From 45bf58754aeafc828f19c29c79b25a6524076373 Mon Sep 17 00:00:00 2001 From: Greg Landrum Date: Fri, 17 Apr 2020 14:34:23 +0200 Subject: [PATCH] Cleanup some cmake dependencies (#3077) * change minimal cmake version to a consistent 3.5 * progress towards a cleanup * get the basic python deps working * two more libs * another round of changes all tests pass at this point * next round of changes all tests pass at this point * close to done all tests pass * very close * almost done * shift the RDBoost dependencies around a bit * remove an extraneous python linkage this is trying to get the mac builds working again * Only link to python if it was built shared (#3091) * change in response to review Co-Authored-By: Ric * move that suppression of the maybe-uninitialized warning to BoostStartInclude.h Co-authored-by: Brian Kelley Co-authored-by: Ric --- CMakeLists.txt | 38 +++++++++++++------ Code/ChemicalFeatures/CMakeLists.txt | 2 +- Code/ChemicalFeatures/Wrap/CMakeLists.txt | 2 +- .../MetricMatrixCalc/Wrap/CMakeLists.txt | 2 +- Code/DataStructs/CMakeLists.txt | 6 +-- Code/DataStructs/Wrap/CMakeLists.txt | 2 +- .../Demos/RDKit/GettingStarted/CMakeLists.txt | 2 +- Code/DistGeom/CMakeLists.txt | 2 +- Code/DistGeom/Wrap/CMakeLists.txt | 2 +- Code/ForceField/MMFF/CMakeLists.txt | 5 +-- Code/ForceField/UFF/CMakeLists.txt | 5 +-- Code/ForceField/Wrap/CMakeLists.txt | 3 +- Code/Geometry/CMakeLists.txt | 6 +-- Code/Geometry/Wrap/CMakeLists.txt | 2 +- Code/GraphMol/CMakeLists.txt | 36 ++++++++---------- Code/GraphMol/ChemReactions/CMakeLists.txt | 17 +++------ .../ChemReactions/Wrap/CMakeLists.txt | 5 +-- Code/GraphMol/ChemTransforms/CMakeLists.txt | 11 ++---- Code/GraphMol/Depictor/CMakeLists.txt | 4 +- Code/GraphMol/Depictor/Wrap/CMakeLists.txt | 2 +- Code/GraphMol/Descriptors/CMakeLists.txt | 30 +++++++-------- Code/GraphMol/Descriptors/Wrap/CMakeLists.txt | 3 +- Code/GraphMol/DistGeomHelpers/CMakeLists.txt | 7 ++-- .../DistGeomHelpers/Wrap/CMakeLists.txt | 2 +- Code/GraphMol/FMCS/CMakeLists.txt | 5 +-- Code/GraphMol/FMCS/Test/CMakeLists.txt | 2 +- Code/GraphMol/FMCS/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/FileParsers/CMakeLists.txt | 22 +++++------ Code/GraphMol/FilterCatalog/CMakeLists.txt | 6 +-- .../FilterCatalog/Wrap/CMakeLists.txt | 5 +-- Code/GraphMol/Fingerprints/CMakeLists.txt | 18 ++++----- .../GraphMol/Fingerprints/Wrap/CMakeLists.txt | 6 +-- .../CrystalFF/CMakeLists.txt | 2 +- .../ForceFieldHelpers/MMFF/CMakeLists.txt | 8 ++-- .../ForceFieldHelpers/UFF/CMakeLists.txt | 6 +-- .../ForceFieldHelpers/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/FragCatalog/CMakeLists.txt | 4 +- Code/GraphMol/FragCatalog/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/MMPA/CMakeLists.txt | 5 +-- Code/GraphMol/MMPA/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/MolAlign/CMakeLists.txt | 6 +-- Code/GraphMol/MolAlign/Wrap/CMakeLists.txt | 6 +-- Code/GraphMol/MolCatalog/CMakeLists.txt | 2 +- Code/GraphMol/MolCatalog/Wrap/CMakeLists.txt | 4 +- .../MolChemicalFeatures/CMakeLists.txt | 7 +--- .../MolChemicalFeatures/Wrap/CMakeLists.txt | 6 +-- Code/GraphMol/MolDraw2D/CMakeLists.txt | 21 +++------- Code/GraphMol/MolDraw2D/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/MolHash/CMakeLists.txt | 2 +- Code/GraphMol/MolHash/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/MolInterchange/CMakeLists.txt | 2 +- .../MolInterchange/Wrap/CMakeLists.txt | 2 +- Code/GraphMol/MolStandardize/CMakeLists.txt | 33 +++++----------- .../MolStandardize/Wrap/CMakeLists.txt | 3 +- Code/GraphMol/MolTransforms/CMakeLists.txt | 6 +-- .../MolTransforms/Wrap/CMakeLists.txt | 5 +-- Code/GraphMol/PartialCharges/CMakeLists.txt | 5 +-- .../PartialCharges/Wrap/CMakeLists.txt | 4 +- .../RGroupDecomposition/CMakeLists.txt | 6 +-- .../RGroupDecomposition/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/ReducedGraphs/CMakeLists.txt | 8 +--- .../ReducedGraphs/Wrap/CMakeLists.txt | 2 +- Code/GraphMol/SLNParse/CMakeLists.txt | 6 +-- Code/GraphMol/SLNParse/Wrap/CMakeLists.txt | 3 +- Code/GraphMol/ScaffoldNetwork/CMakeLists.txt | 6 +-- .../ScaffoldNetwork/Wrap/CMakeLists.txt | 3 +- Code/GraphMol/ShapeHelpers/CMakeLists.txt | 5 +-- .../GraphMol/ShapeHelpers/Wrap/CMakeLists.txt | 5 +-- Code/GraphMol/SmilesParse/CMakeLists.txt | 12 +++--- Code/GraphMol/StructChecker/CMakeLists.txt | 6 +-- .../StructChecker/Wrap/CMakeLists.txt | 4 +- Code/GraphMol/Subgraphs/CMakeLists.txt | 6 +-- Code/GraphMol/Substruct/CMakeLists.txt | 8 ++-- Code/GraphMol/SubstructLibrary/CMakeLists.txt | 6 +-- .../SubstructLibrary/Wrap/CMakeLists.txt | 5 +-- Code/GraphMol/Trajectory/CMakeLists.txt | 7 ++-- Code/GraphMol/Wrap/CMakeLists.txt | 7 ++-- Code/JavaWrappers/gmwrapper/CMakeLists.txt | 2 +- Code/ML/Cluster/Murtagh/CMakeLists.txt | 2 +- Code/ML/Data/CMakeLists.txt | 2 +- Code/ML/InfoTheory/Wrap/CMakeLists.txt | 2 +- Code/Numerics/Alignment/CMakeLists.txt | 2 +- Code/Numerics/Alignment/Wrap/CMakeLists.txt | 2 +- Code/Numerics/CMakeLists.txt | 2 +- Code/Numerics/EigenSolvers/CMakeLists.txt | 2 +- Code/Numerics/Optimizer/CMakeLists.txt | 4 +- Code/PgSQL/rdkit/CMakeLists.txt | 2 - Code/RDBoost/CMakeLists.txt | 10 +++-- Code/RDGeneral/BoostStartInclude.h | 1 + Code/RDGeneral/CMakeLists.txt | 3 +- Code/RDStreams/CMakeLists.txt | 5 +-- Code/SimDivPickers/CMakeLists.txt | 4 +- Code/SimDivPickers/Wrap/CMakeLists.txt | 4 +- Code/cmake/Modules/RDKitUtils.cmake | 13 ++----- Docs/Book/C++Examples/CMakeLists.txt | 2 +- External/AvalonTools/CMakeLists.txt | 7 ++-- External/AvalonTools/Wrap/CMakeLists.txt | 4 +- External/FreeSASA/CMakeLists.txt | 6 +-- External/FreeSASA/Wrap/CMakeLists.txt | 2 +- External/INCHI-API/CMakeLists.txt | 11 ++---- External/INCHI-API/Wrap/CMakeLists.txt | 3 +- External/YAeHMOP/CMakeLists.txt | 5 +-- External/YAeHMOP/Wrap/CMakeLists.txt | 3 +- 103 files changed, 252 insertions(+), 385 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 595c6f596..82ad430ec 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.1) +cmake_minimum_required(VERSION 3.5) project (RDKit) @@ -216,7 +216,6 @@ endif(MSVC) # extra boost versions if(MSVC) # FIX: do we still need this? - SET(Boost_ADDITIONAL_VERSIONS "1.48" "1.48.0" "1.45" "1.45.0" "1.44" "1.44.0" "1.43" "1.43.0" "1.42" "1.42.0" "1.41" "1.41.0" "1.40" "1.40.0") target_compile_definitions(rdkit_base INTERFACE "-DBOOST_ALL_NO_LIB") endif(MSVC) @@ -225,6 +224,8 @@ if(RDK_BUILD_INCHI_SUPPORT) endif(RDK_BUILD_INCHI_SUPPORT) if(RDK_BUILD_PYTHON_WRAPPERS) + add_library(rdkit_py_base INTERFACE) + #------- # pull in python: find_package(PythonInterp) @@ -238,6 +239,19 @@ if(RDK_BUILD_PYTHON_WRAPPERS) find_package(PythonLibs) target_include_directories(rdkit_base INTERFACE ${PYTHON_INCLUDE_DIR}) + + # determine linkage of python + execute_process( + COMMAND + ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))" + OUTPUT_VARIABLE Py_ENABLE_SHARED + OUTPUT_STRIP_TRAILING_WHITESPACE + ) + + if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1") + target_link_libraries(rdkit_py_base INTERFACE ${PYTHON_LIBRARIES} ) + endif() + find_package(NumPy REQUIRED) target_include_directories(rdkit_base INTERFACE ${PYTHON_NUMPY_INCLUDE_PATH}) @@ -251,18 +265,20 @@ if(RDK_BUILD_PYTHON_WRAPPERS) list(APPEND Boost_Python_Names "python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}") # Try each potential boost-python name until one works - foreach(Boost_Python_Lib ${Boost_Python_Names}) - find_package(Boost 1.56.0 COMPONENTS "${Boost_Python_Lib}" QUIET) + foreach(Boost_Python_LibN ${Boost_Python_Names}) + find_package(Boost 1.56.0 COMPONENTS "${Boost_Python_LibN}" QUIET) if(Boost_FOUND) + set(Boost_Python_Lib ${Boost_Python_LibN}) break() endif() endforeach() - # Finally just try "python" and hope it is a compatible version if(NOT Boost_FOUND) find_package(Boost 1.56.0 COMPONENTS python REQUIRED) + set(Boost_Python_Lib "python") endif() + target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib}) if(RDK_INSTALL_INTREE) set(RDKit_PythonDir "${CMAKE_SOURCE_DIR}/rdkit") @@ -301,13 +317,6 @@ if(RDK_BUILD_PYTHON_WRAPPERS) endif(RDK_INSTALL_INTREE) - # determine linkage of python - execute_process( - COMMAND - ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))" - OUTPUT_VARIABLE Py_ENABLE_SHARED - OUTPUT_STRIP_TRAILING_WHITESPACE - ) if(NOT WIN32) # See https://bugs.python.org/msg277944 # The "command to create shared modules". Used as variable in the "Makefile (and similar) templates to build python modules" @@ -323,6 +332,10 @@ if(RDK_BUILD_PYTHON_WRAPPERS) message("PYTHON Py_ENABLE_SHARED: ${Py_ENABLE_SHARED}") message("PYTHON USING LINK LINE: ${PYTHON_LDSHARED}") endif() + + install(TARGETS rdkit_py_base EXPORT ${RDKit_EXPORTED_TARGETS} + COMPONENT dev ) + else(RDK_BUILD_PYTHON_WRAPPERS) find_package(Boost 1.56.0 REQUIRED) endif(RDK_BUILD_PYTHON_WRAPPERS) @@ -351,6 +364,7 @@ if(RDK_BUILD_THREADSAFE_SSS) if(RDK_TEST_MULTITHREADED) target_compile_definitions(rdkit_base INTERFACE "-DRDK_TEST_MULTITHREADED") endif() + target_link_libraries(rdkit_base INTERFACE Threads::Threads) else() if(RDK_TEST_MULTITHREADED) message("RDK_TEST_MULTITHREADED does not make sense without RD_BUILD_THREADSAFE_SSS, disabling it.") diff --git a/Code/ChemicalFeatures/CMakeLists.txt b/Code/ChemicalFeatures/CMakeLists.txt index bbbd9bf0e..9bbc0a4e6 100644 --- a/Code/ChemicalFeatures/CMakeLists.txt +++ b/Code/ChemicalFeatures/CMakeLists.txt @@ -7,7 +7,7 @@ rdkit_headers(ChemicalFeature.h FreeChemicalFeature.h DEST ChemicalFeatures) rdkit_test(testChemicalFeatures testChemicalFeatures.cpp - LINK_LIBRARIES ChemicalFeatures RDGeneral) + LINK_LIBRARIES ChemicalFeatures) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/ChemicalFeatures/Wrap/CMakeLists.txt b/Code/ChemicalFeatures/Wrap/CMakeLists.txt index 25c8ff433..c78b954d0 100644 --- a/Code/ChemicalFeatures/Wrap/CMakeLists.txt +++ b/Code/ChemicalFeatures/Wrap/CMakeLists.txt @@ -3,7 +3,7 @@ rdkit_python_extension(rdChemicalFeatures rdChemicalFeatures.cpp FreeChemicalFeature.cpp DEST Chem LINK_LIBRARIES - ChemicalFeatures GraphMol RDGeometryLib RDGeneral RDBoost) + ChemicalFeatures GraphMol) add_pytest(pyFeatures ${CMAKE_CURRENT_SOURCE_DIR}/testFeatures.py) diff --git a/Code/DataManip/MetricMatrixCalc/Wrap/CMakeLists.txt b/Code/DataManip/MetricMatrixCalc/Wrap/CMakeLists.txt index c8c83bdbb..51bf29f30 100644 --- a/Code/DataManip/MetricMatrixCalc/Wrap/CMakeLists.txt +++ b/Code/DataManip/MetricMatrixCalc/Wrap/CMakeLists.txt @@ -1,7 +1,7 @@ rdkit_python_extension(rdMetricMatrixCalc rdMetricMatrixCalc.cpp DEST DataManip/Metric LINK_LIBRARIES - RDGeneral DataStructs RDBoost) + DataStructs) add_pytest(pyMatCalc ${CMAKE_CURRENT_SOURCE_DIR}/testMatricCalc.py) diff --git a/Code/DataStructs/CMakeLists.txt b/Code/DataStructs/CMakeLists.txt index 741c82cf2..029e73fd6 100644 --- a/Code/DataStructs/CMakeLists.txt +++ b/Code/DataStructs/CMakeLists.txt @@ -27,13 +27,13 @@ rdkit_headers(base64.h DEST DataStructs) rdkit_test(testDataStructs testDatastructs.cpp - LINK_LIBRARIES DataStructs RDGeneral) + LINK_LIBRARIES DataStructs ) rdkit_test(testFPB testFPB.cpp - LINK_LIBRARIES DataStructs