revert ringinfo level checks

rdkit · May 9, 2024 · 56eed01 · 56eed01
1 parent 61d4fc5
commit 56eed01
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Showing 27 changed files with 84 additions and 101 deletions.
diff --git a/Code/GraphMol/Aromaticity.cpp b/Code/GraphMol/Aromaticity.cpp
@@ -912,7 +912,7 @@ int setAromaticity(RWMol &mol, AromaticityModel model, int (*func)(RWMol &)) {
 
   // first find the all the simple rings in the molecule
   VECT_INT_VECT srings;
-  if (mol.getRingInfo()->isSymmSssr()) {
+  if (mol.getRingInfo()->isInitialized()) {
     srings = mol.getRingInfo()->atomRings();
   } else {
     MolOps::symmetrizeSSSR(mol, srings);

diff --git a/Code/GraphMol/Canon.cpp b/Code/GraphMol/Canon.cpp
@@ -1028,7 +1028,7 @@ void canonicalizeFragment(ROMol &mol, int atomIdx,
 
   // we need ring information; make sure findSSSR has been called before
   // if not call now
-  if (!mol.getRingInfo()->isSssrOrBetter()) {
+  if (!mol.getRingInfo()->isInitialized()) {
     MolOps::findSSSR(mol);
   }
   mol.getAtomWithIdx(atomIdx)->setProp(common_properties::_TraversalStartPoint,

diff --git a/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp b/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp
@@ -69,8 +69,8 @@ RDKit::SparseIntVect<std::uint32_t> *generateFingerprint(
       delete tmp2;
     } break;
     case RDKit::MorganFP: {
-      if (!mol.getRingInfo()->isSssrOrBetter()) {
-        mol.updatePropertyCache(false);
+      if (!mol.getRingInfo()->isInitialized()) {
+        mol.updatePropertyCache();
         RDKit::MolOps::findSSSR(mol);
       }
       res = RDKit::MorganFingerprints::getHashedFingerprint(mol, 2, fpSize);
@@ -101,8 +101,8 @@ ExplicitBitVect *generateFingerprintAsBitVect(RDKit::ROMol &mol,
           mol, fpSize);
       break;
     case RDKit::MorganFP: {
-      if (!mol.getRingInfo()->isSssrOrBetter()) {
-        mol.updatePropertyCache(false);
+      if (!mol.getRingInfo()->isInitialized()) {
+        mol.updatePropertyCache();
         RDKit::MolOps::findSSSR(mol);
       }
       res = RDKit::MorganFingerprints::getFingerprintAsBitVect(mol, 2, fpSize);

diff --git a/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py b/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py
@@ -1153,9 +1153,7 @@ def testCDXML(self):
     self.assertEqual(len(rxns), 1)
     self.assertEqual(
       AllChem.ReactionToSmarts(rxns[0]),
-      "[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](-[#17&D1]):[#6&D2:5]:[#6&D2:6]:1."
-      "[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>"
-      "[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](-[#6&D3:7]2:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:2):[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1"
+      "[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](:[#6&D2:5]:[#6&D2:6]:1)-[#17&D1].[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](:[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1)-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1"
     )
 
     rxns = AllChem.ReactionsFromCDXMLFile('does-not-exist.cdxml')
@@ -1167,9 +1165,7 @@ def testCDXML(self):
     self.assertEqual(len(rxns), 1)
     self.assertEqual(
       AllChem.ReactionToSmarts(rxns[0]),
-      "[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](-[#17&D1]):[#6&D2:5]:[#6&D2:6]:1."
-      "[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>"
-      "[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](-[#6&D3:7]2:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:2):[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1"
+      "[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](:[#6&D2:5]:[#6&D2:6]:1)-[#17&D1].[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](:[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1)-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1"
     )
 
     rxns = AllChem.ReactionsFromCDXMLBlock('')

diff --git a/Code/GraphMol/ChemReactions/catch_tests.cpp b/Code/GraphMol/ChemReactions/catch_tests.cpp
@@ -1304,9 +1304,7 @@ TEST_CASE("CDXML Parser") {
     auto smarts = ChemicalReactionToRxnSmarts(*rxns[0]);
     CHECK(
         smarts ==
-        ("[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](-[#17&D1]):[#6&D2:5]:[#6&D2:6]:1."
-         "[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>"
-         "[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](-[#6&D3:7]2:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:2):[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1"));
+        "[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](:[#6&D2:5]:[#6&D2:6]:1)-[#17&D1].[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](:[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1)-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1");
   }
 }
 

