Support allenes in canonicalizing double bonds, fixes #7044

Code/GraphMol/Canon.cpp

@@ -212,6 +212,15 @@ void canonicalizeDoubleBond(Bond *dblBond, UINT_VECT &bondVisitOrders,
         secondNeighborBond = bond;
       }
     }
+    if (!firstNeighborBond) {
+      // allene
+      for (const auto bond : mol.atomBonds(atom)) {
+        if (bond == dblBond) {
+          continue;
+        }
+        firstNeighborBond = bond;
+      }
+    }
   };
 
   findNeighborBonds(atom1, firstFromAtom1, secondFromAtom1, dir1Set);

Code/GraphMol/MolStandardize/testTautomer.cpp

@@ -316,6 +316,10 @@ void testEnumerator() {
   checkAns("C/C=C/C(C)=O", {"C=C(O)C=CC", "C=CC=C(C)O", "C=CCC(=C)O",
                             "C=CCC(C)=O", "CC=CC(C)=O"});
 
+  // // Remove stereochemistry from conjugated double bonds to nitro
+  // checkAns("c1ccnc(c1)/C=C/[N+](=O)[O-]", {"O=[N+]([O-])C=Cc1ccccn1",
+  //                                          "[O-][N+](O)=C=Cc1ccccn1"});
+
   // Remove stereochemistry from mobile double bonds
   std::string smi66 = "C/C=C\\C(C)=O";
   ROMOL_SPTR m66(SmilesToMol(smi66));
@@ -334,7 +338,7 @@ void testEnumerator() {
   std::sort(ans66.begin(), ans66.end());
   TEST_ASSERT(sm66 == ans66);
 
-  // Gaunine tautomers
+  // Guanine tautomers
   std::string smi67 = "N1C(N)=NC=2N=CNC2C1=O";
   ROMOL_SPTR m67(SmilesToMol(smi67));
   TautomerEnumeratorResult res67 = te.enumerate(*m67);
@@ -490,6 +494,56 @@ void testEnumeratorParams() {
       }
     }
   }
+  std::string eOximeSmi = "c1ccnc(c1)/C=N/O";
+  ROMOL_SPTR eOxime(SmilesToMol(eOximeSmi));
+  TEST_ASSERT(eOxime->getBondWithIdx(6)->getStereo() == Bond::STEREOE);
+  {
+    // test remove oxime E stereochemistry
+    CleanupParameters params;
+    params.tautomerRemoveBondStereo = true;
+    TautomerEnumerator te(params);
+    TautomerEnumeratorResult res = te.enumerate(*eOxime);
+    for (const auto &taut : res) {
+      TEST_ASSERT(taut->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
+    }
+  }
+  {
+    // test retain enol E stereochemistry
+    CleanupParameters params;
+    params.tautomerRemoveBondStereo = false;
+    TautomerEnumerator te(params);
+    TautomerEnumeratorResult res = te.enumerate(*eOxime);
+    for (const auto &taut : res) {
+      if (taut->getBondWithIdx(6)->getBondType() == Bond::DOUBLE) {
+        TEST_ASSERT(taut->getBondWithIdx(6)->getStereo() == Bond::STEREOE);
+      }
+    }
+  }
+  ROMOL_SPTR zOxime = "c1ccnc(c1)/C=N\\O"_smiles;
+  // zOxime->debugMol(std::cerr);
+  TEST_ASSERT(zOxime->getBondWithIdx(6)->getStereo() == Bond::STEREOZ);
+  {
+    // test remove enol Z stereochemistry
+    CleanupParameters params;
+    params.tautomerRemoveBondStereo = true;
+    TautomerEnumerator te(params);
+    TautomerEnumeratorResult res = te.enumerate(*zOxime);
+    for (const auto &taut : res) {
+      TEST_ASSERT(taut->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
+    }
+  }
+  {
+    // test retain enol Z stereochemistry
+    CleanupParameters params;
+    params.tautomerRemoveBondStereo = false;
+    TautomerEnumerator te(params);
+    TautomerEnumeratorResult res = te.enumerate(*zOxime);
+    for (const auto &taut : res) {
+      if (taut->getBondWithIdx(6)->getBondType() == Bond::DOUBLE) {
+        TEST_ASSERT(taut->getBondWithIdx(6)->getStereo() == Bond::STEREOZ);
+      }
+    }
+  }
   ROMOL_SPTR chembl2024142 =
       "[2H]C1=C(C(=C2C(=C1[2H])C(=O)C(=C(C2=O)C([2H])([2H])[2H])C/C=C(\\C)/CC([2H])([2H])/C=C(/CC/C=C(\\C)/CCC=C(C)C)\\C([2H])([2H])[2H])[2H])[2H]"_smiles;
   MolOps::RemoveHsParameters hparams;