passing all tests

Code/GraphMol/Aromaticity.cpp

@@ -546,13 +546,14 @@ namespace {
           nelec--;
         }
       }
-      if (nelec%2 == 1) {
+      if (nelec%2 == 1 || at->getNumRadicalElectrons()==1) {
         res = OneElectronDonorType;
       }
       else {
         res = TwoElectronDonorType;
       }
     }
+    //std::cerr<<"  "<<at->getIdx()<<" "<<at->getAtomicNum()<<" "<<res<<std::endl;;
     return(res);
   }
 }// end of local utility namespace

Code/GraphMol/Atom.cpp

@@ -208,7 +208,7 @@ int Atom::calcExplicitValence(bool strict) {
   // check accum is greater than the default valence
   int chr = getFormalCharge();
   if(d_atomicNum>1){
-    unsigned int dv = PeriodicTable::getTable()->getDefaultValence(d_atomicNum-chr);
+    int dv = PeriodicTable::getTable()->getDefaultValence(d_atomicNum-chr);
     if (accum > dv && this->getIsAromatic()){
       // this needs some explanation : if the atom is aromatic and
       // accum > (dv + chr) we assume that no hydrogen can be added
@@ -398,14 +398,19 @@ int Atom::calcImplicitValence(bool strict) {
   else {
     // non-aromatic case we are allowed to have non default valences
     // and be able to add hydrogens
-    res = -1;
     const INT_VECT &valens = PeriodicTable::getTable()->getValenceList(d_atomicNum-chg);
-    for (INT_VECT_CI vi = valens.begin();
-	 vi != valens.end() && *vi>=0; ++vi) {
-      int tot = (*vi);
-      if (explicitPlusRadV <= tot) {
-        res = tot - explicitPlusRadV;
-        break;
+    if(valens.size()==1 && valens[0]==-1){
+      // no default valence, set res to zero
+      res = 0;
+    } else {
+      res = -1;
+      for (INT_VECT_CI vi = valens.begin();
+           vi != valens.end() && *vi>=0; ++vi) {
+        int tot = (*vi);
+        if (explicitPlusRadV <= tot) {
+          res = tot - explicitPlusRadV;
+          break;
+        }
       }
     }
     if (res < 0) {
@@ -415,7 +420,7 @@ int Atom::calcImplicitValence(bool strict) {
         std::ostringstream errout;
         errout << "Explicit valence for atom # " << getIdx() 
                << " " << PeriodicTable::getTable()->getElementSymbol(d_atomicNum)
-               << " greater than permitted";
+               << ", " << res <<", greater than permitted";
         std::string msg = errout.str();
         BOOST_LOG(rdErrorLog) << msg << std::endl;
         throw MolSanitizeException(msg);

Code/GraphMol/molopstest.cpp

@@ -2546,7 +2546,7 @@ void testAromaticityEdges()
   RWMol *m;
 
   std::string smi;
-
+#if 1
   // ------
   // this was sf.net bug 1934360
   smi = "C1=C=NC=N1";
@@ -2652,6 +2652,25 @@ void testAromaticityEdges()
   TEST_ASSERT(m->getAtomWithIdx(1)->getIsAromatic());
   TEST_ASSERT(m->getBondBetweenAtoms(1,2)->getIsAromatic());
   delete m;
+#endif
+  
+  // ------
+  // Caused problems from InChI
+  smi = "C[N]C1=CC=NC=C1";
+  m = SmilesToMol(smi);
+  TEST_ASSERT(m);
+  TEST_ASSERT(m->getNumAtoms()==8);
+  TEST_ASSERT(m->getAtomWithIdx(5)->getNumRadicalElectrons()==0);
+  TEST_ASSERT(m->getAtomWithIdx(5)->getIsAromatic());
+  delete m;
+
+  smi = "CN=C1C=C[N]C=C1";
+  m = SmilesToMol(smi);
+  TEST_ASSERT(m);
+  TEST_ASSERT(m->getNumAtoms()==8);
+  TEST_ASSERT(m->getAtomWithIdx(5)->getNumRadicalElectrons()==1);
+  TEST_ASSERT(!m->getAtomWithIdx(5)->getIsAromatic());
+  delete m;
 
 
   BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
@@ -4468,7 +4487,6 @@ int main(){
   testSFNetIssue3185548();
   testSFNetIssue3349243();
   testFastFindRings();
-#endif
   testSanitizeNonringAromatics();  
   testAtomAtomMatch();
   testSFNetIssue3349243();
@@ -4483,12 +4501,12 @@ int main(){
   testGitHubIssue42();
   testGitHubIssue65();
   testSFNetIssue2952255();
-  testAromaticityEdges();
-#endif
   testBareHs();
   testGitHubIssue72();
   testRenumberAtoms();
   testGithubIssue141();
+#endif
+  testAromaticityEdges();
 
   return 0;
 }

External/INCHI-API/test.cpp

@@ -226,16 +226,48 @@ void testGithubIssue68(){
   BOOST_LOG(rdInfoLog) <<"done" << std::endl;
 }
 
+void testMiscValenceProblems(){
+  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) <<"testing miscellaneous valence problems" << std::endl;
+  {
+    ExtraInchiReturnValues tmp;
+    std::string inchi="InChI=1S/Ga/q+3";
+    ROMol *m = InchiToMol(inchi,tmp);
+    TEST_ASSERT(m);
+    TEST_ASSERT(m->getNumAtoms()==1);
+    TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge()==3);
+    
+    delete m;
+  }
+  {
+    ExtraInchiReturnValues tmp;
+    std::string inchi="InChI=1S/C6H7N2/c1-7-6-2-4-8-5-3-6/h2-5H,1H3";
+    ROMol *m = InchiToMol(inchi,tmp);
+    TEST_ASSERT(m);
+    TEST_ASSERT(m->getNumAtoms()==8);
+    TEST_ASSERT(m->getAtomWithIdx(7)->getNumRadicalElectrons()==1);
+    TEST_ASSERT(!m->getAtomWithIdx(7)->getIsAromatic());
+    
+    delete m;
+  }
+  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
+}
+
+
 
 //-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
 //
 //-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
 int main(){
   RDLog::InitLogs();
+#if 1
   testMultiThread();
   testGithubIssue3();
   testGithubIssue8();
   testGithubIssue40();
   testGithubIssue67();
   testGithubIssue68();
+#endif
+  testMiscValenceProblems();
+
 }

rdkit/Chem/UnitTestInchi.py

@@ -224,7 +224,7 @@ class TestCase(unittest.TestCase):
                                 )
                             )
                 except:
-                    print '>>> mol failed:',midx,MolToSmiles(m,True),x
+                    print '>>> mol(%d), cid(%s) failed:'%(midx,cid),MolToSmiles(m,True),x
                     y = ''
                 if y == '':
                     # metal involved?
@@ -295,8 +295,8 @@ class TestCase(unittest.TestCase):
                     same += 1
             print green + "InChI Read Summary: %d identical, %d  variance, %d reasonable variance" % (same, diff, reasonable) + reset
             self.assertEqual(same, 544)
-            self.assertEqual(diff, 1)
-            self.assertEqual(reasonable, 636)
+            self.assertEqual(diff, 0)
+            self.assertEqual(reasonable, 637)
 
     def test2InchiOptions(self):
         m = MolFromSmiles("CC=C(N)C")