RDGeneral) + LINK_LIBRARIES DataStructs ) rdkit_test(testMultiFPB testMultiFPB.cpp - LINK_LIBRARIES DataStructs RDGeneral) + LINK_LIBRARIES DataStructs ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/DataStructs/Wrap/CMakeLists.txt b/Code/DataStructs/Wrap/CMakeLists.txt index 865333ac6..294324112 100644 --- a/Code/DataStructs/Wrap/CMakeLists.txt +++ b/Code/DataStructs/Wrap/CMakeLists.txt @@ -6,7 +6,7 @@ rdkit_python_extension(cDataStructs wrap_Utils.cpp DEST DataStructs LINK_LIBRARIES - RDGeneral DataStructs RDBoost) + DataStructs) add_pytest(pyBV ${CMAKE_CURRENT_SOURCE_DIR}/testBV.py) diff --git a/Code/Demos/RDKit/GettingStarted/CMakeLists.txt b/Code/Demos/RDKit/GettingStarted/CMakeLists.txt index 7baf7ef69..ddef0933c 100644 --- a/Code/Demos/RDKit/GettingStarted/CMakeLists.txt +++ b/Code/Demos/RDKit/GettingStarted/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 3.5) project (GettingStartedDemo) find_package (RDKit 1.2011.09 REQUIRED) diff --git a/Code/DistGeom/CMakeLists.txt b/Code/DistGeom/CMakeLists.txt index 28f563147..e50755d63 100644 --- a/Code/DistGeom/CMakeLists.txt +++ b/Code/DistGeom/CMakeLists.txt @@ -16,7 +16,7 @@ rdkit_headers(BoundsMatrix.h TriangleSmooth.h DEST DistGeom) rdkit_test(testDistGeom testDistGeom.cpp -LINK_LIBRARIES DistGeometry EigenSolvers ForceField ForceFieldHelpers Optimizer RDGeneral RDGeometryLib ) +LINK_LIBRARIES DistGeometry ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/DistGeom/Wrap/CMakeLists.txt b/Code/DistGeom/Wrap/CMakeLists.txt index 9c338b532..18c5b3f87 100644 --- a/Code/DistGeom/Wrap/CMakeLists.txt +++ b/Code/DistGeom/Wrap/CMakeLists.txt @@ -1,7 +1,7 @@ remove_definitions(-DRDKIT_DISTGEOMETRY_BUILD) rdkit_python_extension(DistGeom DistGeom.cpp DEST DistanceGeometry -LINK_LIBRARIES DistGeometry EigenSolvers ForceField ForceFieldHelpers Optimizer RDGeneral RDGeometryLib RDBoost ) +LINK_LIBRARIES DistGeometry ) add_pytest(pyDistGeom ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) diff --git a/Code/ForceField/MMFF/CMakeLists.txt b/Code/ForceField/MMFF/CMakeLists.txt index fbc0de218..1bdda2ead 100644 --- a/Code/ForceField/MMFF/CMakeLists.txt +++ b/Code/ForceField/MMFF/CMakeLists.txt @@ -8,7 +8,6 @@ if(RDK_TEST_MMFF_COMPLIANCE) endif() rdkit_test(testMMFFForceField testMMFFForceField.cpp LINK_LIBRARIES - DistGeomHelpers DistGeometry ForceFieldHelpers ForceField - FileParsers MolTransforms SmilesParse SubstructMatch MolAlign - Optimizer EigenSolvers Alignment GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS} ) + DistGeomHelpers ForceFieldHelpers + FileParsers MolTransforms SmilesParse SubstructMatch MolAlign ) endif(RDK_TEST_MMFF_COMPLIANCE) diff --git a/Code/ForceField/UFF/CMakeLists.txt b/Code/ForceField/UFF/CMakeLists.txt index 2972c73e4..f68ec4002 100644 --- a/Code/ForceField/UFF/CMakeLists.txt +++ b/Code/ForceField/UFF/CMakeLists.txt @@ -1,4 +1,3 @@ rdkit_test(testUFFForceField testUFFForceField.cpp -LINK_LIBRARIES ForceField Optimizer RDGeometryLib RDGeneral - EigenSolvers SmilesParse SubstructMatch GraphMol - FileParsers MolTransforms ForceFieldHelpers ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES ForceFieldHelpers SmilesParse SubstructMatch + FileParsers MolTransforms ) diff --git a/Code/ForceField/Wrap/CMakeLists.txt b/Code/ForceField/Wrap/CMakeLists.txt index 3f2bfe2be..3253778be 100644 --- a/Code/ForceField/Wrap/CMakeLists.txt +++ b/Code/ForceField/Wrap/CMakeLists.txt @@ -1,6 +1,5 @@ remove_definitions(-DRDKIT_FORCEFIELD_BUILD) rdkit_python_extension(rdForceField ForceField.cpp DEST ForceField - LINK_LIBRARIES GraphMol ForceField ForceFieldHelpers Optimizer - RDGeneral RDGeometryLib RDBoost) + LINK_LIBRARIES ForceFieldHelpers ) add_pytest(pyForceFieldConstraints ${CMAKE_CURRENT_SOURCE_DIR}/testConstraints.py) diff --git a/Code/Geometry/CMakeLists.txt b/Code/Geometry/CMakeLists.txt index 39d9798d7..31f131fff 100644 --- a/Code/Geometry/CMakeLists.txt +++ b/Code/Geometry/CMakeLists.txt @@ -14,10 +14,10 @@ rdkit_headers(Grid3D.h UniformGrid3D.h Utils.h DEST Geometry) -rdkit_test(testTransforms testTransforms.cpp LINK_LIBRARIES RDGeometryLib DataStructs RDGeneral ) -rdkit_test(testGrid testGrid.cpp LINK_LIBRARIES RDGeometryLib DataStructs RDGeneral ) +rdkit_test(testTransforms testTransforms.cpp LINK_LIBRARIES RDGeometryLib ) +rdkit_test(testGrid testGrid.cpp LINK_LIBRARIES RDGeometryLib) rdkit_catch_test(geometryTestsCatch catch_tests.cpp - LINK_LIBRARIES RDGeometryLib RDGeneral) + LINK_LIBRARIES RDGeometryLib) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/Geometry/Wrap/CMakeLists.txt b/Code/Geometry/Wrap/CMakeLists.txt index 6db5dd9cc..87ffd3f76 100644 --- a/Code/Geometry/Wrap/CMakeLists.txt +++ b/Code/Geometry/Wrap/CMakeLists.txt @@ -2,7 +2,7 @@ remove_definitions(-DRDKIT_RDGEOMETRYLIB_BUILD) rdkit_python_extension(rdGeometry Point.cpp UniformGrid3D.cpp rdGeometry.cpp DEST Geometry - LINK_LIBRARIES RDGeometryLib DataStructs RDGeneral RDBoost) + LINK_LIBRARIES RDGeometryLib) add_pytest(testPyGeometry ${CMAKE_CURRENT_SOURCE_DIR}/testGeometry.py) diff --git a/Code/GraphMol/CMakeLists.txt b/Code/GraphMol/CMakeLists.txt index b0c117c2f..fb7b8c785 100644 --- a/Code/GraphMol/CMakeLists.txt +++ b/Code/GraphMol/CMakeLists.txt @@ -10,11 +10,7 @@ rdkit_library(GraphMol Renumber.cpp AdjustQuery.cpp Resonance.cpp StereoGroup.cpp new_canon.cpp SubstanceGroup.cpp SHARED - LINK_LIBRARIES RDGeometryLib RDGeneral - ${RDKit_THREAD_LIBS} ) - -target_link_libraries(GraphMol PUBLIC ${RDKit_THREAD_LIBS}) - + LINK_LIBRARIES RDGeometryLib RDGeneral ) if(RDK_USE_URF) target_link_libraries(GraphMol PUBLIC ${RDK_URF_LIBS}) endif() @@ -111,46 +107,46 @@ add_subdirectory(ScaffoldNetwork) rdkit_test(graphmolTest1 test1.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol -RDGeometryLib RDGeneral SubstructMatch ForceFieldHelpers ForceField) + SubstructMatch ForceFieldHelpers ForceField) -rdkit_test(graphmolcpTest cptest.cpp LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral) +rdkit_test(graphmolcpTest cptest.cpp LINK_LIBRARIES SmilesParse GraphMol) -rdkit_test(graphmolqueryTest querytest.cpp LINK_LIBRARIES SubstructMatch SmilesParse GraphMol RDGeometryLib RDGeneral) +rdkit_test(graphmolqueryTest querytest.cpp LINK_LIBRARIES SubstructMatch SmilesParse GraphMol) rdkit_test(graphmolMolOpsTest molopstest.cpp LINK_LIBRARIES SubstructMatch FileParsers - SmilesParse GraphMol RDGeometryLib RDGeneral) + SmilesParse GraphMol ) rdkit_test(graphmoltestChirality testChirality.cpp LINK_LIBRARIES SmilesParse FileParsers - GraphMol RDGeometryLib RDGeneral) + GraphMol ) rdkit_test(graphmoltestPickler testPickler.cpp - LINK_LIBRARIES SmilesParse SubstructMatch FileParsers GraphMol RDGeometryLib RDGeneral) + LINK_LIBRARIES SmilesParse SubstructMatch FileParsers GraphMol ) rdkit_test(graphmoltestPicklerGlobalSetting testPicklerGlobalSettings.cpp - LINK_LIBRARIES SmilesParse SubstructMatch FileParsers GraphMol RDGeometryLib RDGeneral) + LINK_LIBRARIES SmilesParse SubstructMatch FileParsers GraphMol ) -rdkit_test(graphmolIterTest itertest.cpp LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral) +rdkit_test(graphmolIterTest itertest.cpp LINK_LIBRARIES SmilesParse GraphMol ) rdkit_test(hanoiTest hanoitest.cpp LINK_LIBRARIES SubstructMatch SmilesParse FileParsers GraphMol - RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS} ) + ) -rdkit_test(graphmolMemTest1 memtest1.cpp LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral) +rdkit_test(graphmolMemTest1 memtest1.cpp LINK_LIBRARIES SmilesParse GraphMol ) rdkit_test(resMolSupplierTest resMolSupplierTest.cpp - LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral SubstructMatch FileParsers) + LINK_LIBRARIES SmilesParse GraphMol SubstructMatch FileParsers) rdkit_test(molBundleTest testMolBundle.cpp - LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral SubstructMatch FileParsers) + LINK_LIBRARIES SmilesParse GraphMol SubstructMatch FileParsers) rdkit_test(testSGroup testSGroup.cpp LINK_LIBRARIES FileParsers GraphMol) -rdkit_test(test-valgrind test-valgrind.cpp LINK_LIBRARIES SmilesParse GraphMol RDGeneral) +rdkit_test(test-valgrind test-valgrind.cpp LINK_LIBRARIES SmilesParse GraphMol ) rdkit_catch_test(graphmolTestsCatch catch_graphmol.cpp catch_main.cpp - LINK_LIBRARIES SubstructMatch FileParsers SmilesParse GraphMol RDGeometryLib RDGeneral) + LINK_LIBRARIES SubstructMatch FileParsers SmilesParse GraphMol ) rdkit_catch_test(graphmolSGroupCatch catch_sgroups.cpp catch_main.cpp - LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral) + LINK_LIBRARIES SmilesParse GraphMol ) diff --git a/Code/GraphMol/ChemReactions/CMakeLists.txt b/Code/GraphMol/ChemReactions/CMakeLists.txt index f7191c1ba..d2ecf9031 100644 --- a/Code/GraphMol/ChemReactions/CMakeLists.txt +++ b/Code/GraphMol/ChemReactions/CMakeLists.txt @@ -20,10 +20,9 @@ rdkit_library(ChemReactions Enumerate/Enumerate.cpp Enumerate/EnumerationPickler.cpp Enumerate/EvenSamplePairs.cpp - LINK_LIBRARIES FilterCatalog Descriptors Fingerprints DataStructs Depictor - FileParsers SubstructMatch ChemTransforms ${RDKit_SERIALIZATION_LIBS}) + FileParsers SubstructMatch ChemTransforms GraphMol ${RDKit_SERIALIZATION_LIBS}) rdkit_headers(Reaction.h ReactionParser.h @@ -46,21 +45,15 @@ rdkit_headers(Enumerate/Enumerate.h DEST GraphMol/ChemReactions/Enumerate) rdkit_test(testReaction testReaction.cpp LINK_LIBRARIES - ChemReactions ChemTransforms Descriptors Fingerprints -Subgraphs DataStructs FileParsers SmilesParse SubstructMatch -GraphMol RDGeneral RDGeometryLib ${RDKit_SERIALIZATION_LIBS}) + ChemReactions ) rdkit_test(testReactionFingerprints testReactionFingerprints.cpp LINK_LIBRARIES -ChemReactions Descriptors Fingerprints Subgraphs DataStructs ChemTransforms FileParsers SmilesParse SubstructMatch -GraphMol RDGeneral RDGeometryLib ${RDKit_SERIALIZATION_LIBS}) +ChemReactions ) rdkit_test(testEnumeration Enumerate/testEnumerate.cpp LINK_LIBRARIES -ChemReactions ChemTransforms Descriptors Fingerprints Subgraphs DataStructs FileParsers SmilesParse SubstructMatch -GraphMol RDGeneral RDGeometryLib ${RDKit_SERIALIZATION_LIBS} ) +ChemReactions ) -rdkit_catch_test(rxnTestCatch catch_tests.cpp LINK_LIBRARIES ChemReactions ChemTransforms Descriptors Fingerprints -Subgraphs DataStructs FileParsers SmilesParse SubstructMatch -GraphMol RDGeneral RDGeometryLib ${RDKit_SERIALIZATION_LIBS} ) +rdkit_catch_test(rxnTestCatch catch_tests.cpp LINK_LIBRARIES ChemReactions ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/ChemReactions/Wrap/CMakeLists.txt b/Code/GraphMol/ChemReactions/Wrap/CMakeLists.txt index 044540487..40d94f07f 100644 --- a/Code/GraphMol/ChemReactions/Wrap/CMakeLists.txt +++ b/Code/GraphMol/ChemReactions/Wrap/CMakeLists.txt @@ -4,10 +4,7 @@ rdkit_python_extension(rdChemReactions rdChemReactions.cpp DEST Chem LINK_LIBRARIES -ChemReactions - FilterCatalog ChemTransforms -Descriptors Fingerprints Subgraphs DataStructs Depictor FileParsers SmilesParse SubstructMatch -GraphMol Catalogs FilterCatalog RDGeneral RDGeometryLib RDBoost ) +ChemReactions ) add_pytest(pyChemReactions ${CMAKE_CURRENT_SOURCE_DIR}/testReactionWrapper.py) diff --git