make ringdecomposerlib a mandatory dependency (#9209)

Code/GraphMol/CMakeLists.txt

@@ -12,11 +12,10 @@ rdkit_library(GraphMol
         SHARED
         LINK_LIBRARIES RDGeometryLib RDGeneral)
 target_compile_definitions(GraphMol PRIVATE RDKIT_GRAPHMOL_BUILD)
-if (RDK_USE_URF)
-    target_link_libraries(GraphMol PUBLIC ${RDK_URF_LIBS})
-    if (RDK_INSTALL_STATIC_LIBS AND NOT RDK_BUILD_STATIC_LIBS_ONLY)
+
+target_link_libraries(GraphMol PUBLIC ${RDK_URF_LIBS})
+if (RDK_INSTALL_STATIC_LIBS AND NOT RDK_BUILD_STATIC_LIBS_ONLY)
         target_link_libraries(GraphMol_static PUBLIC ${RDK_URF_LIBS}_static)
-    endif ()
 endif ()
 
 rdkit_headers(Atom.h

Code/GraphMol/FindRings.cpp

@@ -1157,7 +1157,6 @@ void fastFindRings(const ROMol &mol) {
   FindRings::storeRingsInfo(mol, res);
 }
 
-#ifdef RDK_USE_URF
 void findRingFamilies(const ROMol &mol, bool includeDativeBonds,
                       bool includeHydrogenBonds) {
   if (mol.getRingInfo()->isInitialized()) {
@@ -1214,13 +1213,6 @@ void findRingFamilies(const ROMol &mol, bool includeDativeBonds,
     free(edges);
   }
 }
-#else
-void findRingFamilies(const ROMol &mol, bool includeDativeBonds,
-                      bool includeHydrogenBonds) {
-  BOOST_LOG(rdErrorLog)
-      << "This version of the RDKit was built without URF support" << std::endl;
-}
-#endif
 }  // namespace MolOps
 
 }  // namespace RDKit

Code/GraphMol/RingInfo.cpp

@@ -267,7 +267,6 @@ void RingInfo::initFusedRings() {
   }
 }
 
-#ifdef RDK_USE_URF
 unsigned int RingInfo::numRingFamilies() const {
   PRECONDITION(df_init, "RingInfo not initialized");
   return d_atomRingFamilies.size();
@@ -288,7 +287,6 @@ unsigned int RingInfo::addRingFamily(const INT_VECT &atomIndices,
 
   return rdcast<unsigned int>(d_atomRingFamilies.size());
 }
-#endif
 
 void RingInfo::initialize(RDKit::FIND_RING_TYPE ringType) {
   df_init = true;
@@ -304,10 +302,9 @@ void RingInfo::reset() {
   d_bondMembers.clear();
   d_atomRings.clear();
   d_bondRings.clear();
-#ifdef RDK_USE_URF
+
   d_atomRingFamilies.clear();
   d_bondRingFamilies.clear();
-#endif
 }
 void RingInfo::preallocate(unsigned int numAtoms, unsigned int numBonds) {
   d_atomMembers.resize(numAtoms);

Code/GraphMol/RingInfo.h

@@ -15,13 +15,9 @@
 #include <vector>
 #include <RDGeneral/BoostStartInclude.h>
 #include <boost/dynamic_bitset.hpp>
-#ifdef RDK_USE_URF
 #include <boost/shared_ptr.hpp>
-#endif
 #include <RDGeneral/BoostEndInclude.h>
-#ifdef RDK_USE_URF
 #include <RingDecomposerLib.h>
-#endif
 
 namespace RDKit {
 //! A class to store information about a molecule's rings
@@ -270,7 +266,6 @@ class RDKIT_GRAPHMOL_EXPORT RingInfo {
   */
   std::vector<unsigned int> fusedRingNeighbors(unsigned int ringIdx);
 
-#ifdef RDK_USE_URF
   //! adds a ring family to our data
   /*!
     \param atomIndices the integer indices of the atoms involved in the
@@ -317,7 +312,6 @@ class RDKIT_GRAPHMOL_EXPORT RingInfo {
 
   //! check if the ring families have been initialized
   bool areRingFamiliesInitialized() const { return dp_urfData != nullptr; }
-#endif
 
   //! @}
 
@@ -333,10 +327,8 @@ class RDKIT_GRAPHMOL_EXPORT RingInfo {
   std::vector<boost::dynamic_bitset<>> d_fusedRings;
   std::vector<unsigned int> d_numFusedBonds;
 
-#ifdef RDK_USE_URF
  public:
   boost::shared_ptr<RDL_data> dp_urfData;
-#endif
 };
 }  // namespace RDKit
 

Code/GraphMol/Wrap/MolOps.cpp

@@ -1322,7 +1322,6 @@ struct molops_wrapper {
     python::def("FastFindRings", MolOps::fastFindRings, docString.c_str(),
                 python::args("mol"));
 
-#ifdef RDK_USE_URF
     docString =
         "Generate Unique Ring Families.\n\
 \n\
@@ -1338,7 +1337,6 @@ struct molops_wrapper {
                 (python::args("mol"), python::arg("includeDativeBonds") = false,
                  python::arg("includeHydrogenBonds") = false),
                 docString.c_str());
-#endif
 
     // ------------------------------------------------------------------------
     docString = R"DOC(Parameters controlling H addition.)DOC";

Code/GraphMol/Wrap/RingInfo.cpp

@@ -46,7 +46,6 @@ python::object bondRingSizes(const RingInfo *self, unsigned int idx) {
   return python::tuple(self->bondRingSizes(idx));
 }
 
