Fix Uncharger applying to already neutralized perhalic groups (#7211)

Code/GraphMol/MolStandardize/Charge.cpp

@@ -406,7 +406,7 @@ void Uncharger::unchargeInPlace(RWMol &mol) {
   // insert the elements from a_atoms, but make sure that
   // the anions of monoprotic acids are not protonated multiple
   // times
-  boost::dynamic_bitset<> skipChargeSep(mol.getNumAtoms());
+  std::vector<int> skipChargeSep(mol.getNumAtoms());
   for (const auto &pair : a_atoms) {
     unsigned int idx = pair.second;
     Atom *atom = mol.getAtomWithIdx(idx);
@@ -415,20 +415,22 @@ void Uncharger::unchargeInPlace(RWMol &mol) {
       const auto &nbr = (mol)[nbri];
       auto nbrIdx = nbr->getIdx();
       // if the neighbor has a positive charge,
-      // neutralize only once (e.g., NO3-)
-      if (nbr->getFormalCharge() > 0) {
-        if (!skipChargeSep.test(nbrIdx)) {
-          skipChargeSep.set(nbrIdx);
-        } else {
-          skipChargeSep.set(idx);
+      // neutralize only the negative charges that are not
+      // already balanced within the functional group
+      // (normally, at most once e.g., NO3-)
+      auto nbrFormalCharge = nbr->getFormalCharge();
+      if (nbrFormalCharge > 0) {
+        if (skipChargeSep[nbrIdx] < nbrFormalCharge) {
+          skipChargeSep[nbrIdx] += 1;
+          skipChargeSep[idx] = 1;
         }
         break;
       }
     }
   }
   for (const auto &pair : a_atoms) {
     unsigned int idx = pair.second;
-    if (skipChargeSep.test(idx)) {
+    if (skipChargeSep[idx]) {
       continue;
     }
     neg_atoms.push_back(pair);

Code/GraphMol/MolStandardize/testCharge.cpp

@@ -285,6 +285,12 @@ void testInorganicAcids() {
     TEST_ASSERT(perhalate);
     res.reset(uncharger.uncharge(*perhalate));
     TEST_ASSERT(MolToSmiles(*res) == "[O-][" + halogen + "+3]([O-])([O-])O");
+    // also test uncharging the already neutralized acid
+    std::unique_ptr<ROMol> perhalic_acid(
+        SmilesToMol("[" + halogen + "](=O)(=O)(=O)O"));
+    TEST_ASSERT(perhalic_acid);
+    res.reset(uncharger.uncharge(*perhalic_acid));
+    TEST_ASSERT(MolToSmiles(*res) == "[O-][" + halogen + "+3]([O-])([O-])O");
   }
   {
     auto hyponitrite = "[O-]N=N[O-]"_smiles;