a/Code/GraphMol/ChemTransforms/CMakeLists.txt b/Code/GraphMol/ChemTransforms/CMakeLists.txt index f5e4faf2f..b8adedf27 100644 --- a/Code/GraphMol/ChemTransforms/CMakeLists.txt +++ b/Code/GraphMol/ChemTransforms/CMakeLists.txt @@ -2,8 +2,7 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_CHEMTRANSFORMS_BUILD) rdkit_library(ChemTransforms ChemTransforms.cpp MolFragmenter.cpp LINK_LIBRARIES - SubstructMatch SmilesParse - ${RDKit_THREAD_LIBS}) + GraphMol SubstructMatch SmilesParse ) rdkit_headers(ChemTransforms.h MolFragmenter.h @@ -12,11 +11,7 @@ rdkit_headers(ChemTransforms.h # there's no Wrap subdirectory on the main trunk (but in "minimal" there is).. #add_subdirectory(Wrap) -#rdkit_test(testChemTransforms testChemTransforms.cpp -# LINK_LIBRARIES ChemTransforms FileParsers SmilesParse SubstructMatch GraphMol RDGeometryLib RDGeneral ) rdkit_test(testChemTransforms testChemTransforms.cpp - LINK_LIBRARIES ChemTransforms FileParsers SmilesParse SubstructMatch - GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS}) + LINK_LIBRARIES ChemTransforms FileParsers) -rdkit_catch_test(chemTransformsTestCatch catch_tests.cpp LINK_LIBRARIES ChemTransforms FileParsers SmilesParse - SubstructMatch GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS} ) +rdkit_catch_test(chemTransformsTestCatch catch_tests.cpp LINK_LIBRARIES ChemTransforms FileParsers) diff --git a/Code/GraphMol/Depictor/CMakeLists.txt b/Code/GraphMol/Depictor/CMakeLists.txt index 85475305e..eeaef8516 100644 --- a/Code/GraphMol/Depictor/CMakeLists.txt +++ b/Code/GraphMol/Depictor/CMakeLists.txt @@ -15,14 +15,14 @@ endif() rdkit_library(Depictor RDDepictor.cpp EmbeddedFrag.cpp DepictUtils.cpp - LINK_LIBRARIES ${RDK_COORDGEN_LIBS} SubstructMatch GraphMol) + LINK_LIBRARIES ${RDK_COORDGEN_LIBS} SubstructMatch GraphMol RDGeneral) rdkit_headers(DepictUtils.h EmbeddedFrag.h RDDepictor.h DEST GraphMol/Depictor) rdkit_test(testDepictor testDepictor.cpp - LINK_LIBRARIES Depictor ChemTransforms FileParsers SmilesParse GraphMol RDGeometryLib RDGeneral ) + LINK_LIBRARIES Depictor ChemTransforms FileParsers SmilesParse ) FILE(GLOB TEST_OUTPUT_FILES "${CMAKE_CURRENT_SOURCE_DIR}/test_data/*.out.sdf") get_directory_property(extra_clean_files ADDITIONAL_MAKE_CLEAN_FILES) diff --git a/Code/GraphMol/Depictor/Wrap/CMakeLists.txt b/Code/GraphMol/Depictor/Wrap/CMakeLists.txt index 289eb6efb..921d4a272 100644 --- a/Code/GraphMol/Depictor/Wrap/CMakeLists.txt +++ b/Code/GraphMol/Depictor/Wrap/CMakeLists.txt @@ -3,6 +3,6 @@ rdkit_python_extension(rdDepictor rdDepictor.cpp DEST Chem LINK_LIBRARIES - Depictor SmilesParse FileParsers SubstructMatch GraphMol RDGeometryLib RDGeneral RDBoost ) + Depictor ) add_pytest(pyDepictor ${CMAKE_CURRENT_SOURCE_DIR}/testDepictor.py) diff --git a/Code/GraphMol/Descriptors/CMakeLists.txt b/Code/GraphMol/Descriptors/CMakeLists.txt index 24540e455..2bdb5c2ed 100644 --- a/Code/GraphMol/Descriptors/CMakeLists.txt +++ b/Code/GraphMol/Descriptors/CMakeLists.txt @@ -16,7 +16,7 @@ rdkit_library(Descriptors USRDescriptor.cpp AtomFeat.cpp ${DESC3D_SOURCES} LINK_LIBRARIES PartialCharges SmilesParse FileParsers Subgraphs SubstructMatch MolTransforms GraphMol - EigenSolvers ${RDKit_THREAD_LIBS}) + EigenSolvers RDGeneral) rdkit_headers(Crippen.h BCUT.h Lipinski.h MolDescriptors.h @@ -30,40 +30,40 @@ rdkit_headers(Crippen.h BCUT.h Lipinski.h DEST GraphMol/Descriptors) rdkit_test(testDescriptors test.cpp -LINK_LIBRARIES PartialCharges Descriptors FileParsers SmilesParse Subgraphs SubstructMatch MolTransforms GraphMol EigenSolvers DataStructs RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES PartialCharges Descriptors ) rdkit_test(testAUTOCORR2D testAUTOCORR2D.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testATF testATF.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) if(RDK_HAS_EIGEN) rdkit_test(testBCUT testBCUT.cpp - LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) + LINK_LIBRARIES Descriptors ) endif(RDK_HAS_EIGEN) if(RDK_BUILD_DESCRIPTORS3D) rdkit_test(testEEM testEEM.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testPBF testPBF.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testRDFcustom testRDFcustom.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testRDF testRDF.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testMORSE testMORSE.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(test3D test3D.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testWHIM testWHIM.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testGETAWAY testGETAWAY.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testAUTOCORR3D testAUTOCORR3D.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ) rdkit_test(testCoulombMat testCoulombMat.cpp -LINK_LIBRARIES Descriptors FileParsers SmilesParse MolTransforms PartialCharges GraphMol DataStructs EigenSolvers RDGeneral RDGeometryLib ForceField ForceFieldHelpers Optimizer DistGeomHelpers ${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES Descriptors ForceFieldHelpers DistGeomHelpers ) endif(RDK_BUILD_DESCRIPTORS3D) diff --git a/Code/GraphMol/Descriptors/Wrap/CMakeLists.txt b/Code/GraphMol/Descriptors/Wrap/CMakeLists.txt index 56e249964..dd1dd6c1d 100644 --- a/Code/GraphMol/Descriptors/Wrap/CMakeLists.txt +++ b/Code/GraphMol/Descriptors/Wrap/CMakeLists.txt @@ -2,8 +2,7 @@ remove_definitions(-DRDKIT_DESCRIPTORS_BUILD) rdkit_python_extension(rdMolDescriptors rdMolDescriptors.cpp DEST Chem LINK_LIBRARIES -LINK_LIBRARIES Descriptors PartialCharges Fingerprints FileParsers SmilesParse Subgraphs -SubstructMatch MolTransforms GraphMol EigenSolvers DataStructs RDGeneral RDGeometryLib RDBoost ) +LINK_LIBRARIES Descriptors Fingerprints ) add_pytest(pyMolDescriptors ${CMAKE_CURRENT_SOURCE_DIR}/testMolDescriptors.py) add_pytest(pyMolDescriptors3D ${CMAKE_CURRENT_SOURCE_DIR}/test3D.py) diff --git a/Code/GraphMol/DistGeomHelpers/CMakeLists.txt b/Code/GraphMol/DistGeomHelpers/CMakeLists.txt index 7cc9caa42..d576f45d8 100644 --- a/Code/GraphMol/DistGeomHelpers/CMakeLists.txt +++ b/Code/GraphMol/DistGeomHelpers/CMakeLists.txt @@ -2,16 +2,15 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_DISTGEOMHELPERS_BUILD) rdkit_library(DistGeomHelpers BoundsMatrixBuilder.cpp Embedder.cpp - LINK_LIBRARIES ForceFieldHelpers DistGeometry Alignment - ${RDKit_THREAD_LIBS}) + LINK_LIBRARIES ForceFieldHelpers GraphMol DistGeometry Alignment + ) rdkit_headers(BoundsMatrixBuilder.h Embedder.h DEST GraphMol/DistGeomHelpers) rdkit_test(testDistGeomHelpers testDgeomHelpers.cpp LINK_LIBRARIES - DistGeomHelpers DistGeometry ForceFieldHelpers ForceField - MolAlign MolTransforms FileParsers SmilesParse SubstructMatch Optimizer EigenSolvers Alignment GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS} ) + DistGeomHelpers MolAlign MolTransforms FileParsers SmilesParse SubstructMatch ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/DistGeomHelpers/Wrap/CMakeLists.txt b/Code/GraphMol/DistGeomHelpers/Wrap/CMakeLists.txt index efb4859a2..afa5f17dd 100644 --- a/Code/GraphMol/DistGeomHelpers/Wrap/CMakeLists.txt +++ b/Code/GraphMol/DistGeomHelpers/Wrap/CMakeLists.txt @@ -5,6 +5,6 @@ rdkit_python_extension(rdDistGeom rdDistGeom.cpp DEST Chem LINK_LIBRARIES LINK_LIBRARIES - DistGeomHelpers DistGeometry FileParsers MolTransforms SmilesParse SubstructMatch ForceFieldHelpers ForceField MolAlign Optimizer EigenSolvers Alignment GraphMol DataStructs RDGeometryLib RDGeneral RDBoost) + DistGeomHelpers FileParsers MolTransforms SmilesParse SubstructMatch MolAlign EigenSolvers) add_pytest(pyDistGeomHelpers ${CMAKE_CURRENT_SOURCE_DIR}/testDistGeom.py) diff --git a/Code/GraphMol/FMCS/CMakeLists.txt b/Code/GraphMol/FMCS/CMakeLists.txt index 41a787eeb..acc2076c2 100644 --- a/Code/GraphMol/FMCS/CMakeLists.txt +++ b/Code/GraphMol/FMCS/CMakeLists.txt @@ -3,15 +3,14 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_FMCS_BUILD) rdkit_library(FMCS FMCS.cpp Seed.cpp MaximumCommonSubgraph.cpp SubstructMatchCustom.cpp - LINK_LIBRARIES Depictor FileParsers ChemTransforms SubstructMatch) + LINK_LIBRARIES Depictor SmilesParse FileParsers ChemTransforms SubstructMatch GraphMol ) rdkit_headers(FMCS.h Graph.h DEST GraphMol/FMCS) rdkit_test(testFMCS testFMCS_Unit.cpp LINK_LIBRARIES -FMCS ChemTransforms Depictor FileParsers SmilesParse -GraphMol RDGeneral RDGeometryLib SubstructMatch ${RDKit_THREAD_LIBS}) +FMCS ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/FMCS/Test/CMakeLists.txt b/Code/GraphMol/FMCS/Test/CMakeLists.txt index e2eaedab9..c92490ba6 100644 --- a/Code/GraphMol/FMCS/Test/CMakeLists.txt +++ b/Code/GraphMol/FMCS/Test/CMakeLists.txt @@ -1,2 +1,2 @@ rdkit_test(FMCStest testFMCS.cpp LINK_LIBRARIES -FMCS FileParsers SmilesParse GraphMol SubstructMatch DataStructs RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS}) +FMCS ) diff --git a/Code/GraphMol/FMCS/Wrap/CMakeLists.txt b/Code/GraphMol/FMCS/Wrap/CMakeLists.txt index aab78c66f..6e9408b20 100644 --- a/Code/GraphMol/FMCS/Wrap/CMakeLists.txt +++ b/Code/GraphMol/FMCS/Wrap/CMakeLists.txt @@ -2,8 +2,6 @@ remove_definitions(-DRDKIT_FMCS_BUILD) rdkit_python_extension(rdFMCS rdFMCS.cpp DEST Chem - LINK_LIBRARIES FMCS -SmilesParse SubstructMatch GraphMol DataStructs RDGeometryLib RDGeneral -RDBoost) + LINK_LIBRARIES FMCS) add_pytest(pyFMCS ${CMAKE_CURRENT_SOURCE_DIR}/testFMCS.py) diff --git a/Code/GraphMol/FileParsers/CMakeLists.txt b/Code/GraphMol/FileParsers/CMakeLists.txt index a40889623..e4dc10f18 100644 --- a/Code/GraphMol/FileParsers/CMakeLists.txt +++ b/Code/GraphMol/FileParsers/CMakeLists.txt @@ -56,26 +56,26 @@ rdkit_headers(FileParsers.h DEST GraphMol/FileParsers) rdkit_test(fileParsersTest1 test1.cpp - LINK_LIBRARIES FileParsers SmilesParse - SubstructMatch GraphMol RDGeneral RDGeometryLib ${maeparser_var}) + LINK_LIBRARIES FileParsers SubstructMatch ) rdkit_test(testMolSupplier testMolSupplier.cpp - LINK_LIBRARIES FileParsers SmilesParse SubstructMatch - GraphMol RDGeneral RDGeometryLib RDStreams) + LINK_LIBRARIES FileParsers RDStreams) -rdkit_test(testMolWriter testMolWriter.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_test(testMolWriter testMolWriter.cpp LINK_LIBRARIES FileParsers ) -rdkit_test(testTplParser testTpls.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_test(testTplParser testTpls.cpp LINK_LIBRARIES FileParsers ) -rdkit_test(testMol2ToMol testMol2ToMol.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_test(testMol2ToMol testMol2ToMol.cpp LINK_LIBRARIES FileParsers ) -rdkit_test(testSequence testSequence.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_test(testSequence testSequence.cpp LINK_LIBRARIES FileParsers ) rdkit_test(testExtendedStereoParsing testExtendedStereoParsing.cpp - LINK_LIBRARIES FileParsers Depictor GraphMol RDGeneral RDGeometryLib ) + LINK_LIBRARIES FileParsers ) -rdkit_catch_test(fileParsersCatchTest file_parsers_catch.cpp catch_main.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_catch_test(fileParsersCatchTest file_parsers_catch.cpp catch_main.cpp + LINK_LIBRARIES FileParsers ) -rdkit_catch_test(testPropertyLists testPropertyLists.cpp catch_main.