-#ifdef RDK_USE_URF
 python::object atomRingFamilies(const RingInfo *self) {
   python::list res;
   for (const auto &ring : self->atomRingFamilies()) {
@@ -61,7 +60,6 @@ python::object bondRingFamilies(const RingInfo *self) {
   }
   return python::tuple(res);
 }
-#endif
 
 void addRing(RingInfo *self, python::object atomRing, python::object bondRing) {
   unsigned int nAts = boost::python::len(atomRing);
@@ -121,7 +119,6 @@ struct ringinfo_wrapper {
         .def("BondMembers", bondMembers, python::args("self", "idx"))
         .def("AtomRingSizes", atomRingSizes, python::args("self", "idx"))
         .def("BondRingSizes", bondRingSizes, python::args("self", "idx"))
-#ifdef RDK_USE_URF
         .def("NumRingFamilies", &RingInfo::numRingFamilies,
              python::args("self"))
         .def("NumRelevantCycles", &RingInfo::numRelevantCycles,
@@ -130,7 +127,6 @@ struct ringinfo_wrapper {
         .def("BondRingFamilies", bondRingFamilies, python::args("self"))
         .def("AreRingFamiliesInitialized",
              &RingInfo::areRingFamiliesInitialized, python::args("self"))
-#endif
         .def("AddRing", addRing,
              (python::arg("self"), python::arg("atomIds"),
               python::arg("bondIds")),

Code/GraphMol/catch_molops.cpp

@@ -681,7 +681,6 @@ TEST_CASE("Github #8945") {
   }
 }
 
-#ifdef RDK_USE_URF
 TEST_CASE("Test findRingFamilies") {
   SECTION("basic check") {
     auto m = R"SMI(c1ccc2c(c1)C3CC3C4CC5CC4CC25)SMI"_smiles;
@@ -770,4 +769,3 @@ TEST_CASE("Test findRingFamilies") {
     CHECK(r->bondRingFamilies().size() == numRings);
   }
 }
-#endif

Code/GraphMol/molopstest.cpp

@@ -7754,7 +7754,6 @@ M  END)CTAB";
   REQUIRE(v86.dotProduct(v16) < -1e-4);
 }
 
-#ifdef RDK_USE_URF
 TEST_CASE("Testing ring family calculation") {
   {
     constexpr const char *smiles = "C(C1C2C3C41)(C2C35)C45";  // cubane
@@ -7799,7 +7798,6 @@ TEST_CASE("Testing ring family calculation") {
     delete m;
   }
 }
-#endif
 
 TEST_CASE("Testing adding coordinates to a terminal atom") {
   auto mol = R"CTAB(

Code/JavaWrappers/CMakeLists.txt

@@ -37,9 +37,7 @@ set(swigRDKitLibList "${swigRDKitLibList}"
   "ForceFieldHelpers;ForceField;EigenSolvers;Optimizer;MolAlign;O3AAlign;"
   "Alignment;SimDivPickers;RDGeometryLib;RDStreams;RDGeneral;"
 )
-if(RDK_USE_URF)
-  set(swigRDKitLibList "${swigRDKitLibList};${RDK_URF_LIBS};")
-endif(RDK_USE_URF)
+set(swigRDKitLibList "${swigRDKitLibList};${RDK_URF_LIBS};")
 set(swigRDKitLibs "")
 foreach(swigRDKitLib ${swigRDKitLibList})
   set(swigRDKitLibs "${swigRDKitLibs}${swigRDKitLib}${swigRDKitLibSuffix};")

Code/MinimalLib/CMakeLists.txt

@@ -61,9 +61,7 @@ if(RDK_BUILD_CFFI_LIB)
         add_definitions(-DRDK_BUILD_INCHI_SUPPORT)
         list(APPEND LIBS_TO_USE RDInchiLib)
     endif()
-    if(RDK_URF_LIBS)
-        list(APPEND LIBS_TO_USE RingDecomposerLib)
-    endif()
+    list(APPEND LIBS_TO_USE RingDecomposerLib)
     
     if(RDK_CFFI_STATIC AND ((NOT WIN32) OR (WIN32 AND RDK_INSTALL_DLLS_MSVC)))
         set(staticLibSuffix "_static")

Code/PgSQL/rdkit/CMakeLists.txt

@@ -143,9 +143,7 @@ set(pgRDKitLibList "${pgRDKitLibList}"
     "FileParsers;SmilesParse;Fingerprints;Subgraphs;Descriptors;"
     "PartialCharges;SubstructMatch;GraphMol;EigenSolvers;DataStructs;Depictor;"
     "RDGeometryLib;RDGeneral")
-if(RDK_USE_URF)
-  set(pgRDKitLibList "${pgRDKitLibList};${RDK_URF_LIBS}")
-endif(RDK_USE_URF)
+set(pgRDKitLibList "${pgRDKitLibList};${RDK_URF_LIBS}")
 set (pgRDKitLibs "")
 foreach(pgRDKitLib ${pgRDKitLibList})
   if (NOT pgRDKitLibs STREQUAL "")

Code/RDGeneral/RDConfig.h.cmake

@@ -40,8 +40,6 @@
 
 #cmakedefine RDK_BUILD_FREETYPE_SUPPORT
 
-#cmakedefine RDK_USE_URF
-
 #cmakedefine RDK_BUILD_YAEHMOP_SUPPORT
 
 #cmakedefine RDK_BUILD_XYZ2MOL_SUPPORT