Enhanced Stereochemistry canonicalization errors

Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py

@@ -2,7 +2,6 @@
 
 from rdkit import Chem
 
-
 class TestCase(unittest.TestCase):
 
   def testLabelAtomsList(self):

Code/GraphMol/CIPLabeler/catch_tests.cpp

@@ -809,7 +809,7 @@ TEST_CASE("AssignMandP", "[accurateCIP]") {
         "C1(N2C(C)=CC=C2Br)=C(C)C(C)=C(N2C(C)=CC=C2Br)C(C)=C1C |(-0.0002,1.5403,;-0.0002,3.0805,;-1.334,3.8508,;-2.6678,3.0807,;-1.334,5.391,;1.3338,5.391,;1.3338,3.8508,;2.6676,3.0807,;-1.3338,0.7702,;-2.6678,1.5403,;-1.3338,-0.7702,;-2.6678,-1.5401,;-0.0002,-1.5403,;-0.0002,-3.0805,;1.3338,-3.8508,;2.6676,-3.0805,;1.3338,-5.391,;-1.334,-5.391,;-1.334,-3.8508,;-2.6678,-3.0805,;1.3338,-0.7702,;2.6678,-1.5403,;1.3338,0.7702,;2.6678,1.5404,),wU:1.6,13.14|",
         "0-1=m:12-13=m:");
   }
-  SECTION("psuedo") {
+  SECTION("pseudo") {
     testOneAtropIomerMandP(
         "N1(n2c(C)ccc2Br)C(=O)[C@H](C)[C@H](C)C1=O |(-11.1517,1.8306,;-11.1517,3.3708,;-12.4855,4.1411,;-13.8193,3.371,;-12.4855,5.6813,;-9.8177,5.6813,;-9.8177,4.1411,;-8.4839,3.371,;-12.3975,0.9252,;-13.8622,1.4011,;-11.9217,-0.5394,;-12.8269,-1.7852,;-10.3817,-0.5394,;-9.4765,-1.7852,;-9.9059,0.9252,;-8.4413,1.4011,),wU:0.8,10.11,12.13|",
         "0-1=p:");

Code/GraphMol/CIPLabeler/rules/Rule5New.cpp

@@ -58,7 +58,7 @@ int Rule5New::compare(const Edge *a, const Edge *b) const {
     fillPairs(bEnd, listSB);
     int cmpR = listRA.compareTo(listRB);
     int cmpS = listSA.compareTo(listSB);
-    // -2/+2 for psuedo-asymetric
+    // -2/+2 for pseudo-asymetric
     // -1/+1 if not (e.g. the R > R and S > S lists)
     if (cmpR < 0) {
       return cmpS < 0 ? -1 : -2;

Code/GraphMol/Chirality.cpp

@@ -3196,8 +3196,6 @@ void assignChiralTypesFrom3D(ROMol &mol, int confId, bool replaceExistingTags) {
   }
 
   for (auto atom : mol.atoms()) {
-    // see if only the explicitly wedged atoms are to be used
-
     // if we aren't replacing existing tags and the atom is already tagged,
     // punt:
     if (!replaceExistingTags && atom->getChiralTag() != Atom::CHI_UNSPECIFIED) {

Code/GraphMol/DetermineBonds/catch_tests.cpp

@@ -136,7 +136,15 @@ TEST_CASE("Determine Connectivity") {
       std::string smiles = mol->getProp<std::string>("_FileComments");
       std::unique_ptr<RWMol> orig(SmilesToMol(smiles));
       REQUIRE(orig);
-      SmilesWriteParams params = {false, false, true, false, false, false, -1};
+      SmilesWriteParams params;
+      params.doIsomericSmiles = false;
+      params.doKekule = false;
+      params.canonical = true;
+      params.allBondsExplicit = false;
+      params.allHsExplicit = false;
+      params.doRandom = false;
+      params.rootedAtAtom = -1;
+
       std::string canonSmiles = MolToSmiles(*orig, params);
       int charge = MolOps::getFormalCharge(*orig);
 
@@ -180,7 +188,14 @@ TEST_CASE("Determine Connectivity") {
       std::string smiles = mol->getProp<std::string>("_FileComments");
       std::unique_ptr<RWMol> orig(SmilesToMol(smiles));
       REQUIRE(orig);
-      SmilesWriteParams params = {false, false, true, false, false, false, -1};
+      SmilesWriteParams params;
+      params.doIsomericSmiles = false;
+      params.doKekule = false;
+      params.canonical = true;
+      params.allBondsExplicit = false;
+      params.allHsExplicit = false;
+      params.doRandom = false;
+      params.rootedAtAtom = -1;
       std::string canonSmiles = MolToSmiles(*orig, params);
       int charge = MolOps::getFormalCharge(*orig);
 

Code/GraphMol/FileParsers/file_parsers_catch.cpp

@@ -6276,7 +6276,7 @@ TEST_CASE("MaeWriter basic testing", "[mae][MaeWriter][writer]") {
     auto ctBlockStart = mae.find("f_m_ct");
     REQUIRE(ctBlockStart != std::string::npos);
 
-    std::string_view ctBlock(&mae[ctBlockStart]);
+    std::string ctBlock(&mae[ctBlockStart]);
 
     CHECK(ctBlock == MaeWriter::getText(*mol));
   }

Code/GraphMol/MarvinParse/MarvinParser.cpp

@@ -57,7 +57,8 @@ class MarvinCMLReader {
   ~MarvinCMLReader(){};
 
   std::unique_ptr<RWMol> parseMolecule(boost::property_tree::ptree molTree,
-                       bool sanitize = false, bool removeHs = false) {
+                                       bool sanitize = false,
+                                       bool removeHs = false) {
     boost::property_tree::ptree molSection;
 
     try {