Removing stereoatoms requires removing CIS/Trans stereo flags (rdkit#…

…6901) * Removing stereoatoms requires removing CIS/Trans stereo flags * Added test when removing nbrs of cis/trans bonds --------- Co-authored-by: Brian Kelley <bkelley@relaytx.com>
e-kwsm · Nov 21, 2023 · ee8c35a · ee8c35a
1 parent ab7b8dd
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Showing 3 changed files with 43 additions and 1 deletion.
diff --git a/Code/GraphMol/MMPA/MMPA_UnitTest.cpp b/Code/GraphMol/MMPA/MMPA_UnitTest.cpp
@@ -49,6 +49,7 @@
 #include <iostream>
 #include <RDGeneral/RDLog.h>
 #include <RDGeneral/utils.h>
+#include <GraphMol/Chirality.h>
 #include "../RDKitBase.h"
 #include "../FileParsers/FileParsers.h"  //MOL single molecule !
 #include "../FileParsers/MolSupplier.h"  //SDF
@@ -690,6 +691,14 @@ std::endl;
 //====================================================================================================
 //====================================================================================================
 
+void testGithub6900 () {
+  RDKit::Chirality::setUseLegacyStereoPerception(false);
+  //auto mol = "CN1CCCN=C1/C=C/c1cccs1"_smiles;
+  auto mol = "N/C=C/C"_smiles;
+  std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> res;
+  RDKit::MMPA::fragmentMol(*mol, res, 3);
+  RDKit::Chirality::setUseLegacyStereoPerception(true);
+}
 int main() {
   BOOST_LOG(rdInfoLog)
       << "*******************************************************\n";
@@ -703,14 +712,15 @@ int main() {
 #else
   setpriority(PRIO_PROCESS, getpid(), -20);
 #endif
-
+  testGithub6900();
   T0 = nanoClock();
   t0 = nanoClock();
 
   testCase_1();
   // /*
   test2();
   test3();
+
   //    test4();
   // */
   //    debugTest1("C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O");

diff --git a/Code/GraphMol/RWMol.cpp b/Code/GraphMol/RWMol.cpp
@@ -468,6 +468,12 @@ void RWMol::removeBond(unsigned int aid1, unsigned int aid2) {
     }
     if (std::find(obnd->getStereoAtoms().begin(), obnd->getStereoAtoms().end(),
                   aid2) != obnd->getStereoAtoms().end()) {
+      // github #6900 if we remove stereo atoms we need to remove
+      //  the CIS and or TRANS since this requires stereo atoms
+      if (obnd->getStereo() == Bond::BondStereo::STEREOCIS ||
+          obnd->getStereo() == Bond::BondStereo::STEREOTRANS ) {
+          obnd->setStereo(Bond::BondStereo::STEREONONE);
+      }
       obnd->getStereoAtoms().clear();
     }
   }
@@ -484,6 +490,12 @@ void RWMol::removeBond(unsigned int aid1, unsigned int aid2) {
     }
     if (std::find(obnd->getStereoAtoms().begin(), obnd->getStereoAtoms().end(),
                   aid1) != obnd->getStereoAtoms().end()) {
+      // github #6900 if we remove stereo atoms we need to remove
+      //  the CIS and or TRANS since this requires stereo atoms
+      if (obnd->getStereo() == Bond::BondStereo::STEREOCIS ||
+        obnd->getStereo() == Bond::BondStereo::STEREOTRANS ) {
+        obnd->setStereo(Bond::BondStereo::STEREONONE);
+      }
       obnd->getStereoAtoms().clear();
     }
   }

diff --git a/Code/GraphMol/catch_chirality.cpp b/Code/GraphMol/catch_chirality.cpp
@@ -1297,6 +1297,26 @@ TEST_CASE("ring stereo finding is overly aggressive", "[chirality][bug]") {
         Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
     CHECK(stereoInfo.size() == 2);
   }
+  SECTION("Removal of stereoatoms requires removing CIS/TRANS when using legacy stereo") {
+      UseLegacyStereoPerceptionFixture reset_stereo_perception;
+      Chirality::setUseLegacyStereoPerception(false);
+
+    {
+      auto mol = "N/C=C/C"_smiles;
+      CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
+      auto rwmol = dynamic_cast<RWMol*>(mol.get());
+      rwmol->removeBond(0,1);
+      CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::BondStereo::STEREONONE);
+    }
+    {
+      auto mol = "N/C=C/C"_smiles;
+      CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
+      auto rwmol = dynamic_cast<RWMol*>(mol.get());
+      rwmol->removeBond(2,3);
+      CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREONONE);
+    }
+
+  }
 }
 
 TEST_CASE(