diff --git a/Code/GraphMol/ChemTransforms/ChemTransforms.cpp b/Code/GraphMol/ChemTransforms/ChemTransforms.cpp
@@ -407,8 +407,8 @@ int findNbrBond(RWMol &mol, Bond *bond, Atom *bondAtom, const INT_VECT &bring,
 
 void setSubMolBrokenRingStereo(RWMol &mol,
                                const boost::dynamic_bitset<> &removedAtoms) {
-  PRECONDITION(mol.getRingInfo() && mol.getRingInfo()->isSssrOrBetter(),
-               "insufficient ringinfo");
+  PRECONDITION(mol.getRingInfo() && mol.getRingInfo()->isInitialized(),
+               "bad ringinfo");
 
   for (const auto &bring : mol.getRingInfo()->bondRings()) {
     // check whether or not this bond ring is affected by the removal
@@ -718,7 +718,7 @@ ROMol *replaceCore(const ROMol &mol, const ROMol &core,
       newMol->removeAtom(at);
       removedAtoms.set(at->getIdx());
       if (!removedRingAtom && mol.getRingInfo() &&
-          mol.getRingInfo()->isSssrOrBetter() &&
+          mol.getRingInfo()->isInitialized() &&
           mol.getRingInfo()->numAtomRings(at->getIdx())) {
         removedRingAtom = true;
       }

diff --git a/Code/GraphMol/Chirality.cpp b/Code/GraphMol/Chirality.cpp
@@ -1375,7 +1375,7 @@ bool atomIsCandidateForRingStereochem(const ROMol &mol, const Atom *atom) {
   std::set<unsigned int> nbrRanks;
   if (!atom->getPropIfPresent(common_properties::_ringStereochemCand, res)) {
     const RingInfo *ringInfo = mol.getRingInfo();
-    if (ringInfo->isSssrOrBetter() && ringInfo->numAtomRings(atom->getIdx())) {
+    if (ringInfo->isInitialized() && ringInfo->numAtomRings(atom->getIdx())) {
       // three-coordinate N additional requirements:
       //   in a ring of size 3  (from InChI)
       // OR
@@ -1438,7 +1438,7 @@ void findChiralAtomSpecialCases(ROMol &mol,
   PRECONDITION(possibleSpecialCases.size() >= mol.getNumAtoms(),
                "bit vector too small");
   possibleSpecialCases.reset();
-  if (!mol.getRingInfo()->isSymmSssr()) {
+  if (!mol.getRingInfo()->isInitialized()) {
     VECT_INT_VECT sssrs;
     MolOps::symmetrizeSSSR(mol, sssrs);
   }
@@ -2181,7 +2181,7 @@ void legacyStereoPerception(ROMol &mol, bool cleanIt,
 
   // later we're going to need ring information, get it now if we don't
   // have it already:
-  if (!mol.getRingInfo()->isFindFastOrBetter()) {
+  if (!mol.getRingInfo()->isInitialized()) {
     MolOps::fastFindRings(mol);
   }
 

diff --git a/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp b/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp
@@ -220,7 +220,7 @@ void set12Bounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat,
     if (bond->getIsConjugated() &&
         (bond->getBeginAtom()->getAtomicNum() > 10 ||
          bond->getEndAtom()->getAtomicNum() > 10) &&
-        mol.getRingInfo() && mol.getRingInfo()->isSssrOrBetter() &&
+        mol.getRingInfo() && mol.getRingInfo()->isInitialized() &&
         mol.getRingInfo()->isBondInRingOfSize(bond->getIdx(), 5)) {
       squishAtoms.set(bond->getBeginAtomIdx());
       squishAtoms.set(bond->getEndAtomIdx());

