Support new coordgen option to not always make bonds to metals zero-order (#3769)

* bump version of coordgen we're installing

* default to not set bonds to metals to be ZOBs
but add an option to change that

External/CoordGen/CMakeLists.txt

@@ -82,24 +82,24 @@ if(RDK_BUILD_COORDGEN_SUPPORT)
     endif()
 
     if(NOT EXISTS "${COORDGEN_DIR}/sketcherMinimizer.h")
-        set(RELEASE_NO "1.4.1")
-        set(MD5 "d9a925c9569bc08e241a01669f43d639")
+        set(RELEASE_NO "1.4.2")
+        set(MD5 "47aa5fe6d8186b6c8d3b871d4400218a")
         downloadAndCheckMD5("https://github.com/schrodinger/coordgenlibs/archive/v${RELEASE_NO}.tar.gz"
               "${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz" ${MD5})
         execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
           ${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz
           WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
         
-        # FIX: this is a workaround until https://github.com/schrodinger/coordgenlibs/pull/76
-        # is merged and a new coordgen release is done
         file(RENAME "coordgenlibs-${RELEASE_NO}" "${COORDGEN_DIR}")
-        set(fileToPatch "${COORDGEN_DIR}/CoordgenFragmenter.h")
-        configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
-        file(READ "${fileToPatch}" buffer)
-        string(REPLACE "class CoordgenFragmenter"
-          "#include \"CoordgenConfig.hpp\"\nclass EXPORT_COORDGEN CoordgenFragmenter" 
-          buffer "${buffer}")
-        file(WRITE "${fileToPatch}" "${buffer}")
+        # # FIX: this is a workaround until https://github.com/schrodinger/coordgenlibs/pull/76
+        # # is merged and a new coordgen release is done
+        # set(fileToPatch "${COORDGEN_DIR}/CoordgenFragmenter.h")
+        # configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
+        # file(READ "${fileToPatch}" buffer)
+        # string(REPLACE "class CoordgenFragmenter"
+        #   "#include \"CoordgenConfig.hpp\"\nclass EXPORT_COORDGEN CoordgenFragmenter" 
+        #   buffer "${buffer}")
+        # file(WRITE "${fileToPatch}" "${buffer}")
     else()
       message("-- Found coordgenlibs source in ${COORDGEN_DIR}")
     endif()

External/CoordGen/CoordGen.h

@@ -34,10 +34,12 @@ struct CoordGenParams {
   // length of 50.
   std::string templateFileDir = "";
   float minimizerPrecision =
-      sketcherCoarsePrecision;  // controls sketch precision
-  bool dbg_useConstrained = true;   // debugging
-  bool dbg_useFixed = false;        // debugging
-  bool minimizeOnly = false;        // don't actually generate full coords
+      sketcherCoarsePrecision;     // controls sketch precision
+  bool dbg_useConstrained = true;  // debugging
+  bool dbg_useFixed = false;       // debugging
+  bool minimizeOnly = false;       // don't actually generate full coords
+  bool treatBondsToMetalAsZeroOrder =
+      false;  // set all bonds to metal atoms to be zero-order bonds
 };
 
 static CoordGenParams defaultParams;
@@ -75,6 +77,8 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
   sketcherMinimizer minimizer(params->minimizerPrecision);
   auto min_mol = new sketcherMinimizerMolecule();
 
+  minimizer.setTreatAllBondsToMetalAsZOBs(params->treatBondsToMetalAsZeroOrder);
+
   // FIX: only do this check once.
   // std::cerr << "  TEMPLATES: " << templateFileDir << std::endl;
   if (templateFileDir != "") {

