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Release_2018_09
rdkit/Code/JavaWrappers/gmwrapper/CMakeLists.txt
Susan Leung 956fdf268c Dev/GSOC2018_MolVS_Integration (#2002) 
* short test file for MolVS standardize_sm

* short test file for MolVS fragment

* short test file for MolVS metals

* short test file for MolVS normalize

* short test file for MolVS reionize

* short test file for MolVS tautomer

* short test file for MolVS validate

* long test file for MolVS standardize smiles

* long test file for MolVS fragment

* long test file for MolVS metals

* long test file for MolVS normalize

* long test file for MolVS reionize

* long test file for MolVS tautomer

* long test file for MolVS validate

* Unit tests for MolVS steps

* dropping support for Python2

* molvs/__init__.py

* molvs/charge.py

* molvs/errors.py

* molvs/fragment.py

* molvs/metal.py

* molvs/normalize.py

* molvs/resonance.py

* molvs/standardize.py

* molvs/tautomer.py

* molvs/utils.py

* molvs/validate.py

* molvs/validations.py

* molvs/cli.py

* adapted and renamed molvs/cli.py to work within $RDBASE/Contrib/MolVS/

* setup MolStandardize directories, source with empty cleanup function, header, CMake files

* corrections to empty source, header and test1.cpp

* adding empty functions and initializers to MolStandardize

* empty Metal source, header and added test

* added most of Metal.cpp functionality and made some more tests

* empty functions and initializers to Normalize

* empty functions and initializers to Validate

* added most code for RDKitDefault mode, along with some tests

* restructure for abstract base class ValidateMethod

* written in isNoneValidation for MolVSValidation

* took out isNoneValidation, put in noAtomValidation, neutralValidation, isotopeValidation for MolVSValidation

* added in AllowedAtoms

* added in disallowedAtoms

* corrections to Validate

* added code for FragmentRemover

* extended fragment functionality to include choose largest fragment, added in tests for fragment catalog, fragment remover. Also added fragmentValidation method in MolStandardize

* added another test to testValidate test_fragment

* corrections to fragment

* corrections to Metal

* added code for Normalize

* added normalize member function to MolStandardize and added tests

* added multi fragment functionality to Normalize.cpp and additional tests

* TransformCatalog

* tests for Normalize.cpp

* first bit of cleanup

* added most of Charge functionality and some tests

* some corrections to Charge.cpp and some more tests to testCharge.cpp

* corrections to Charge.cpp

* start of Tautomer Enumerate with some tests

* added BondType option to Tautomer Enumeration

* correcting for some memory leakage

* a few alterations to formatting

* sorting out some memory leaks

* sorting out some memory leaks

* some corrections for PCS test set

* redo tests with updated RDKit

* fixing memory leak

* more fixes after 100kPCS set testing

* using tab as delimiter in CSVs rather than comma

* tutorial for MolStandardize

* still working on Tautomer enumeration

* deleted some empty tests

* starting writing tautomer canonicalize

* rename test_data -> data (the source still needs to be updated)

* automatic source reformatting

* adjust to directory rename

* move the fragment catalog test into the MolStandardize directory
do not create separate library for FragmentCatalog

* stop building separate libraries for the catalogs

* move the CleanupParameters into the MolStandardize namespace

* first pass at python wrapper

* move the py module to the correct dir;
add some python tests;
add standardizeSmiles to python wrapper

* disabling the compareMolVSTest since that requires command line arguments to run

* get this building on windows

* put the python lib in the right place

* further work on python wrapper for rdMolStandardize

* added get and set functions to Metal and wrapped them

* added get and set functions to Metal and wrapped them

* changed construstor of Reionizer class and input args for reionize, wrapped this default

* overload Reionizer constructor so user can input own AcidBaseFile from python

* added Uncharger class to Charge and added test for Uncharger

* wrapped Fragment, fixed some memory leakage, changed some args and return types, added some tests

* wrapped Normalized and changed how Normalizer class is initiated

* changing MolVSValidation structure so user can choose which MolVS submethod they want