diff --git a/Code/GraphMol/DistGeomHelpers/Embedder.cpp b/Code/GraphMol/DistGeomHelpers/Embedder.cpp
@@ -1052,7 +1052,7 @@ void findChiralSets(const ROMol &mol, DistGeom::VECT_CHIRALSET &chiralCenters,
           chiralCenters.push_back(cptr);
         } else {
           if ((coordMap && coordMap->find(atom->getIdx()) != coordMap->end()) ||
-              (mol.getRingInfo()->isSssrOrBetter() &&
+              (mol.getRingInfo()->isInitialized() &&
                (mol.getRingInfo()->numAtomRings(atom->getIdx()) < 2 ||
                 mol.getRingInfo()->isAtomInRingOfSize(atom->getIdx(), 3)))) {
             // we only want to these tests for ring atoms that are not part of

diff --git a/Code/GraphMol/FMCS/Wrap/testFMCS.py b/Code/GraphMol/FMCS/Wrap/testFMCS.py
@@ -1234,7 +1234,7 @@ def test21ShouldAcceptMCS(self):
     mcs = rdFMCS.FindMCS(mols1, params)
     self.assertEqual(mcs.numAtoms, 11)
     self.assertEqual(mcs.numBonds, 12)
-    self.assertEqual(mcs.smartsString, "[#6]1:&@[#6]:&@[#6]2:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2:&@[#6](-&!@[#0,#6]):&@[#6]:&@1")
+    self.assertEqual(mcs.smartsString, "[#6]1:&@[#6]:&@[#6]2:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2:&@[#6](:&@[#6]:&@1)-&!@[#0,#6]")
     self.assertGreater(params.ProgressCallback.callCount, 0)
     self.assertGreater(params.FinalMatchChecker.callCount, 0)
     params.AtomCompareParameters.RingMatchesRingOnly = True

diff --git a/Code/GraphMol/FMCS/testFMCS_Unit.cpp b/Code/GraphMol/FMCS/testFMCS_Unit.cpp
@@ -2035,7 +2035,7 @@ void testGitHub2731_comment546175466() {
       TEST_ASSERT(res.NumBonds == 14);
       TEST_ASSERT(
           res.SmartsString ==
-          "[#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6]2:&@[#6;r6,!R1]:&@[#6](:&@[#6]:&@[#6]):&@[#6](:&@[#6]):&@[#7;r6,!R1]:&@[#6]:&@2:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1");
+          "[#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6]2:&@[#6;r6,!R1]:&@[#6](:&@[#6]:&@[#6]):&@[#6](:&@[#7;r6,!R1]:&@[#6]:&@2:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1):&@[#6]");
     }
     {
       MCSParameters p;
@@ -2329,7 +2329,7 @@ void testGitHub3458() {
       TEST_ASSERT(res.NumBonds == 18);
       TEST_ASSERT(
           res.SmartsString ==
-          "[#6&R]:&@[#6&R]:&@[#6]1:&@[#6](-&!@[#7&!R]-&!@[#6]2:&@[#6]:&@[#6]:&@[#6]:&@[#6](-&!@[#35&!R]):&@[#6]:&@2):&@[#7]:&@[#6]:&@[#7]:&@[#6]:&@1:&@[#6&R]");
+          "[#6&R]:&@[#6&R]:&@[#6]1:&@[#6](-&!@[#7&!R]-&!@[#6]2:&@[#6]:&@[#6]:&@[#6]:&@[#6](:&@[#6]:&@2)-&!@[#35&!R]):&@[#7]:&@[#6]:&@[#7]:&@[#6]:&@1:&@[#6&R]");
     }
     {
       MCSParameters p;
@@ -2682,7 +2682,7 @@ void testCustomShouldAcceptMCS() {
   TEST_ASSERT(mcs.NumBonds == 12);
   TEST_ASSERT(
       mcs.SmartsString ==
-      "[#6]1:&@[#6]:&@[#6]2:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2:&@[#6](-&!@[#0,#6]):&@[#6]:&@1");
+      "[#6]1:&@[#6]:&@[#6]2:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2:&@[#6](:&@[#6]:&@1)-&!@[#0,#6]");
 }
 