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_catch_test(testPropertyLists testPropertyLists.cpp catch_main.cpp + LINK_LIBRARIES FileParsers ) diff --git a/Code/GraphMol/FilterCatalog/CMakeLists.txt b/Code/GraphMol/FilterCatalog/CMakeLists.txt index 993558932..3c30441e2 100644 --- a/Code/GraphMol/FilterCatalog/CMakeLists.txt +++ b/Code/GraphMol/FilterCatalog/CMakeLists.txt @@ -31,7 +31,7 @@ rdkit_library(FilterCatalog FilterMatchers.cpp FunctionalGroupHierarchy.cpp LINK_LIBRARIES Subgraphs SubstructMatch SmilesParse - GraphMol RDGeometryLib Catalogs RDGeneral ${RDKit_SERIALIZATION_LIBS} ) + GraphMol Catalogs ${RDKit_SERIALIZATION_LIBS} ) rdkit_headers(FilterCatalogEntry.h FilterCatalog.h @@ -45,6 +45,4 @@ add_subdirectory(Wrap) endif() rdkit_test(filterCatalogTest filtercatalogtest.cpp - LINK_LIBRARIES FilterCatalog - Catalogs SubstructMatch FileParsers SmilesParse GraphMol RDGeometryLib RDGeneral - ${RDKit_SERIALIZATION_LIBS}) + LINK_LIBRARIES FilterCatalog SmilesParse FileParsers ) diff --git a/Code/GraphMol/FilterCatalog/Wrap/CMakeLists.txt b/Code/GraphMol/FilterCatalog/Wrap/CMakeLists.txt index fd9b4f717..e0280217f 100644 --- a/Code/GraphMol/FilterCatalog/Wrap/CMakeLists.txt +++ b/Code/GraphMol/FilterCatalog/Wrap/CMakeLists.txt @@ -4,9 +4,6 @@ rdkit_python_extension(rdfiltercatalog FilterCatalog.cpp DEST Chem LINK_LIBRARIES - FilterCatalog -Subgraphs SubstructMatch SmilesParse Catalogs FileParsers GraphMol DataStructs -RDGeometryLib RDGeneral RDBoost -) + FilterCatalog ) add_pytest(pyFilterCatalog ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) diff --git a/Code/GraphMol/Fingerprints/CMakeLists.txt b/Code/GraphMol/Fingerprints/CMakeLists.txt index a5de27c36..f8da00485 100644 --- a/Code/GraphMol/Fingerprints/CMakeLists.txt +++ b/Code/GraphMol/Fingerprints/CMakeLists.txt @@ -6,8 +6,8 @@ rdkit_library(Fingerprints AtomPairs.cpp MACCS.cpp MHFP.cpp FingerprintGenerator.cpp AtomPairGenerator.cpp MorganGenerator.cpp RDKitFPGenerator.cpp FingerprintUtil.cpp TopologicalTorsionGenerator.cpp - LINK_LIBRARIES Subgraphs SubstructMatch SmilesParse GraphMol - ${RDKit_THREAD_LIBS} ) + LINK_LIBRARIES DataStructs Subgraphs SubstructMatch SmilesParse GraphMol RDGeneral + ) rdkit_headers(AtomPairs.h Fingerprints.h @@ -23,19 +23,15 @@ rdkit_headers(AtomPairs.h DEST GraphMol/Fingerprints) rdkit_test(testFingerprints test1.cpp LINK_LIBRARIES - Fingerprints FileParsers SubstructMatch SmilesParse - Subgraphs GraphMol DataStructs RDGeometryLib - RDGeneral ${RDKit_THREAD_LIBS} ) + Fingerprints FileParsers ) rdkit_test(testMHFPFingerprint testMHFPFingerprint.cpp LINK_LIBRARIES - Fingerprints SmilesParse GraphMol DataStructs FileParsers - RDGeneral ) + Fingerprints FileParsers ) rdkit_test(testFingerprintGenerators testFingerprintGenerators.cpp LINK_LIBRARIES - Fingerprints SmilesParse GraphMol DataStructs FileParsers - RDGeneral ) -rdkit_catch_test(fpTestCatch catch_tests.cpp LINK_LIBRARIES Fingerprints SmilesParse GraphMol DataStructs FileParsers - RDGeneral) + Fingerprints FileParsers ) + +rdkit_catch_test(fpTestCatch catch_tests.cpp LINK_LIBRARIES Fingerprints FileParsers) if(RDK_BUILD_PYTHON_WRAPPERS) diff --git a/Code/GraphMol/Fingerprints/Wrap/CMakeLists.txt b/Code/GraphMol/Fingerprints/Wrap/CMakeLists.txt index bbd438d1a..a904fbb84 100644 --- a/Code/GraphMol/Fingerprints/Wrap/CMakeLists.txt +++ b/Code/GraphMol/Fingerprints/Wrap/CMakeLists.txt @@ -1,14 +1,12 @@ rdkit_python_extension(rdFingerprintGenerator FingerprintGeneratorWrapper.cpp DEST Chem - LINK_LIBRARIES Fingerprints - DataStructs RDGeneral RDBoost) + LINK_LIBRARIES Fingerprints ) rdkit_python_extension(rdMHFPFingerprint MHFPWrapper.cpp DEST Chem - LINK_LIBRARIES Fingerprints - DataStructs RDGeneral RDBoost) + LINK_LIBRARIES Fingerprints ) add_pytest(pyTestGenerator ${CMAKE_CURRENT_SOURCE_DIR}/testGenerators.py) add_pytest(pyTestMHFP ${CMAKE_CURRENT_SOURCE_DIR}/testMHFP.py) diff --git a/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeLists.txt b/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeLists.txt index e1690e2a1..e4adcf134 100644 --- a/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeLists.txt +++ b/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeLists.txt @@ -1,4 +1,4 @@ rdkit_test(testCrystalForceField testCrystalFF.cpp LINK_LIBRARIES ForceFieldHelpers - DistGeomHelpers DistGeometry FileParsers MolTransforms SmilesParse SubstructMatch ForceField MolAlign Optimizer EigenSolvers Alignment GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS}) + DistGeomHelpers FileParsers MolTransforms SmilesParse ) diff --git a/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeLists.txt b/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeLists.txt index 9b727441e..3fd9db267 100644 --- a/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeLists.txt +++ b/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeLists.txt @@ -1,9 +1,9 @@ rdkit_test(testMMFFForceFieldHelpers testMMFFHelpers.cpp - LINK_LIBRARIES + LINK_LIBRARIES ForceFieldHelpers -DistGeomHelpers DistGeometry FileParsers MolTransforms SmilesParse SubstructMatch ForceField MolAlign Optimizer EigenSolvers Alignment GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS}) + DistGeomHelpers FileParsers MolTransforms SmilesParse) rdkit_test(testMMFFForceFieldHelpersMultiThread testMultiThread.cpp - LINK_LIBRARIES + LINK_LIBRARIES ForceFieldHelpers -DistGeomHelpers DistGeometry FileParsers MolTransforms SmilesParse SubstructMatch ForceField MolAlign Optimizer EigenSolvers Alignment GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS}) + DistGeomHelpers FileParsers MolTransforms SmilesParse) diff --git a/Code/GraphMol/ForceFieldHelpers/UFF/CMakeLists.txt b/Code/GraphMol/ForceFieldHelpers/UFF/CMakeLists.txt index cffcf2cc1..d34fcf671 100644 --- a/Code/GraphMol/ForceFieldHelpers/UFF/CMakeLists.txt +++ b/Code/GraphMol/ForceFieldHelpers/UFF/CMakeLists.txt @@ -1,7 +1,5 @@ remove_definitions(-DRDKIT_FORCEFIELDHELPERS_BUILD) rdkit_test(testUFFForceFieldHelpers testUFFHelpers.cpp - LINK_LIBRARIES + LINK_LIBRARIES ForceFieldHelpers - DistGeomHelpers DistGeometry FileParsers MolTransforms SmilesParse - SubstructMatch ForceField MolAlign Optimizer EigenSolvers Alignment - GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS}) + DistGeomHelpers FileParsers MolTransforms SmilesParse) diff --git a/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeLists.txt b/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeLists.txt index 25625a9ca..93770cd97 100644 --- a/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeLists.txt +++ b/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeLists.txt @@ -2,9 +2,7 @@ remove_definitions(-DRDKIT_FORCEFIELDHELPERS_BUILD) rdkit_python_extension(rdForceFieldHelpers rdForceFields.cpp DEST Chem LINK_LIBRARIES - ForceFieldHelpers -SmilesParse SubstructMatch GraphMol ForceField Optimizer RDGeometryLib RDGeneral DataStructs -RDBoost) + ForceFieldHelpers ) add_pytest(pyForceFieldHelpers ${CMAKE_CURRENT_SOURCE_DIR}/testHelpers.py) diff --git a/Code/GraphMol/FragCatalog/CMakeLists.txt b/Code/GraphMol/FragCatalog/CMakeLists.txt index 47e7ae1f9..aea9d9f15 100644 --- a/Code/GraphMol/FragCatalog/CMakeLists.txt +++ b/Code/GraphMol/FragCatalog/CMakeLists.txt @@ -4,7 +4,7 @@ add_definitions(-DRDKIT_FRAGCATALOG_BUILD) rdkit_library(FragCatalog FragCatalogUtils.cpp FragCatGenerator.cpp FragCatalogEntry.cpp FragCatParams.cpp FragFPGenerator.cpp - LINK_LIBRARIES Subgraphs SubstructMatch SmilesParse Catalogs GraphMol RDGeometryLib RDGeneral ) + LINK_LIBRARIES Subgraphs SubstructMatch SmilesParse Catalogs GraphMol RDGeneral ) rdkit_headers(FragCatalogEntry.h FragCatalogUtils.h @@ -12,7 +12,7 @@ rdkit_headers(FragCatalogEntry.h FragCatParams.h FragFPGenerator.h DEST GraphMol/FragCatalog) -rdkit_test(testFragCatalog test1.cpp LINK_LIBRARIES FragCatalog Subgraphs SubstructMatch SmilesParse Catalogs FileParsers GraphMol DataStructs RDGeometryLib RDGeneral ) +rdkit_test(testFragCatalog test1.cpp LINK_LIBRARIES FragCatalog FileParsers ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/FragCatalog/Wrap/CMakeLists.txt b/Code/GraphMol/FragCatalog/Wrap/CMakeLists.txt index f9c7dd841..aa9912b26 100644 --- a/Code/GraphMol/FragCatalog/Wrap/CMakeLists.txt +++ b/Code/GraphMol/FragCatalog/Wrap/CMakeLists.txt @@ -4,8 +4,6 @@ rdkit_python_extension(rdfragcatalog FragCatGenerator.cpp FragFPGenerator.cpp DEST Chem LINK_LIBRARIES - FragCatalog -Subgraphs SubstructMatch SmilesParse Catalogs FileParsers GraphMol DataStructs RDGeometryLib RDGeneral - RDBoost) + FragCatalog FileParsers) add_pytest(pyFragCatalog ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) diff --git a/Code/GraphMol/MMPA/CMakeLists.txt b/Code/GraphMol/MMPA/CMakeLists.txt index d69155cfe..28971cf36 100644 --- a/Code/GraphMol/MMPA/CMakeLists.txt +++ b/Code/GraphMol/MMPA/CMakeLists.txt @@ -7,14 +7,13 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_MMPA_BUILD) rdkit_library(MMPA MMPA.cpp - LINK_LIBRARIES SubstructMatch Depictor FileParsers ChemTransforms GraphMol ${RDKit_THREAD_LIBS} ) + LINK_LIBRARIES SubstructMatch Depictor FileParsers ChemTransforms GraphMol RDGeneral ) rdkit_headers(MMPA.h DEST GraphMol/MMPA) rdkit_test(testMMPA MMPA_UnitTest.cpp LINK_LIBRARIES - MMPA ChemTransforms Depictor FileParsers SmilesParse - GraphMol RDGeneral RDGeometryLib SubstructMatch ${RDKit_THREAD_LIBS}) + MMPA SmilesParse ) if(RDK_BUILD_PYTHON_WRAPPERS) diff --git a/Code/GraphMol/MMPA/Wrap/CMakeLists.txt b/Code/GraphMol/MMPA/Wrap/CMakeLists.txt index 4ef517a97..6f042f127 100644 --- a/Code/GraphMol/MMPA/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MMPA/Wrap/CMakeLists.txt @@ -2,8 +2,6 @@ remove_definitions(-DRDKIT_MMPA_BUILD) rdkit_python_extension(rdMMPA rdMMPA.cpp DEST Chem - LINK_LIBRARIES MMPA -SubstructMatch SmilesParse GraphMol DataStructs RDGeometryLib RDGeneral -RDBoost ) + LINK_LIBRARIES MMPA ) add_pytest(pyMMPA ${CMAKE_CURRENT_SOURCE_DIR}/testMMPA.py) diff --git a/Code/GraphMol/MolAlign/CMakeLists.txt b/Code/GraphMol/MolAlign/CMakeLists.txt index e6c6da79f..79c6f94ab 100644 --- a/Code/GraphMol/MolAlign/CMakeLists.txt +++ b/Code/GraphMol/MolAlign/CMakeLists.txt @@ -2,15 +2,13 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_MOLALIGN_BUILD) rdkit_library(MolAlign AlignMolecules.cpp O3AAlignMolecules.cpp - LINK_LIBRARIES MolTransforms SubstructMatch Alignment RDGeometryLib RDGeneral ForceFieldHelpers) + LINK_LIBRARIES MolTransforms SubstructMatch Alignment GraphMol RDGeneral ForceFieldHelpers) rdkit_headers(AlignMolecules.h O3AAlignMolecules.h DEST GraphMol/MolAlign) rdkit_test(testMolAlign testMolAlign.cpp LINK_LIBRARIES MolAlign Descriptors -FileParsers DistGeomHelpers ForceFieldHelpers -SmilesParse DistGeometry ForceField Optimizer SubstructMatch -GraphMol RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS}) +FileParsers DistGeomHelpers SmilesParse) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/MolAlign/Wrap/CMakeLists.txt b/Code/GraphMol/MolAlign/Wrap/CMakeLists.txt index 5791f0651..a9bf40117 100644 --- a/Code/GraphMol/MolAlign/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolAlign/Wrap/CMakeLists.txt @@ -2,11 +2,7 @@ remove_definitions(-DRDKIT_MOLALIGN_BUILD) rdkit_python_extension(rdMolAlign rdMolAlign.cpp DEST Chem LINK_LIBRARIES -MolAlign MolTransforms ForceFieldHelpers ForceField -EigenSolvers Alignment Optimizer SubstructMatch -GraphMol RDGeneral RDGeometryLib DataStructs -Descriptors SmilesParse - RDBoost) +MolAlign DataStructs Descriptors SmilesParse) add_pytest(pyMolAlign ${CMAKE_CURRENT_SOURCE_DIR}/testMolAlign.py) diff --git a/Code/GraphMol/MolCatalog/CMakeLists.txt b/Code/GraphMol/MolCatalog/CMakeLists.txt index b5953d3ff..485ddb676 100644 --- a/Code/GraphMol/MolCatalog/CMakeLists.txt +++ b/Code/GraphMol/MolCatalog/CMakeLists.txt @@ -9,7 +9,7 @@ rdkit_headers(MolCatalogEntry.h MolCatalogParams.h DEST GraphMol/MolCatalog) rdkit_test(testMolCatalog test1.cpp LINK_LIBRARIES -MolCatalog FileParsers Catalogs SmilesParse GraphMol DataStructs RDGeneral RDGeometryLib ) +MolCatalog FileParsers SmilesParse DataStructs ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/MolCatalog/Wrap/CMakeLists.txt b/Code/GraphMol/MolCatalog/Wrap/CMakeLists.txt index a2ef1e840..658972e90 100644 --- a/Code/GraphMol/MolCatalog/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolCatalog/Wrap/CMakeLists.txt @@ -1,9 +1,7 @@ remove_definitions(-DRDKIT_MOLCATALOG_BUILD) rdkit_python_extension(rdMolCatalog rdMolCatalog.cpp DEST Chem - LINK_LIBRARIES -MolCatalog FileParsers Catalogs SmilesParse GraphMol DataStructs RDGeneral RDGeometryLib -RDBoost) + LINK_LIBRARIES MolCatalog ) add_pytest(pyMolCatalog ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) diff --git a/Code/GraphMol/MolChemicalFeatures/CMakeLists.txt b/Code/GraphMol/MolChemicalFeatures/CMakeLists.txt index 2e6982cf2..ba39bbb85 100644 --- a/Code/GraphMol/MolChemicalFeatures/CMakeLists.txt +++ b/Code/GraphMol/MolChemicalFeatures/CMakeLists.txt @@ -4,7 +4,7 @@ add_definitions(-DRDKIT_MOLCHEMICALFEATURES_BUILD) rdkit_library(MolChemicalFeatures MolChemicalFeature.cpp MolChemicalFeatureDef.cpp MolChemicalFeatureFactory.cpp FeatureParser.cpp - LINK_LIBRARIES SubstructMatch SmilesParse) + LINK_LIBRARIES SubstructMatch SmilesParse GraphMol) rdkit_headers(FeatureParser.h MolChemicalFeatureFactory.h MolChemicalFeatureDef.h MolChemicalFeature.h @@ -12,10 +12,7 @@ rdkit_headers(FeatureParser.h MolChemicalFeatureFactory.h rdkit_test(testFeatures testFeatures.cpp - LINK_LIBRARIES MolChemicalFeatures Catalogs -FileParsers SmilesParse SubstructMatch DataStructs -GraphMol RDGeometryLib RDGeneral -) + LINK_LIBRARIES MolChemicalFeatures FileParsers ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeLists.txt b/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeLists.txt index 6ed0f523d..4625fc4b2 100644 --- a/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeLists.txt @@ -3,11 +3,7 @@ rdkit_python_extension(rdMolChemicalFeatures rdMolChemicalFeatures.cpp MolChemicalFeature.cpp MolChemicalFeatureFactory.cpp ChemicalFeatureUtils.cpp DEST Chem - LINK_LIBRARIES MolChemicalFeatures -Catalogs -SmilesParse SubstructMatch DataStructs -GraphMol RDGeometryLib RDGeneral -RDBoost) + LINK_LIBRARIES MolChemicalFeatures ) add_pytest(pyChemicalFeatures ${CMAKE_CURRENT_SOURCE_DIR}/testChemicalFeatures.py) diff --git a/Code/GraphMol/MolDraw2D/CMakeLists.txt b/Code/GraphMol/MolDraw2D/CMakeLists.txt index aaa38c285..98cdd829a 100644 --- a/Code/GraphMol/MolDraw2D/CMakeLists.txt +++ b/Code/GraphMol/MolDraw2D/CMakeLists.txt @@ -17,10 +17,8 @@ add_definitions(-DRDKIT_MOLDRAW2D_BUILD) rdkit_library(MolDraw2D MolDraw2D.cpp MolDraw2DSVG.cpp MolDraw2DDetails.cpp MolDraw2DUtils.cpp LINK_LIBRARIES - ChemReactions FileParsers SmilesParse Depictor MolTransforms RDGeometryLib - RDGeneral SubstructMatch Subgraphs GraphMol EigenSolvers -RDGeometryLib - ${RDKit_THREAD_LIBS} ) + ChemReactions FileParsers SmilesParse Depictor MolTransforms + SubstructMatch Subgraphs GraphMol EigenSolvers ) if(RDK_BUILD_QT_SUPPORT) find_package(Qt5 COMPONENTS Widgets OpenGL REQUIRED) @@ -40,22 +38,13 @@ if(RDK_BUILD_CAIRO_SUPPORT) endif(RDK_BUILD_CAIRO_SUPPORT) rdkit_test(moldraw2DTest1 test1.cpp LINK_LIBRARIES - ChemReactions FileParsers SmilesParse Depictor RDGeometryLib - RDGeneral SubstructMatch Subgraphs GraphMol MolTransforms EigenSolvers - RDGeometryLib - MolDraw2D ${RDKit_THREAD_LIBS} ) + MolDraw2D ) rdkit_catch_test(moldraw2DTestCatch catch_tests.cpp LINK_LIBRARIES - ChemReactions FileParsers SmilesParse Depictor RDGeometryLib - RDGeneral SubstructMatch Subgraphs GraphMol MolTransforms EigenSolvers - RDGeometryLib - MolDraw2D ${RDKit_THREAD_LIBS} ) + MolDraw2D ) rdkit_test(moldraw2DRxnTest1 rxn_test1.cpp LINK_LIBRARIES - ChemReactions FileParsers SmilesParse Depictor RDGeometryLib - RDGeneral SubstructMatch Subgraphs GraphMol MolTransforms EigenSolvers - RDGeometryLib - MolDraw2D ${RDKit_THREAD_LIBS} ${EXTRA_LOCAL_LIBS} ) + MolDraw2D ) if(RDK_BUILD_QT_DEMO) add_subdirectory(QTDemo) diff --git a/Code/GraphMol/MolDraw2D/Wrap/CMakeLists.txt b/Code/GraphMol/MolDraw2D/Wrap/CMakeLists.txt index d0b20eec8..fd7900e4a 100644 --- a/Code/GraphMol/MolDraw2D/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolDraw2D/Wrap/CMakeLists.txt @@ -2,8 +2,6 @@ remove_definitions(-DRDKIT_MOLDRAW2D_BUILD) rdkit_python_extension(rdMolDraw2D rdMolDraw2D.cpp DEST Chem/Draw - LINK_LIBRARIES MolDraw2D -Depictor ChemReactions SmilesParse FileParsers SubstructMatch MolTransforms GraphMol -DataStructs EigenSolvers RDGeometryLib RDGeneral RDBoost ${EXTRA_LOCAL_LIBS}) + LINK_LIBRARIES MolDraw2D ) add_pytest(pyMolDraw2D ${CMAKE_CURRENT_SOURCE_DIR}/testMolDraw2D.py) diff --git a/Code/GraphMol/MolHash/CMakeLists.txt b/Code/GraphMol/MolHash/CMakeLists.txt index c90b5b948..6c082d6cc 100644 --- a/Code/GraphMol/MolHash/CMakeLists.txt +++ b/Code/GraphMol/MolHash/CMakeLists.txt @@ -3,7 +3,7 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_MOLHASH_BUILD) rdkit_library(MolHash hashfunctions.cpp normalize.cpp - LINK_LIBRARIES Depictor Descriptors GraphMol RDGeneral) + LINK_LIBRARIES Depictor Descriptors GraphMol) rdkit_headers(MolHash.h nmmolhash.h DEST GraphMol/MolHash) diff --git a/Code/GraphMol/MolHash/Wrap/CMakeLists.txt b/Code/GraphMol/MolHash/Wrap/CMakeLists.txt index 80c1a68ca..2db3da5a4 100644 --- a/Code/GraphMol/MolHash/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolHash/Wrap/CMakeLists.txt @@ -2,8 +2,6 @@ remove_definitions(-DRDKIT_MOLHASH_BUILD) rdkit_python_extension(rdMolHash rdMolHash.cpp DEST Chem - LINK_LIBRARIES MolHash -Descriptors GraphMol DataStructs -RDGeometryLib RDGeneral RDBoost) + LINK_LIBRARIES MolHash) add_pytest(pyMolHash ${CMAKE_CURRENT_SOURCE_DIR}/testMolHash.py) diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt index d85c92e11..29e7975cd 100644 --- a/Code/GraphMol/MolInterchange/CMakeLists.txt +++ b/Code/GraphMol/MolInterchange/CMakeLists.txt @@ -23,7 +23,7 @@ rdkit_headers(MolInterchange.h details.h DEST GraphMol/MolInterchange) rdkit_test(molInterchangeTest1 test1.cpp - LINK_LIBRARIES MolInterchange FileParsers SmilesParse GraphMol RDGeneral) + LINK_LIBRARIES MolInterchange FileParsers SmilesParse) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/MolInterchange/Wrap/CMakeLists.txt b/Code/GraphMol/MolInterchange/Wrap/CMakeLists.txt index 35d350132..a2b483abb 100644 --- a/Code/GraphMol/MolInterchange/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolInterchange/Wrap/CMakeLists.txt @@ -2,6 +2,6 @@ remove_definitions(-DRDKIT_MOLINTERCHANGE_BUILD) rdkit_python_extension(rdMolInterchange rdMolInterchange.cpp DEST Chem - LINK_LIBRARIES MolInterchange GraphMol RDBoost) + LINK_LIBRARIES MolInterchange) add_pytest(pyMolInterchange ${CMAKE_CURRENT_SOURCE_DIR}/testMolInterchange.py) diff --git a/Code/GraphMol/MolStandardize/CMakeLists.txt b/Code/GraphMol/MolStandardize/CMakeLists.txt index e2043ff81..eec2c6498 100644 --- a/Code/GraphMol/MolStandardize/CMakeLists.txt +++ b/Code/GraphMol/MolStandardize/CMakeLists.txt @@ -21,7 +21,7 @@ rdkit_library(MolStandardize TautomerCatalog/TautomerCatalogEntry.cpp TautomerCatalog/TautomerCatalogParams.cpp TautomerCatalog/TautomerCatalogUtils.cpp - LINK_LIBRARIES ChemReactions ChemTransforms GraphMol RDGeneral ) + LINK_LIBRARIES ChemReactions ChemTransforms SmilesParse SubstructMatch Descriptors GraphMol ) rdkit_headers(MolStandardize.h Metal.h @@ -56,28 +56,13 @@ if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) endif() -rdkit_test(molStandardizeTest test1.cpp LINK_LIBRARIES MolStandardize - SmilesParse RDGeneral GraphMol SubstructMatch ) -rdkit_test(molNormalizeTest testNormalize.cpp LINK_LIBRARIES MolStandardize - SmilesParse RDGeneral GraphMol SubstructMatch ) -rdkit_test(molValidateTest testValidate.cpp LINK_LIBRARIES MolStandardize - SmilesParse RDGeneral GraphMol SubstructMatch FileParsers ) -rdkit_test(molChargeTest testCharge.cpp LINK_LIBRARIES MolStandardize - SmilesParse RDGeneral GraphMol SubstructMatch FileParsers ) -rdkit_test(molTautomerTest testTautomer.cpp LINK_LIBRARIES MolStandardize - SmilesParse RDGeneral GraphMol SubstructMatch FileParsers ) -rdkit_test(molStandardizeSmallTest test2.cpp LINK_LIBRARIES MolStandardize - SmilesParse RDGeneral GraphMol SubstructMatch) -rdkit_test(molFragmentTest testFragment.cpp LINK_LIBRARIES MolStandardize - Catalogs SmilesParse RDGeneral GraphMol SubstructMatch FileParsers - ChemTransforms Descriptors) -rdkit_catch_test(molStandardizeCatchTest catch_tests.cpp LINK_LIBRARIES MolStandardize - Catalogs SmilesParse RDGeneral GraphMol SubstructMatch FileParsers - ChemTransforms Descriptors) +rdkit_test(molStandardizeTest test1.cpp LINK_LIBRARIES MolStandardize ) +rdkit_test(molNormalizeTest testNormalize.cpp LINK_LIBRARIES MolStandardize ) +rdkit_test(molValidateTest testValidate.cpp LINK_LIBRARIES MolStandardize ) +rdkit_test(molChargeTest testCharge.cpp LINK_LIBRARIES MolStandardize ) +rdkit_test(molTautomerTest testTautomer.cpp LINK_LIBRARIES MolStandardize ) +rdkit_test(molStandardizeSmallTest test2.cpp LINK_LIBRARIES MolStandardize ) +rdkit_test(molFragmentTest testFragment.cpp LINK_LIBRARIES MolStandardize ) +rdkit_catch_test(molStandardizeCatchTest catch_tests.cpp LINK_LIBRARIES MolStandardize ) -#find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED) -#if (NOT Boost_USE_STATIC_LIBS) -# add_definitions("-DBOOST_IOSTREAMS_DYN_LINK") -#endif() -# rdkit_test(compareMolVSTest testPCS.cpp LINK_LIBRARIES RDGeneral SmilesParse RDGeneral GraphMol MolStandardize ${Boost_LIBRARIES}) diff --git a/Code/GraphMol/MolStandardize/Wrap/CMakeLists.txt b/Code/GraphMol/MolStandardize/Wrap/CMakeLists.txt index 993c9f043..9618b66a8 100644 --- a/Code/GraphMol/MolStandardize/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolStandardize/Wrap/CMakeLists.txt @@ -3,7 +3,6 @@ rdkit_python_extension(rdMolStandardize rdMolStandardize.cpp Validate.cpp Charge.cpp Fragment.cpp Normalize.cpp Metal.cpp Tautomer.cpp DEST Chem/MolStandardize LINK_LIBRARIES -LINK_LIBRARIES MolStandardize SmilesParse -SubstructMatch GraphMol RDGeneral RDGeometryLib RDBoost ) +LINK_LIBRARIES MolStandardize ) add_pytest(pyMolStandardize ${CMAKE_CURRENT_SOURCE_DIR}/testMolStandardize.py) diff --git a/Code/GraphMol/MolTransforms/CMakeLists.txt