertEqual(Chem.MolToSmiles(mol), Chem.MolToSmiles(refMol))
 
+  def test_github3403(self):
+    core1 = "[$(C-!@[a])](=O)(Cl)"
+    sma = Chem.MolFromSmarts(core1)
+    
+    m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
+    self.assertFalse(m.HasSubstructMatch(sma, recursionPossible=False))
+    
+    m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
+    self.assertTrue(m.HasSubstructMatch(sma))
+    
+    m = Chem.MolFromSmiles("c1ccccc1C(=O)Cl")
+    self.assertFalse(m.HasSubstructMatch(sma, recursionPossible=False))
 
+    
 if __name__ == '__main__':
   if "RDTESTCASE" in os.environ:
     suite = unittest.TestSuite()