 void testGitHub5510() {
@@ -2958,7 +2958,7 @@ void testGitHub6578() {
     TEST_ASSERT(mcs.NumBonds == 33);
     TEST_ASSERT(
         mcs.SmartsString ==
-        "[#6]-[#6]1:[#6]:[#6]:[#6]2:[#7](:[#7]:1):[#7]:[#6](-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1):[#6]:2-[#6]1:[#6]:[#6]:[#7]:[#6](-[#7]-[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2):[#7]:1");
+        "[#6]-[#6]1:[#6]:[#6]:[#6]2:[#7](:[#7]:1):[#7]:[#6](:[#6]:2-[#6]1:[#6]:[#6]:[#7]:[#6](:[#7]:1)-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1");
   }
   {
     std::vector<ROMOL_SPTR> mols{
@@ -2972,7 +2972,7 @@ void testGitHub6578() {
     TEST_ASSERT(mcs.NumBonds == 33);
     TEST_ASSERT(
         mcs.SmartsString ==
-        "[#6]-[#6]1:[#6]:[#6]:[#6]2:[#7](:[#7]:1):[#7]:[#6](-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1):[#6]:2-[#6]1:[#6]:[#6]:[#7]:[#6](-[#7]-[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2):[#7]:1");
+        "[#6]-[#6]1:[#6]:[#6]:[#6]2:[#7](:[#7]:1):[#7]:[#6](:[#6]:2-[#6]1:[#6]:[#6]:[#7]:[#6](:[#7]:1)-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1");
   }
   {
     std::vector<ROMOL_SPTR> mols{""_smiles, ""_smiles, ""_smiles, ""_smiles};
@@ -3002,7 +3002,7 @@ void testGitHub6773() {
       TEST_ASSERT(mcs.NumBonds == 11);
       TEST_ASSERT(
           mcs.SmartsString ==
-          "[#8&!R]-&!@[#6;r6,!R1]1-&@[#6;r6,!R1]-&@[#6;r6,!R1]-&@[#6]-&@[#6](-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@[#6&R])-&@[#6;r6,!R1]-&@1");
+          "[#8&!R]-&!@[#6;r6,!R1]1-&@[#6;r6,!R1]-&@[#6;r6,!R1]-&@[#6]-&@[#6](-&@[#6;r6,!R1]-&@1)-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@[#6&R]");
     }
     {
       MCSParameters p;
@@ -3044,8 +3044,7 @@ void testGitHub6773() {
       TEST_ASSERT(mcs.NumBonds == 1);
       TEST_ASSERT(mcs.SmartsString == "[#8&!R]-&!@[#6&R]");
     }
-    mols = std::vector<ROMOL_SPTR>{"C1CC2CCC3CC2C(C1)CCCCCC3"_smiles,
-                                   "C1CC2CCC3CCCC4CCC(C1)C2C34"_smiles};
+    mols = std::vector<ROMOL_SPTR>{"C1CC2CCC3CC2C(C1)CCCCCC3"_smiles, "C1CC2CCC3CCCC4CCC(C1)C2C34"_smiles};
     {
       MCSParameters p;
       p.BondCompareParameters.MatchFusedRingsStrict = true;
@@ -3054,7 +3053,7 @@ void testGitHub6773() {
       TEST_ASSERT(mcs.NumBonds == 16);
       TEST_ASSERT(
           mcs.SmartsString ==
-          "[#6;r6,!R1]1-&@[#6;r6,!R1]-&@[#6]2-&@[#6;r6,!R1]-&@[#6;r6,!R1]-&@[#6](-&@[#6]-&@[#6]-&@[#6])-&@[#6]-&@[#6]-&@2-&@[#6](-&@[#6]-&@[#6])-&@[#6;r6,!R1]-&@1");
+          "[#6;r6,!R1]1-&@[#6;r6,!R1]-&@[#6]2-&@[#6;r6,!R1]-&@[#6;r6,!R1]-&@[#6](-&@[#6]-&@[#6]-&@2-&@[#6](-&@[#6;r6,!R1]-&@1)-&@[#6]-&@[#6])-&@[#6]-&@[#6]-&@[#6]");
     }
     {
       MCSParameters p;
@@ -3079,10 +3078,9 @@ void testGitHub6773() {
 
