fix a problem with reading older pickles (#7180)

Code/GraphMol/MolPickler.cpp

@@ -1106,7 +1106,7 @@ void MolPickler::_pickle(const ROMol *mol, std::ostream &ss,
         streamWrite(ss, BEGINFASTFIND);
         break;
       case RDKit::FIND_RING_TYPE::FIND_RING_TYPE_SSSR:
-    streamWrite(ss, BEGINSSSR);
+        streamWrite(ss, BEGINSSSR);
         break;
       case RDKit::FIND_RING_TYPE::FIND_RING_TYPE_SYMM_SSSR:
         streamWrite(ss, BEGINSYMMSSSR);
@@ -2417,16 +2417,17 @@ void MolPickler::_depickleStereo(std::istream &ss, ROMol *mol, int version) {
         atoms.push_back(mol->getAtomWithIdx(tmpT));
       }
 
-      streamRead(ss, tmpT, version);
-      const auto numBonds = static_cast<unsigned>(tmpT);
-
       std::vector<Bond *> bonds;
-      bonds.reserve(numBonds);
-      for (unsigned i = 0u; i < numBonds; ++i) {
+      if (version > 16000) {
         streamRead(ss, tmpT, version);
-        bonds.push_back(mol->getBondWithIdx(tmpT));
-      }
+        const auto numBonds = static_cast<unsigned>(tmpT);
 
+        bonds.reserve(numBonds);
+        for (unsigned i = 0u; i < numBonds; ++i) {
+          streamRead(ss, tmpT, version);
+          bonds.push_back(mol->getBondWithIdx(tmpT));
+        }
+      }
       groups.emplace_back(groupType, std::move(atoms), std::move(bonds), gId);
     }
 

Code/GraphMol/catch_pickles.cpp

@@ -213,4 +213,19 @@ M  END
     CHECK(mol2.getBondWithIdx(2)->getProp<std::string>(
               common_properties::_MolFileBondEndPts) == "(3 1 2 3)");
   }
-}
+}
+
+TEST_CASE("parsing old pickles with many features") {
+  std::string pklName = getenv("RDBASE");
+  pklName += "/Code/GraphMol/test_data/mol_with_sgroups_and_stereo.pkl";
+
+  auto m =
+      "C/C=C/C[C@H](O)[C@@H](C)F |a:6,o2:4,r,SgD:5:data_pt:4.5::::|"_smiles;
+  REQUIRE(m);
+  std::ifstream inStream(pklName.c_str(), std::ios_base::binary);
+  RWMol m2;
+  // if the mol can be read, the primary problem was addressed
+  MolPickler::molFromPickle(inStream, m2);
+  CHECK(m2.getNumAtoms() == m->getNumAtoms());
+  CHECK(MolToCXSmiles(*m) == MolToCXSmiles(m2));
+}