b/Code/GraphMol/MolTransforms/CMakeLists.txt index 27fb83745..1419799ea 100644 --- a/Code/GraphMol/MolTransforms/CMakeLists.txt +++ b/Code/GraphMol/MolTransforms/CMakeLists.txt @@ -2,15 +2,13 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_MOLTRANSFORMS_BUILD) rdkit_library(MolTransforms MolTransforms.cpp - LINK_LIBRARIES GraphMol EigenSolvers) + LINK_LIBRARIES GraphMol EigenSolvers RDGeneral ) rdkit_headers(MolTransforms.h DEST GraphMol/MolTransforms) rdkit_test(testMolTransforms test1.cpp LINK_LIBRARIES MolTransforms - SubstructMatch - FileParsers SmilesParse - EigenSolvers GraphMol RDGeometryLib RDGeneral ) + FileParsers SmilesParse ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/MolTransforms/Wrap/CMakeLists.txt b/Code/GraphMol/MolTransforms/Wrap/CMakeLists.txt index d7af0609a..8247cfa3c 100644 --- a/Code/GraphMol/MolTransforms/Wrap/CMakeLists.txt +++ b/Code/GraphMol/MolTransforms/Wrap/CMakeLists.txt @@ -2,9 +2,6 @@ remove_definitions(-DRDKIT_MOLTRANSFORMS_BUILD) rdkit_python_extension(rdMolTransforms rdMolTransforms.cpp DEST Chem - LINK_LIBRARIES MolTransforms -EigenSolvers -GraphMol DataStructs RDGeometryLib RDGeneral -RDBoost) + LINK_LIBRARIES MolTransforms ) add_pytest(pyMolTransforms ${CMAKE_CURRENT_SOURCE_DIR}/testMolTransforms.py) diff --git a/Code/GraphMol/PartialCharges/CMakeLists.txt b/Code/GraphMol/PartialCharges/CMakeLists.txt index b0d796b4b..7f3d1998c 100644 --- a/Code/GraphMol/PartialCharges/CMakeLists.txt +++ b/Code/GraphMol/PartialCharges/CMakeLists.txt @@ -3,14 +3,13 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_PARTIALCHARGES_BUILD) rdkit_library(PartialCharges GasteigerCharges.cpp GasteigerParams.cpp - LINK_LIBRARIES GraphMol) + LINK_LIBRARIES GraphMol RDGeneral) rdkit_headers(GasteigerCharges.h GasteigerParams.h DEST GraphMol/PartialCharges) rdkit_test(testPartialCharges test1.cpp LINK_LIBRARIES PartialCharges -SmilesParse GraphMol RDGeometryLib RDGeneral DataStructs -${RDKit_THREAD_LIBS} ) +SmilesParse ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/PartialCharges/Wrap/CMakeLists.txt b/Code/GraphMol/PartialCharges/Wrap/CMakeLists.txt index b3f89b328..0ede2d054 100644 --- a/Code/GraphMol/PartialCharges/Wrap/CMakeLists.txt +++ b/Code/GraphMol/PartialCharges/Wrap/CMakeLists.txt @@ -2,8 +2,6 @@ remove_definitions(-DRDKIT_PARTIALCHARGES_BUILD) rdkit_python_extension(rdPartialCharges rdPartialCharges.cpp DEST Chem - LINK_LIBRARIES PartialCharges -GraphMol RDGeometryLib RDGeneral DataStructs -RDBoost) + LINK_LIBRARIES PartialCharges ) add_pytest(pyPartialCharges ${CMAKE_CURRENT_SOURCE_DIR}/testPartialCharges.py) diff --git a/Code/GraphMol/RGroupDecomposition/CMakeLists.txt b/Code/GraphMol/RGroupDecomposition/CMakeLists.txt index 1962f2436..c77535ae0 100644 --- a/Code/GraphMol/RGroupDecomposition/CMakeLists.txt +++ b/Code/GraphMol/RGroupDecomposition/CMakeLists.txt @@ -4,7 +4,7 @@ add_definitions(-DRDKIT_RGROUPDECOMPOSITION_BUILD) rdkit_library(RGroupDecomposition RGroupDecomp.cpp LINK_LIBRARIES FMCS ChemTransforms SubstructMatch SmilesParse - ${RDKit_THREAD_LIBS}) + GraphMol RDGeneral) rdkit_headers( RGroupDecomp.h @@ -17,6 +17,4 @@ endif() rdkit_test(testRGroupDecomp testRGroupDecomp.cpp - LINK_LIBRARIES RGroupDecomposition ChemTransforms FMCS FileParsers - SmilesParse SubstructMatch GraphMol RDGeometryLib RDGeneral - ${RDKit_THREAD_LIBS}) + LINK_LIBRARIES RGroupDecomposition ) diff --git a/Code/GraphMol/RGroupDecomposition/Wrap/CMakeLists.txt b/Code/GraphMol/RGroupDecomposition/Wrap/CMakeLists.txt index c048cf422..395639886 100644 --- a/Code/GraphMol/RGroupDecomposition/Wrap/CMakeLists.txt +++ b/Code/GraphMol/RGroupDecomposition/Wrap/CMakeLists.txt @@ -3,9 +3,7 @@ rdkit_python_extension(rdRGroupDecomposition rdRGroupComposition.cpp DEST Chem LINK_LIBRARIES - RGroupDecomposition FMCS ChemTransforms SubstructMatch SmilesParse GraphMol - RDGeneral RDGeometryLib RDBoost - ${RDKit_THREAD_LIBS}) + RGroupDecomposition ) diff --git a/Code/GraphMol/ReducedGraphs/CMakeLists.txt b/Code/GraphMol/ReducedGraphs/CMakeLists.txt index 9b8f7cad8..e39390dce 100644 --- a/Code/GraphMol/ReducedGraphs/CMakeLists.txt +++ b/Code/GraphMol/ReducedGraphs/CMakeLists.txt @@ -3,17 +3,13 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_REDUCEDGRAPHS_BUILD) rdkit_library(ReducedGraphs ReducedGraphs.cpp - LINK_LIBRARIES SubstructMatch SmilesParse GraphMol - ${RDKit_THREAD_LIBS} ) + LINK_LIBRARIES SubstructMatch SmilesParse GraphMol RDGeneral) rdkit_headers(ReducedGraphs.h DEST GraphMol/ReducedGraphs) rdkit_test(testReducedGraphs test1.cpp LINK_LIBRARIES - ReducedGraphs - SubstructMatch SmilesParse - GraphMol DataStructs RDGeometryLib - RDGeneral ) + ReducedGraphs ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/ReducedGraphs/Wrap/CMakeLists.txt b/Code/GraphMol/ReducedGraphs/Wrap/CMakeLists.txt index cd9a32230..b144d6f1b 100644 --- a/Code/GraphMol/ReducedGraphs/Wrap/CMakeLists.txt +++ b/Code/GraphMol/ReducedGraphs/Wrap/CMakeLists.txt @@ -2,7 +2,7 @@ remove_definitions(-DRDKIT_REDUCEDGRAPHS_BUILD) rdkit_python_extension(rdReducedGraphs rdReducedGraphs.cpp DEST Chem LINK_LIBRARIES -LINK_LIBRARIES ReducedGraphs SubstructMatch SmilesParse GraphMol DataStructs RDGeneral RDGeometryLib RDBoost ) +LINK_LIBRARIES ReducedGraphs ) add_pytest(pyReducedGraphs ${CMAKE_CURRENT_SOURCE_DIR}/testReducedGraphs.py) diff --git a/Code/GraphMol/SLNParse/CMakeLists.txt b/Code/GraphMol/SLNParse/CMakeLists.txt index 37d0183c8..36e493d3a 100644 --- a/Code/GraphMol/SLNParse/CMakeLists.txt +++ b/Code/GraphMol/SLNParse/CMakeLists.txt @@ -44,16 +44,14 @@ add_definitions(-DRDKIT_SLNPARSE_BUILD) rdkit_library(SLNParse SLNParse.cpp SLNAttribs.cpp ${BISON_OUTPUT_FILES} ${FLEX_OUTPUT_FILES} - LINK_LIBRARIES GraphMol ) + LINK_LIBRARIES GraphMol RDGeneral ) rdkit_headers(SLNAttribs.h SLNParse.h SLNParseOps.h DEST GraphMol/SLNParse) rdkit_test(testSLNParse test.cpp - LINK_LIBRARIES SLNParse SmilesParse SubstructMatch -GraphMol RDGeometryLib RDGeneral -) + LINK_LIBRARIES SLNParse SmilesParse SubstructMatch ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/SLNParse/Wrap/CMakeLists.txt b/Code/GraphMol/SLNParse/Wrap/CMakeLists.txt index 1e3755ae1..611d8d3ef 100644 --- a/Code/GraphMol/SLNParse/Wrap/CMakeLists.txt +++ b/Code/GraphMol/SLNParse/Wrap/CMakeLists.txt @@ -2,7 +2,6 @@ remove_definitions(-DRDKIT_SLNPARSE_BUILD) rdkit_python_extension(rdSLNParse rdSLNParse.cpp DEST Chem LINK_LIBRARIES - SLNParse SmilesParse SubstructMatch GraphMol - RDGeometryLib RDGeneral DataStructs RDBoost ) + SLNParse ) add_pytest(pySLNParse ${CMAKE_CURRENT_SOURCE_DIR}/testSLN.py) diff --git a/Code/GraphMol/ScaffoldNetwork/CMakeLists.txt b/Code/GraphMol/ScaffoldNetwork/CMakeLists.txt index 7d82148a3..af9ae579f 100644 --- a/Code/GraphMol/ScaffoldNetwork/CMakeLists.txt +++ b/Code/GraphMol/ScaffoldNetwork/CMakeLists.txt @@ -2,13 +2,13 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_SCAFFOLDNETWORK_BUILD) rdkit_library(ScaffoldNetwork ScaffoldNetwork.cpp - LINK_LIBRARIES MolStandardize ChemReactions ChemTransforms SmilesParse SubstructMatch GraphMol RDGeneral) + LINK_LIBRARIES MolStandardize ChemReactions ChemTransforms SmilesParse + SubstructMatch GraphMol RDGeneral) rdkit_headers(ScaffoldNetwork.h DEST GraphMol/ScaffoldNetwork) rdkit_catch_test(testScaffoldNetwork catch_main.cpp catch_tests.cpp -LINK_LIBRARIES ScaffoldNetwork SmilesParse GraphMol RDGeneral -${RDKit_THREAD_LIBS} ) +LINK_LIBRARIES ScaffoldNetwork SmilesParse ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeLists.txt b/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeLists.txt index d581b61cd..f2355555b 100644 --- a/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeLists.txt +++ b/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeLists.txt @@ -3,8 +3,7 @@ rdkit_python_extension(rdScaffoldNetwork rdScaffoldNetwork.cpp DEST Chem/Scaffolds LINK_LIBRARIES ScaffoldNetwork -GraphMol RDGeometryLib RDGeneral DataStructs -RDBoost) +GraphMol ) add_pytest(pyScaffoldNetwork ${CMAKE_CURRENT_SOURCE_DIR}/testScaffoldNetwork.py) if (RDK_USE_BOOST_SERIALIZATION) diff --git a/Code/GraphMol/ShapeHelpers/CMakeLists.txt b/Code/GraphMol/ShapeHelpers/CMakeLists.txt index 3e57ae37b..700606820 100644 --- a/Code/GraphMol/ShapeHelpers/CMakeLists.txt +++ b/Code/GraphMol/ShapeHelpers/CMakeLists.txt @@ -2,15 +2,14 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_SHAPEHELPERS_BUILD) rdkit_library(ShapeHelpers ShapeEncoder.cpp ShapeUtils.cpp - LINK_LIBRARIES MolTransforms) + LINK_LIBRARIES MolTransforms GraphMol RDGeneral) rdkit_headers(ShapeEncoder.h ShapeUtils.h DEST GraphMol/ShapeHelpers) rdkit_test(testShapeHelpers testShapeHelpers.cpp LINK_LIBRARIES ShapeHelpers FileParsers MolAlign -SmilesParse FileParsers MolTransforms SubstructMatch EigenSolvers Alignment DataStructs -GraphMol RDGeneral RDGeometryLib ) +SmilesParse FileParsers SubstructMatch ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/GraphMol/ShapeHelpers/Wrap/CMakeLists.txt b/Code/GraphMol/ShapeHelpers/Wrap/CMakeLists.txt index 786eb3774..51b157d76 100644 --- a/Code/GraphMol/ShapeHelpers/Wrap/CMakeLists.txt +++ b/Code/GraphMol/ShapeHelpers/Wrap/CMakeLists.txt @@ -2,10 +2,7 @@ remove_definitions(-DRDKIT_SHAPEHELPERS_BUILD) rdkit_python_extension(rdShapeHelpers rdShapeHelpers.cpp DEST Chem LINK_LIBRARIES - ShapeHelpers -MolTransforms EigenSolvers -DataStructs GraphMol RDGeometryLib RDGeneral -RDBoost) + ShapeHelpers ) add_pytest(pyShapeHelpers ${CMAKE_CURRENT_SOURCE_DIR}/testShapeHelpers.py) diff --git a/Code/GraphMol/SmilesParse/CMakeLists.txt b/Code/GraphMol/SmilesParse/CMakeLists.txt index 7ba0ccfca..8c7c178f8 100644 --- a/Code/GraphMol/SmilesParse/CMakeLists.txt +++ b/Code/GraphMol/SmilesParse/CMakeLists.txt @@ -58,7 +58,7 @@ rdkit_library(SmilesParse SmilesWrite.cpp SmartsWrite.cpp CXSmilesOps.cpp ${BISON_OUTPUT_FILES} ${FLEX_OUTPUT_FILES} - LINK_LIBRARIES GraphMol) + LINK_LIBRARIES GraphMol RDGeneral) rdkit_headers(primes.h SmartsWrite.h @@ -66,9 +66,9 @@ rdkit_headers(primes.h SmilesParseOps.h SmilesWrite.h DEST GraphMol/SmilesParse) -rdkit_test(smiTest1 test.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) -rdkit_test(smiTest2 test2.cpp LINK_LIBRARIES SmilesParse GraphMol RDGeneral RDGeometryLib ) -rdkit_test(cxsmilesTest cxsmiles_test.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_test(smiTest1 test.cpp LINK_LIBRARIES FileParsers SmilesParse ) +rdkit_test(smiTest2 test2.cpp LINK_LIBRARIES SmilesParse ) +rdkit_test(cxsmilesTest cxsmiles_test.cpp LINK_LIBRARIES FileParsers SmilesParse ) -rdkit_test(smaTest1 smatest.cpp LINK_LIBRARIES SmilesParse SubstructMatch GraphMol RDGeneral RDGeometryLib ) -rdkit_catch_test(smiTestCatch catch_tests.