 void testBondCompareCompleteRingsOnly() {
   BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
-  BOOST_LOG(rdInfoLog)
-      << "test CompleteRingsOnly should work also on unsubstituted fused systems"
-      << std::endl;
-  std::vector<ROMOL_SPTR> mols{"C1CCCC2CCCCC12"_smiles, "C1CCC2CCCC12"_smiles};
+  BOOST_LOG(rdInfoLog) << "test CompleteRingsOnly should work also on unsubstituted fused systems" << std::endl;
+  std::vector<ROMOL_SPTR> mols{"C1CCCC2CCCCC12"_smiles,
+                                "C1CCC2CCCC12"_smiles};
   MCSParameters p;
   p.BondCompareParameters.CompleteRingsOnly = true;
   auto mcs = findMCS(mols, &p);

diff --git a/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp b/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp
@@ -510,8 +510,8 @@ TEST_CASE("CDXML") {
     std::vector<std::string> expected = {"*C1=C([H])C([H])=C([H])C([H])=C1[H]",
                                          "*C1=C([H])N([H])=C([H])C([H])=C1[H]"};
     std::vector<std::string> expected_smarts = {
-        "[#6]1(-[H])=[#6](-[H])-[#6](-[H])=[#6](-[H])-[#6](-[H])=[#6]-1-*",
-        "[#6]1(-[H])=[#6](-[H])-[#6](-[H])=[#7](-[H])-[#6](-[H])=[#6]-1-[!#1]",
+        "[#6]1(=[#6](-[#6](=[#6](-[#6](=[#6]-1-*)-[H])-[H])-[H])-[H])-[H]",
+        "[#6]1(=[#6](-[#6](=[#7](-[#6](=[#6]-1-[!#1])-[H])-[H])-[H])-[H])-[H]",
     };
     CDXMLParserParams params;
     params.sanitize = false;

diff --git a/Code/GraphMol/FileParsers/file_parsers_catch.cpp b/Code/GraphMol/FileParsers/file_parsers_catch.cpp
@@ -3076,7 +3076,7 @@ M  END
           "DoubleOrAromaticBond");
 
     auto smarts = MolToSmarts(*m);
-    CHECK(smarts == "[#7]1-[#6][#6]-[#6]=,:[#8]-[#6]-,=1");
+    CHECK(smarts == "[#7]1-,=[#6]-[#8]=,:[#6]-[#6][#6]-1");
   }
   SECTION("basics V2K") {
     auto m = R"CTAB(

diff --git a/Code/GraphMol/Fingerprints/Fingerprints.cpp b/Code/GraphMol/Fingerprints/Fingerprints.cpp
@@ -262,7 +262,7 @@ ExplicitBitVect *LayeredFingerprintMol(
   PRECONDITION(!setOnlyBits || setOnlyBits->getNumBits() == fpSize,
                "bad setOnlyBits size");
 
-  if (!mol.getRingInfo()->isSssrOrBetter()) {
+  if (!mol.getRingInfo()->isInitialized()) {
     MolOps::findSSSR(mol);
   }
 

diff --git a/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp b/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp
@@ -317,7 +317,7 @@ void getExperimentalTorsions(
     // torsions for flat rings
     const RingInfo *rinfo = mol.getRingInfo();
     CHECK_INVARIANT(rinfo, "no ring info");
-    CHECK_INVARIANT(rinfo->isSssrOrBetter(), "sssr ring info not initialized");
+    CHECK_INVARIANT(rinfo->isInitialized(), "ring info not initialized");
     for (const auto &atomRing : rinfo->atomRings()) {
       unsigned int rSize = atomRing.size();
       // we don't need to deal with 3 membered rings

diff --git a/Code/GraphMol/GenericGroups/GenericGroups.cpp b/Code/GraphMol/GenericGroups/GenericGroups.cpp
@@ -382,7 +382,7 @@ bool FusedRingMatch(const ROMol &mol, const Atom &atom,
     return false;
   }
 