External/CoordGen/Wrap/rdCoordGen.cpp

@@ -73,21 +73,26 @@ struct coordgen_wrapper {
                        "uses coordgen's force field to cleanup the 2D "
                        "coordinates of the active conformation")
         .def_readonly("sketcherBestPrecision",
-                       &CoordGen::CoordGenParams::sketcherBestPrecision,
-                       "highest quality (and slowest) precision setting")
+                      &CoordGen::CoordGenParams::sketcherBestPrecision,
+                      "highest quality (and slowest) precision setting")
         .def_readonly("sketcherStandardPrecision",
-                       &CoordGen::CoordGenParams::sketcherStandardPrecision,
-                       "standard quality precision setting, the default for the coordgen project")
+                      &CoordGen::CoordGenParams::sketcherStandardPrecision,
+                      "standard quality precision setting, the default for the "
+                      "coordgen project")
         .def_readonly("sketcherQuickPrecision",
-                       &CoordGen::CoordGenParams::sketcherQuickPrecision,
-                       "faster precision setting")
-        .def_readonly("sketcherCoarsePrecision",
-                       &CoordGen::CoordGenParams::sketcherCoarsePrecision,
-                       "\"coarse\" (fastest) precision setting, produces good-quality coordinates"
-                       " most of the time, this is the default setting for the RDKit")
+                      &CoordGen::CoordGenParams::sketcherQuickPrecision,
+                      "faster precision setting")
+        .def_readonly(
+            "sketcherCoarsePrecision",
+            &CoordGen::CoordGenParams::sketcherCoarsePrecision,
+            "\"coarse\" (fastest) precision setting, produces good-quality "
+            "coordinates"
+            " most of the time, this is the default setting for the RDKit")
         .def_readwrite("minimizerPrecision",
                        &CoordGen::CoordGenParams::minimizerPrecision,
-                       "controls sketcher precision");
+                       "controls sketcher precision")
+        .def_readwrite("treatBondsToMetalAsZOBs",
+                       &CoordGen::CoordGenParams::treatBondsToMetalAsZeroOrder);
     python::def("SetDefaultTemplateFileDir", SetDefaultTemplateFileDir);
     docString =
         "Add 2D coordinates.\n"

External/CoordGen/test.cpp

@@ -559,6 +559,69 @@ M  END
   BOOST_LOG(rdInfoLog) << "done" << std::endl;
 }
 
+void testZOBs() {
+  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "testing the zero-order bond setting with coordgen"
+                       << std::endl;
+  {
+    auto m1 =
+        R"CTAB(
+     RDKit          2D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 8 7 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 Al 0.108450 -0.062175 0.000000 0 VAL=3
+M  V30 2 C 0.976250 -0.558975 0.000000 0
+M  V30 3 C 0.104850 0.937825 0.000000 0
+M  V30 4 C -0.755750 -0.565175 0.000000 0
+M  V30 5 C 1.840650 -0.055775 0.000000 0
+M  V30 6 C -1.623550 -0.068375 0.000000 0
+M  V30 7 C -2.487750 -0.571375 0.000000 0
+M  V30 8 C 1.836850 0.944025 0.000000 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 1 3
+M  V30 3 1 1 4
+M  V30 4 2 2 5
+M  V30 5 2 4 6
+M  V30 6 1 6 7
+M  V30 7 1 5 8
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+)CTAB"_ctab;
+    TEST_ASSERT(m1);
+    TEST_ASSERT(m1->getNumConformers() == 1);
+    CoordGen::addCoords(*m1);
+    TEST_ASSERT(m1->getNumConformers() == 1);
+    {
+      std::unique_ptr<ROMol> nm{MolBlockToMol(MolToMolBlock(*m1))};
+      TEST_ASSERT(nm);
+      TEST_ASSERT(nm->getBondWithIdx(3)->getStereo() ==
+                  m1->getBondWithIdx(3)->getStereo());
+      TEST_ASSERT(nm->getBondWithIdx(4)->getStereo() ==
+                  m1->getBondWithIdx(4)->getStereo());
+    }
+
+    CoordGen::CoordGenParams ps;
+    ps.treatBondsToMetalAsZeroOrder = true;
+    CoordGen::addCoords(*m1, &ps);
+    {
+      // the ZOB behavior screws up the double bond stereo here... detect that
+      std::unique_ptr<ROMol> nm{MolBlockToMol(MolToMolBlock(*m1))};
+      TEST_ASSERT(nm);
+      TEST_ASSERT(nm->getBondWithIdx(3)->getStereo() !=
+                  m1->getBondWithIdx(3)->getStereo());
+      TEST_ASSERT(nm->getBondWithIdx(4)->getStereo() !=
+                  m1->getBondWithIdx(4)->getStereo());
+    }
+  }
+  BOOST_LOG(rdInfoLog) << "done" << std::endl;
+}
+
 int main(int argc, char* argv[]) {
   (void)argc;
   (void)argv;
@@ -570,4 +633,5 @@ int main(int argc, char* argv[]) {
   testGithub3131();
 #endif
   testCoordgenMinimize();
+  testZOBs();
 }