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib ) +rdkit_test(smaTest1 smatest.cpp LINK_LIBRARIES SmilesParse SubstructMatch ) +rdkit_catch_test(smiTestCatch catch_tests.cpp LINK_LIBRARIES FileParsers SmilesParse ) diff --git a/Code/GraphMol/StructChecker/CMakeLists.txt b/Code/GraphMol/StructChecker/CMakeLists.txt index 9bebafdcc..fc9cde5a2 100644 --- a/Code/GraphMol/StructChecker/CMakeLists.txt +++ b/Code/GraphMol/StructChecker/CMakeLists.txt @@ -5,7 +5,7 @@ rdkit_library(StructChecker StructChecker.cpp StructCheckerOptions.cpp StructureFlags.cpp Utilites.cpp Pattern.cpp Stereo.cpp AtomSymbolMatch.cpp StripSmallFragments.cpp ReCharge.cpp Tautomer.cpp LINK_LIBRARIES Depictor SubstructMatch FileParsers ChemTransforms Descriptors - GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS}) + GraphMol RDGeneral ) rdkit_headers(StructChecker.h Utilites.h Pattern.h Stereo.h StripSmallFragments.h ReCharge.h Tautomer.h DEST GraphMol/StructChecker) @@ -15,6 +15,4 @@ add_subdirectory(Wrap) endif() rdkit_test(testStructChecker testStructChecker.cpp - LINK_LIBRARIES StructChecker ChemTransforms Depictor Descriptors - SubstructMatch FileParsers SmilesParse - GraphMol RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS}) + LINK_LIBRARIES StructChecker SmilesParse ) diff --git a/Code/GraphMol/StructChecker/Wrap/CMakeLists.txt b/Code/GraphMol/StructChecker/Wrap/CMakeLists.txt index b9416fd9f..8f110923f 100644 --- a/Code/GraphMol/StructChecker/Wrap/CMakeLists.txt +++ b/Code/GraphMol/StructChecker/Wrap/CMakeLists.txt @@ -2,7 +2,5 @@ remove_definitions(-DRDKIT_STRUCTCHECKER_BUILD) rdkit_python_extension(rdStructChecker structchecker.cpp DEST Chem - LINK_LIBRARIES StructChecker ChemTransforms Depictor Descriptors - SubstructMatch FileParsers SmilesParse - GraphMol RDGeneral RDGeometryLib) + LINK_LIBRARIES StructChecker ) add_pytest(pyStructChecker ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) diff --git a/Code/GraphMol/Subgraphs/CMakeLists.txt b/Code/GraphMol/Subgraphs/CMakeLists.txt index 0482d707b..917eb4e19 100644 --- a/Code/GraphMol/Subgraphs/CMakeLists.txt +++ b/Code/GraphMol/Subgraphs/CMakeLists.txt @@ -2,12 +2,12 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_SUBGRAPHS_BUILD) rdkit_library(Subgraphs Subgraphs.cpp SubgraphUtils.cpp - LINK_LIBRARIES GraphMol ) + LINK_LIBRARIES GraphMol RDGeneral ) rdkit_headers(Subgraphs.h SubgraphUtils.h DEST GraphMol/Subgraphs) target_include_directories(Subgraphs PUBLIC $) -rdkit_test(testSubgraphs1 test1.cpp LINK_LIBRARIES Subgraphs SmilesParse GraphMol RDGeometryLib RDGeneral ) -rdkit_test(testSubgraphs2 test2.cpp LINK_LIBRARIES SmilesParse Subgraphs GraphMol RDGeometryLib RDGeneral ) +rdkit_test(testSubgraphs1 test1.cpp LINK_LIBRARIES Subgraphs SmilesParse ) +rdkit_test(testSubgraphs2 test2.cpp LINK_LIBRARIES SmilesParse Subgraphs ) diff --git a/Code/GraphMol/Substruct/CMakeLists.txt b/Code/GraphMol/Substruct/CMakeLists.txt index 92e2e94fd..c7bad7158 100644 --- a/Code/GraphMol/Substruct/CMakeLists.txt +++ b/Code/GraphMol/Substruct/CMakeLists.txt @@ -3,14 +3,12 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_SUBSTRUCTMATCH_BUILD) rdkit_library(SubstructMatch SubstructMatch.cpp SubstructUtils.cpp - LINK_LIBRARIES GraphMol - ${RDKit_THREAD_LIBS} ) + LINK_LIBRARIES GraphMol RDGeneral ) rdkit_headers(SubstructMatch.h SubstructUtils.h DEST GraphMol/Substruct) -rdkit_test(testSubstructMatch test1.cpp LINK_LIBRARIES FileParsers SmilesParse SubstructMatch -GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS} ) +rdkit_test(testSubstructMatch test1.cpp LINK_LIBRARIES FileParsers SmilesParse SubstructMatch ) rdkit_catch_test(substructTestCatch catch_tests.cpp LINK_LIBRARIES FileParsers SmilesParse -SubstructMatch GraphMol RDGeneral RDGeometryLib ${RDKit_THREAD_LIBS}) +SubstructMatch ) diff --git a/Code/GraphMol/SubstructLibrary/CMakeLists.txt b/Code/GraphMol/SubstructLibrary/CMakeLists.txt index 4817bba2a..0b649d722 100644 --- a/Code/GraphMol/SubstructLibrary/CMakeLists.txt +++ b/Code/GraphMol/SubstructLibrary/CMakeLists.txt @@ -13,7 +13,7 @@ rdkit_library(SubstructLibrary SubstructLibrary.cpp PatternFactory.cpp LINK_LIBRARIES Fingerprints SubstructMatch SmilesParse - GraphMol RDGeometryLib Catalogs RDGeneral DataStructs ${RDKit_SERIALIZATION_LIBS}) + GraphMol Catalogs DataStructs RDGeneral ${RDKit_SERIALIZATION_LIBS}) rdkit_headers(SubstructLibrary.h SubstructLibrarySerialization.h @@ -25,8 +25,6 @@ add_subdirectory(Wrap) endif() rdkit_test(substructLibraryTest substructLibraryTest.cpp - LINK_LIBRARIES SubstructLibrary Fingerprints - SubstructMatch FileParsers SmilesParse GraphMol RDGeometryLib RDGeneral DataStructs - ${RDKit_SERIALIZATION_LIBS}) + LINK_LIBRARIES SubstructLibrary FileParsers ) endif(RDK_BUILD_THREADSAFE_SSS) diff --git a/Code/GraphMol/SubstructLibrary/Wrap/CMakeLists.txt b/Code/GraphMol/SubstructLibrary/Wrap/CMakeLists.txt index d0a67b40a..6d2c74dd9 100644 --- a/Code/GraphMol/SubstructLibrary/Wrap/CMakeLists.txt +++ b/Code/GraphMol/SubstructLibrary/Wrap/CMakeLists.txt @@ -4,9 +4,6 @@ rdkit_python_extension(rdSubstructLibrary SubstructLibraryWrap.cpp DEST Chem LINK_LIBRARIES - SubstructLibrary -Fingerprints SubstructMatch SmilesParse Catalogs FileParsers GraphMol DataStructs -RDGeometryLib RDGeneral RDBoost -) + SubstructLibrary ) add_pytest(pySubstructLibrary ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) diff --git a/Code/GraphMol/Trajectory/CMakeLists.txt b/Code/GraphMol/Trajectory/CMakeLists.txt index b5b37e522..29389453c 100644 --- a/Code/GraphMol/Trajectory/CMakeLists.txt +++ b/Code/GraphMol/Trajectory/CMakeLists.txt @@ -2,11 +2,10 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD) add_definitions(-DRDKIT_TRAJECTORY_BUILD) rdkit_library(Trajectory Trajectory.cpp - LINK_LIBRARIES RDGeneral RDGeometryLib GraphMol) + LINK_LIBRARIES GraphMol RDGeneral ) rdkit_headers(Snapshot.h Trajectory.h DEST GraphMol/Trajectory) rdkit_test(trajectoryTest trajectoryTest.cpp - LINK_LIBRARIES Trajectory RDGeneral RDGeometryLib - GraphMol FileParsers - SmilesParse SubstructMatch ForceFieldHelpers ForceField) + LINK_LIBRARIES Trajectory FileParsers + SmilesParse SubstructMatch ForceFieldHelpers ) diff --git a/Code/GraphMol/Wrap/CMakeLists.txt b/Code/GraphMol/Wrap/CMakeLists.txt index e8487ad5d..7ffbc8954 100644 --- a/Code/GraphMol/Wrap/CMakeLists.txt +++ b/Code/GraphMol/Wrap/CMakeLists.txt @@ -5,7 +5,7 @@ rdkit_python_extension(rdchem ResonanceMolSupplier.cpp MolBundle.cpp StereoGroup.cpp SubstanceGroup.cpp DEST Chem LINK_LIBRARIES - SmilesParse ChemTransforms SubstructMatch GraphMol RDGeometryLib RDGeneral RDBoost) + SmilesParse ChemTransforms SubstructMatch GraphMol) rdkit_python_extension(rdmolops rdmolops.cpp MolOps.cpp @@ -13,14 +13,13 @@ rdkit_python_extension(rdmolops LINK_LIBRARIES ChemReactions MolDraw2D Depictor FileParsers SubstructMatch Fingerprints ChemTransforms - Catalogs Subgraphs SmilesParse MolTransforms GraphMol EigenSolvers -RDGeometryLib DataStructs RDGeneral RDBoost ) + Subgraphs SmilesParse MolTransforms GraphMol ) rdkit_python_extension(rdqueries rdqueries.cpp Queries.cpp DEST Chem LINK_LIBRARIES - GraphMol RDGeometryLib DataStructs RDGeneral RDBoost ) + GraphMol ) if(RDK_BUILD_COORDGEN_SUPPORT) set (maesupplier MaeMolSupplier.cpp) diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt index 9db69e5cf..3613d81c9 100644 --- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt +++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.8) +cmake_minimum_required(VERSION 3.5) project (jGraphMolJava Java) diff --git a/Code/ML/Cluster/Murtagh/CMakeLists.txt b/Code/ML/Cluster/Murtagh/CMakeLists.txt index b1e219d8f..19dab7a55 100644 --- a/Code/ML/Cluster/Murtagh/CMakeLists.txt +++ b/Code/ML/Cluster/Murtagh/CMakeLists.txt @@ -7,7 +7,7 @@ set_target_properties(hc PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) rdkit_python_extension(Clustering Clustering.cpp DEST ML/Cluster LINK_LIBRARIES - hc RDGeneral RDBoost) + hc RDGeneral) diff --git a/Code/ML/Data/CMakeLists.txt b/Code/ML/Data/CMakeLists.txt index a0fc569c8..da8305f34 100644 --- a/Code/ML/Data/CMakeLists.txt +++ b/Code/ML/Data/CMakeLists.txt @@ -1,3 +1,3 @@ rdkit_python_extension(cQuantize cQuantize.cpp DEST ML/Data - LINK_LIBRARIES InfoTheory RDGeneral RDBoost ) + LINK_LIBRARIES InfoTheory RDGeneral) diff --git a/Code/ML/InfoTheory/Wrap/CMakeLists.txt b/Code/ML/InfoTheory/Wrap/CMakeLists.txt index 3f2ef64dd..ceb60a7b1 100644 --- a/Code/ML/InfoTheory/Wrap/CMakeLists.txt +++ b/Code/ML/InfoTheory/Wrap/CMakeLists.txt @@ -4,6 +4,6 @@ rdkit_python_extension(rdInfoTheory rdInfoTheory.cpp DEST ML/InfoTheory LINK_LIBRARIES - InfoTheory RDGeneral DataStructs RDBoost) + InfoTheory) add_pytest(pyRanker ${CMAKE_CURRENT_SOURCE_DIR}/testRanker.py) diff --git a/Code/Numerics/Alignment/CMakeLists.txt b/Code/Numerics/Alignment/CMakeLists.txt index 6a72ae268..d25fe8362 100644 --- a/Code/Numerics/Alignment/CMakeLists.txt +++ b/Code/Numerics/Alignment/CMakeLists.txt @@ -4,7 +4,7 @@ rdkit_library(Alignment AlignPoints.cpp LINK_LIBRARIES RDGeometryLib) rdkit_headers(AlignPoints.h DEST Numerics/Alignment) -rdkit_test(testAlignment testAlignment.cpp LINK_LIBRARIES Alignment RDGeometryLib RDGeneral ) +rdkit_test(testAlignment testAlignment.cpp LINK_LIBRARIES Alignment ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/Code/Numerics/Alignment/Wrap/CMakeLists.txt b/Code/Numerics/Alignment/Wrap/CMakeLists.txt index 3e476cc28..984809025 100644 --- a/Code/Numerics/Alignment/Wrap/CMakeLists.txt +++ b/Code/Numerics/Alignment/Wrap/CMakeLists.txt @@ -2,7 +2,7 @@ remove_definitions(-DRDKIT_ALIGNMENT_BUILD) rdkit_python_extension(rdAlignment rdAlignment.cpp DEST Numerics - LINK_LIBRARIES Alignment RDGeneral RDGeometryLib RDBoost) + LINK_LIBRARIES Alignment) add_pytest(pyAlignment ${CMAKE_CURRENT_SOURCE_DIR}/testAlignment.py) diff --git a/Code/Numerics/CMakeLists.txt b/Code/Numerics/CMakeLists.txt index fb183ae59..7c6d77456 100644 --- a/Code/Numerics/CMakeLists.txt +++ b/Code/Numerics/CMakeLists.txt @@ -9,4 +9,4 @@ rdkit_headers(Matrix.h Conrec.h DEST Numerics) rdkit_test(testMatrices testMatrices.cpp LINK_LIBRARIES RDGeneral) -rdkit_catch_test(testConrec testConrec.cpp LINK_LIBRARIES RDGeometryLib RDGeneral) +rdkit_catch_test(testConrec testConrec.cpp LINK_LIBRARIES RDGeometryLib ) diff --git a/Code/Numerics/EigenSolvers/CMakeLists.txt b/Code/Numerics/EigenSolvers/CMakeLists.txt index 576a1aaad..bac68eea7 100644 --- a/Code/Numerics/EigenSolvers/CMakeLists.txt +++ b/Code/Numerics/EigenSolvers/CMakeLists.txt @@ -6,6 +6,6 @@ rdkit_headers(PowerEigenSolver.h DEST Numerics/EigenSolvers) IF (LAPACK_FOUND) rdkit_test(tesEigensolvers testEigenSolvers.cpp - LINK_LIBRARIES EigenSolvers RDGeneral ) + LINK_LIBRARIES EigenSolvers ) target_include_directories(tesEigenSolvers PUBLIC ${CMAKE_SOURCE_DIR}/External/boost-numeric-bindings) ENDIF (LAPACK_FOUND) diff --git a/Code/Numerics/Optimizer/CMakeLists.txt b/Code/Numerics/Optimizer/CMakeLists.txt index d35a59c3b..298587008 100644 --- a/Code/Numerics/Optimizer/CMakeLists.txt +++ b/Code/Numerics/Optimizer/CMakeLists.txt @@ -2,10 +2,10 @@ add_definitions(-DRDKIT_OPTIMIZER_BUILD) rdkit_library(Optimizer BFGSOpt.cpp LinearSearch.cpp - LINK_LIBRARIES RDGeometryLib Trajectory) + LINK_LIBRARIES RDGeometryLib Trajectory RDGeneral) rdkit_headers(BFGSOpt.h DEST Numerics/Optimizer) -rdkit_test(testOptimizer testOptimizer.cpp LINK_LIBRARIES Optimizer RDGeometryLib RDGeneral ) +rdkit_test(testOptimizer testOptimizer.cpp LINK_LIBRARIES Optimizer ) diff --git a/Code/PgSQL/rdkit/CMakeLists.txt b/Code/PgSQL/rdkit/CMakeLists.txt index