-  if (!mol.getRingInfo() || !mol.getRingInfo()->isSssrOrBetter()) {
+  if (!mol.getRingInfo() || !mol.getRingInfo()->isInitialized()) {
     MolOps::findSSSR(mol);
   }
   if (!mol.getRingInfo()->numAtomRings(atom.getIdx())) {

diff --git a/Code/GraphMol/Kekulize.cpp b/Code/GraphMol/Kekulize.cpp
@@ -566,7 +566,7 @@ void KekulizeFragment(RWMol &mol, const boost::dynamic_bitset<> &atomsToUse,
     // first find all the simple rings in the molecule that are not
     // completely composed of dummy atoms
     VECT_INT_VECT allringsSSSR;
-    if (!mol.getRingInfo()->isSssrOrBetter()) {
+    if (!mol.getRingInfo()->isInitialized()) {
       MolOps::findSSSR(mol, allringsSSSR);
     }
     const VECT_INT_VECT &allrings =
@@ -640,7 +640,7 @@ void KekulizeFragment(RWMol &mol, const boost::dynamic_bitset<> &atomsToUse,
   if (markAtomsBonds) {
     // if we want the atoms and bonds to be marked non-aromatic do
     // that here.
-    if (!mol.getRingInfo()->isSssrOrBetter()) {
+    if (!mol.getRingInfo()->isInitialized()) {
       MolOps::findSSSR(mol);
     }
     for (auto bond : mol.bonds()) {

diff --git a/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp b/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp
@@ -40,7 +40,7 @@ bool isAtomCandForChiralH(const RWMol &mol, const Atom *atom) {
   // conditions for needing a chiral H:
   //   - stereochem specified
   //   - in at least two rings
-  return mol.getRingInfo()->isSssrOrBetter() &&
+  return mol.getRingInfo()->isInitialized() &&
          mol.getRingInfo()->numAtomRings(atom->getIdx()) > 1u &&
          (atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW ||
           atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW);

diff --git a/Code/GraphMol/MolEnumerator/enumerator_catch.cpp b/Code/GraphMol/MolEnumerator/enumerator_catch.cpp
@@ -625,7 +625,7 @@ M  END
     auto bundle = MolEnumerator::enumerate(*mol1);
     CHECK(bundle.size() == 2);
     std::vector<std::string> tsmas = {"[#6]1-[#6]-[#7]=[#6]-[#7]-1-[!#1]",
-                                      "[#6]1-[#6]-[#7](-[!#1])=[#6]-[#7]-1"};
+                                      "[#6]1-[#6]-[#7](=[#6]-[#7]-1)-[!#1]"};
     for (const auto &molp : bundle.getMols()) {
       auto smarts = MolToSmarts(*molp);
       CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());
@@ -663,7 +663,7 @@ M  END
     auto bundle = MolEnumerator::enumerate(*mol1);
     CHECK(bundle.size() == 2);
     std::vector<std::string> tsmas = {"[#6]1-[#6]-[#7]=[#6]-[#7]-1-[!#1]",
-                                      "[#6]1-[#6]-[#7](-[!#1])=[#6]-[#7]-1"};
+                                      "[#6]1-[#6]-[#7](=[#6]-[#7]-1)-[!#1]"};
     for (const auto &molp : bundle.getMols()) {
       auto smarts = MolToSmarts(*molp);
       CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());
@@ -701,7 +701,7 @@ M  END
     auto bundle = MolEnumerator::enumerate(*mol1);
     CHECK(bundle.size() == 2);
     std::vector<std::string> tsmas = {"[#6]1-[#6]-[#7]=[#6]-[#7]-1-*",
-                                      "[#6]1-[#6]-[#7](-*)=[#6]-[#7]-1"};
+                                      "[#6]1-[#6]-[#7](=[#6]-[#7]-1)-*"};
     for (const auto &molp : bundle.getMols()) {
       auto smarts = MolToSmarts(*molp);
       CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());
@@ -742,7 +742,7 @@ M  END
     auto bundle = MolEnumerator::enumerate(*mol1);
     CHECK(bundle.size() == 2);
     std::vector<std::string> tsmas = {"[#6]1:[#6]:[#7]:[#6]:[#7]:1-[#6]",
-                                      "[#6]1:[#6]:[#7](-[#6]):[#6]:[#7]:1"};
+                                      "[#6]1:[#6]:[#7](:[#6]:[#7]:1)-[#6]"};
     for (const auto &molp : bundle.getMols()) {
       auto smarts = MolToSmarts(*molp);
       CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());