c0c870c7b..317c21e24 100644 --- a/Code/PgSQL/rdkit/CMakeLists.txt +++ b/Code/PgSQL/rdkit/CMakeLists.txt @@ -1,5 +1,3 @@ -cmake_minimum_required(VERSION 3.1) - if(APPLE) set (EXTENSION_PREFIX "") set (EXTENSION_SUFFIX ".so") diff --git a/Code/RDBoost/CMakeLists.txt b/Code/RDBoost/CMakeLists.txt index 8d3bb567b..4b784de71 100644 --- a/Code/RDBoost/CMakeLists.txt +++ b/Code/RDBoost/CMakeLists.txt @@ -2,15 +2,14 @@ if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1") add_definitions(-DRDKIT_RDBOOST_BUILD) rdkit_library(RDBoost Wrap.cpp - LINK_LIBRARIES RDGeneral ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}) + LINK_LIBRARIES RDGeneral rdkit_py_base rdkit_base) else() add_definitions(-DRDKIT_RDBOOST_BUILD) rdkit_library(RDBoost Wrap.cpp - LINK_LIBRARIES RDGeneral ${Boost_LIBRARIES}) + LINK_LIBRARIES RDGeneral rdkit_base) if("${PYTHON_LDSHARED}" STREQUAL "") - else() - # fixes an apple issue + else() # fixes an apple issue STRING(REGEX REPLACE "-bundle" "" LDSHARED ${PYTHON_LDSHARED}) set_target_properties(RDBoost PROPERTIES LINK_FLAGS ${LDSHARED}) endif() @@ -24,6 +23,9 @@ rdkit_headers(Wrap.h PySequenceHolder.h DEST RDBoost) if(RDK_BUILD_PYTHON_WRAPPERS) +if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13.0") + cmake_policy(SET CMP0079 NEW) +endif() add_subdirectory(Wrap) endif() diff --git a/Code/RDGeneral/BoostStartInclude.h b/Code/RDGeneral/BoostStartInclude.h index 30d342416..44b869d46 100644 --- a/Code/RDGeneral/BoostStartInclude.h +++ b/Code/RDGeneral/BoostStartInclude.h @@ -63,6 +63,7 @@ #pragma GCC diagnostic ignored "-Wmissing-field-initializers" #pragma GCC diagnostic ignored "-Wsign-compare" #pragma GCC diagnostic ignored "-Wconversion" +#pragma GCC diagnostic ignored "-Wmaybe-uninitialized" #if (__GNUC__ > 4 || __GNUC_MINOR__ > 7) #pragma GCC diagnostic ignored "-Wunused-local-typedefs" #endif diff --git a/Code/RDGeneral/CMakeLists.txt b/Code/RDGeneral/CMakeLists.txt index 94c7525aa..a3cd03cbb 100644 --- a/Code/RDGeneral/CMakeLists.txt +++ b/Code/RDGeneral/CMakeLists.txt @@ -9,8 +9,7 @@ CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/RDConfig.h.cmake add_definitions(-DRDKIT_RDGENERAL_BUILD) rdkit_library(RDGeneral Invariant.cpp types.cpp utils.cpp RDLog.cpp - LocaleSwitcher.cpp versions.cpp SHARED - LINK_LIBRARIES ${RDKit_THREAD_LIBS}) + LocaleSwitcher.cpp versions.cpp SHARED) if(MINGW) set(hasMSVCRuntime "FALSE") diff --git a/Code/RDStreams/CMakeLists.txt b/Code/RDStreams/CMakeLists.txt index 3bd675b94..8e2bab1d7 100644 --- a/Code/RDStreams/CMakeLists.txt +++ b/Code/RDStreams/CMakeLists.txt @@ -1,8 +1,7 @@ if(RDK_USE_BOOST_IOSTREAMS) ADD_DEFINITIONS("-DRDK_USE_BOOST_IOSTREAMS") -find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED) -set (link_iostreams ${Boost_LIBRARIES}) +find_package(Boost 1.56.0 COMPONENTS iostreams REQUIRED) if (NOT Boost_USE_STATIC_LIBS) add_definitions("-DBOOST_IOSTREAMS_DYN_LINK") endif() @@ -24,5 +23,5 @@ endif() add_definitions(-DRDKIT_RDSTREAMS_BUILD) endif(RDK_USE_BOOST_IOSTREAMS) rdkit_library(RDStreams streams.cpp - LINK_LIBRARIES ${Boost_LIBRARIES} ${link_iostreams} ${zlib_lib}) + LINK_LIBRARIES Boost::iostreams ${zlib_lib}) rdkit_headers(streams.h DEST RDStreams) diff --git a/Code/SimDivPickers/CMakeLists.txt b/Code/SimDivPickers/CMakeLists.txt index f6f6db6b6..e37b39023 100644 --- a/Code/SimDivPickers/CMakeLists.txt +++ b/Code/SimDivPickers/CMakeLists.txt @@ -8,10 +8,10 @@ rdkit_headers(DistPicker.h LeaderPicker.h HierarchicalClusterPicker.h MaxMinPicker.h DEST SimDivPickers) -rdkit_test(testSimDivPickers testPickers.cpp LINK_LIBRARIES SimDivPickers RDGeneral) +rdkit_test(testSimDivPickers testPickers.cpp LINK_LIBRARIES SimDivPickers) rdkit_catch_test(pickersTestsCatch catch_tests.cpp - LINK_LIBRARIES SimDivPickers DataStructs RDGeneral) + LINK_LIBRARIES SimDivPickers DataStructs) if(RDK_BUILD_PYTHON_WRAPPERS) diff --git a/Code/SimDivPickers/Wrap/CMakeLists.txt b/Code/SimDivPickers/Wrap/CMakeLists.txt index 3718a7c6f..934cdbcca 100644 --- a/Code/SimDivPickers/Wrap/CMakeLists.txt +++ b/Code/SimDivPickers/Wrap/CMakeLists.txt @@ -3,9 +3,7 @@ rdkit_python_extension(rdSimDivPickers MaxMinPicker.cpp LeaderPicker.cpp HierarchicalClusterPicker.cpp rdSimDivPickers.cpp DEST SimDivFilters - LINK_LIBRARIES SimDivPickers -hc DataStructs -RDGeneral RDBoost) + LINK_LIBRARIES SimDivPickers DataStructs) add_pytest(pySimDivPickers ${CMAKE_CURRENT_SOURCE_DIR}/testPickers.py) diff --git a/Code/cmake/Modules/RDKitUtils.cmake b/Code/cmake/Modules/RDKitUtils.cmake index 97925982b..4ba0f8328 100644 --- a/Code/cmake/Modules/RDKitUtils.cmake +++ b/Code/cmake/Modules/RDKitUtils.cmake @@ -125,16 +125,11 @@ macro(rdkit_python_extension) ${RDK_PYTHON_OUTPUT_DIRECTORY}/${RDKPY_DEST}) endif(WIN32) - if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1") - target_link_libraries(${RDKPY_NAME} ${RDKPY_LINK_LIBRARIES} - ${PYTHON_LIBRARIES} ${Boost_LIBRARIES} ) + target_link_libraries(${RDKPY_NAME} ${RDKPY_LINK_LIBRARIES} + RDBoost rdkit_py_base rdkit_base ) + if("${PYTHON_LDSHARED}" STREQUAL "") else() - target_link_libraries(${RDKPY_NAME} ${RDKPY_LINK_LIBRARIES} - ${Boost_LIBRARIES} ) - if("${PYTHON_LDSHARED}" STREQUAL "") - else() - set_target_properties(${RDKPY_NAME} PROPERTIES LINK_FLAGS ${PYTHON_LDSHARED}) - endif() + set_target_properties(${RDKPY_NAME} PROPERTIES LINK_FLAGS ${PYTHON_LDSHARED}) endif() INSTALL(TARGETS ${RDKPY_NAME} diff --git a/Docs/Book/C++Examples/CMakeLists.txt b/Docs/Book/C++Examples/CMakeLists.txt index b2a138c0d..2af89dd24 100644 --- a/Docs/Book/C++Examples/CMakeLists.txt +++ b/Docs/Book/C++Examples/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required( VERSION 2.8.9 ) +cmake_minimum_required( VERSION 3.5 ) project(RDKitSV) diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLists.txt index 018727bc1..2659a40c6 100644 --- a/External/AvalonTools/CMakeLists.txt +++ b/External/AvalonTools/CMakeLists.txt @@ -94,12 +94,11 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR}) include_directories(${AVALON_SRC_PATH}) add_definitions(-DRDKIT_AVALONLIB_BUILD) -rdkit_library(AvalonLib AvalonTools.cpp SHARED LINK_LIBRARIES avalon_clib FileParsers SmilesParse GraphMol DataStructs RDGeometryLib RDGeneral ) +rdkit_library(AvalonLib AvalonTools.cpp SHARED + LINK_LIBRARIES avalon_clib FileParsers SmilesParse GraphMol DataStructs ) rdkit_headers(AvalonTools.h DEST GraphMol) rdkit_test(testAvalonLib1 test1.cpp - LINK_LIBRARIES AvalonLib avalon_clib - SubstructMatch - FileParsers SmilesParse GraphMol DataStructs RDGeometryLib RDGeneral) + LINK_LIBRARIES AvalonLib SubstructMatch ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/External/AvalonTools/Wrap/CMakeLists.txt b/External/AvalonTools/Wrap/CMakeLists.txt index 00c9fe748..0ff81c1d6 100644 --- a/External/AvalonTools/Wrap/CMakeLists.txt +++ b/External/AvalonTools/Wrap/CMakeLists.txt @@ -3,8 +3,6 @@ rdkit_python_extension(pyAvalonTools pyAvalonTools.cpp DEST Avalon LINK_LIBRARIES - AvalonLib avalon_clib - SubstructMatch - SmilesParse FileParsers GraphMol DataStructs RDGeometryLib RDGeneral RDBoost) + AvalonLib ) add_pytest(pyAvalonTools ${CMAKE_CURRENT_SOURCE_DIR}/testAvalonTools.py) diff --git a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt index b57f831fb..78f76bac8 100644 --- a/External/FreeSASA/CMakeLists.txt +++ b/External/FreeSASA/CMakeLists.txt @@ -90,12 +90,12 @@ if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) endif() include_directories("${FREESASA_SRC_DIR}/src") -rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED LINK_LIBRARIES freesasa_clib GraphMol DataStructs RDGeometryLib RDGeneral ) +rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED + LINK_LIBRARIES freesasa_clib GraphMol ) rdkit_headers(RDFreeSASA.h DEST GraphMol) rdkit_test(testFreeSASALib testFreeSASA.cpp - LINK_LIBRARIES FreeSASALib freesasa_clib FileParsers SmilesParse - GraphMol DataStructs RDGeometryLib RDGeneral) + LINK_LIBRARIES FreeSASALib FileParsers SmilesParse ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/External/FreeSASA/Wrap/CMakeLists.txt b/External/FreeSASA/Wrap/CMakeLists.txt index bfe32cd67..bd4ecbf9f 100644 --- a/External/FreeSASA/Wrap/CMakeLists.txt +++ b/External/FreeSASA/Wrap/CMakeLists.txt @@ -3,6 +3,6 @@ rdkit_python_extension(rdFreeSASA rdFreeSASA.cpp DEST Chem LINK_LIBRARIES - FreeSASALib freesasa_clib GraphMol DataStructs RDGeometryLib RDGeneral RDBoost) + FreeSASALib ) add_pytest(pyFreeSASA ${CMAKE_CURRENT_SOURCE_DIR}/testFreeSASA.py) diff --git a/External/INCHI-API/CMakeLists.txt b/External/INCHI-API/CMakeLists.txt index cca6a03c0..ff5ee328a 100644 --- a/External/INCHI-API/CMakeLists.txt +++ b/External/INCHI-API/CMakeLists.txt @@ -74,8 +74,8 @@ if(RDK_BUILD_INCHI_SUPPORT) endif() add_definitions(-DRDKIT_RDINCHILIB_BUILD) rdkit_library(RDInchiLib inchi.cpp SHARED LINK_LIBRARIES ${INCHI_LIBRARIES} - GraphMol RDGeneral Depictor SubstructMatch SmilesParse - ${RDKit_THREAD_LIBS}) + GraphMol RDGeneral Depictor SubstructMatch SmilesParse ) + rdkit_headers(inchi.h DEST GraphMol) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) @@ -85,11 +85,8 @@ if(RDK_BUILD_INCHI_SUPPORT) rdkit_test(testInchi test.cpp LINK_LIBRARIES - ${INCHI_LIBRARIES} - RDInchiLib ${INCHI_LIBRARIES} - FileParsers SmilesParse Descriptors Depictor SubstructMatch GraphMol - RDGeneral DataStructs RDGeneral RDGeometryLib - ${RDKit_THREAD_LIBS}) + RDInchiLib + FileParsers SmilesParse Descriptors ) endif(RDK_BUILD_INCHI_SUPPORT) if(RDK_BUILD_PYTHON_WRAPPERS) diff --git a/External/INCHI-API/Wrap/CMakeLists.txt b/External/INCHI-API/Wrap/CMakeLists.txt index 65a4e8984..8075ff86e 100644 --- a/External/INCHI-API/Wrap/CMakeLists.txt +++ b/External/INCHI-API/Wrap/CMakeLists.txt @@ -2,5 +2,4 @@ rdkit_python_extension(rdinchi pyInchi.cpp DEST Chem LINK_LIBRARIES - RDInchiLib ${INCHI_LIBRARIES} SmilesParse SubstructMatch Depictor - GraphMol DataStructs RDGeometryLib RDGeneral RDBoost ${RDKit_THREAD_LIBS}) + RDInchiLib ) diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt index 7f7951c0b..cec14faa1 100644 --- a/External/YAeHMOP/CMakeLists.txt +++ b/External/YAeHMOP/CMakeLists.txt @@ -40,12 +40,11 @@ message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") add_definitions(-DRDKIT_EHTLIB_BUILD) -rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol DataStructs RDGeometryLib RDGeneral ) +rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol ) add_dependencies(EHTLib yaehmop_project) rdkit_headers(EHTTools.h DEST GraphMol) rdkit_catch_test(testEHTLib1 test1.cpp - LINK_LIBRARIES EHTLib yaehmop_eht - FileParsers SmilesParse GraphMol DataStructs RDGeometryLib RDGeneral) + LINK_LIBRARIES EHTLib FileParsers SmilesParse ) if(RDK_BUILD_PYTHON_WRAPPERS) add_subdirectory(Wrap) diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt index fd5954fad..759a9f360 100644 --- a/External/YAeHMOP/Wrap/CMakeLists.txt +++ b/External/YAeHMOP/Wrap/CMakeLists.txt @@ -3,8 +3,7 @@ rdkit_python_extension(rdEHTTools rdEHTTools.cpp DEST Chem LINK_LIBRARIES - EHTLib yaehmop_eht - GraphMol DataStructs RDGeometryLib RDGeneral RDBoost) + EHTLib ) add_pytest(pyEHTTools ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)