* starting to write Wrap for Validate

* now it compiles with Wrap/Validate.cpp

* a couple refactorings around validate

* move the validate code into the rdMolStandardize module

* make sure a valid pointer is returned for standardizeSmiles

* rdMolStandardize.MolVSValidation done and tests added

* half way through AllowedAtomsValidation

* finished AllowedAtomsValidation and DisallowedAtomsValidation

* moved charge, fragment, metal, normalize into the rdMolStandardize module

* changed tutorial to use wrapped code

* added copyrights

* added copyrights

* move the data files

* modify source files to adjust to the move

* added validateSmiles functionality

* removed std::cout

* redid some of the 100k PCS tests

* working on the tutorial

* adding some documentation

* deleting some comment lines

* some changes after pull review

* More changes after pull review

* start of trying to make java wrap

* remove some warnings, add some questions

* additional warning removals, a bit more reporting

* some test cleanups

* enable testing of the java code
2018-09-28 11:24:25 +02:00

361 lines
15 KiB
CMake
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cmake_minimum_required(VERSION 3.8)
project (jGraphMolJava Java)
include_directories( ${RDKit_ExternalDir} )
find_package(Java REQUIRED)
find_package(JNI REQUIRED)
include(UseJava)
# Make sure we can access the junit.jar -- needed for compiling/running tests
find_jar(JUNIT_JAR junit PATHS ${RDKit_JavaLibDir})
if (NOT JUNIT_JAR)
if(NOT DEFINED JUNIT_URL)
set(JUNIT_URL "http://central.maven.org/maven2/junit/junit/4.10/junit-4.10.jar")
endif()
if(NOT DEFINED JUNIT_MD5SUM)
set(JUNIT_MD5SUM "68380001b88006ebe49be50cef5bb23a")
endif()
downloadAndCheckMD5(${JUNIT_URL} "${RDKit_JavaLibDir}/junit.jar" ${JUNIT_MD5SUM})
find_jar(JUNIT_JAR junit PATHS ${RDKit_JavaLibDir})
if (NOT JUNIT_JAR)
MESSAGE ("junit.jar was not found in classpath or ${RDKit_JavaLibDir}. Please add it to this directory and rerun cmake.")
MESSAGE(FATAL_ERROR "Cannot find required JUnit library (junit.jar)")
endif()
endif (NOT JUNIT_JAR)
# Likewise for javadoc
find_program(JAVADOC_EXE javadoc PATH _JAVA_PATHS _JAVA_HINTS /usr/bin /usr/local/bin)
if (NOT JAVADOC_EXE)
MESSAGE ("javadoc (executable) is not found. Please add it to PATH and rerun cmake.")
MESSAGE(FATAL_ERROR "Cannot find required javadoc executable (javadoc)")
endif (NOT JAVADOC_EXE)
INCLUDE_DIRECTORIES(${JNI_INCLUDE_DIRS})
# java8 raises errors while creating the documentation
if(Java_VERSION_MAJOR GREATER 1 OR Java_VERSION_MINOR GREATER 7)
set(X_DOCLINT_NONE "-Xdoclint:none")
execute_process(COMMAND ${JAVADOC_EXE} ${X_DOCLINT_NONE}
OUTPUT_VARIABLE null
ERROR_VARIABLE err
ERROR_STRIP_TRAILING_WHITESPACE)
if (NOT ${err} MATCHES "invalid flag")
SET(DOCLINT_FLAGS ${X_DOCLINT_NONE})
endif()
endif()
SET_SOURCE_FILES_PROPERTIES(GraphMolJava.i PROPERTIES CPLUSPLUS ON )
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../*.java COPY_SOURCE)
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/org/RDKit COPY_DEST)
# Setup a few variables for environment-specific things
if(WIN32)
ADD_DEFINITIONS("/W3 /wd4716 /bigobj")
SET(PATH_SEP ";")
SET(COPY_CMD xcopy ${COPY_SOURCE} ${COPY_DEST} /Y /I)
else()
SET(PATH_SEP ":")
SET(COPY_CMD cp -p ${COPY_SOURCE} ${COPY_DEST})
endif()
# Coax SWIG into playing nicely with Apple environments
if(APPLE)
SET(CMAKE_SIZEOF_VOID_P 4)
endif(APPLE)
if(CMAKE_SIZEOF_VOID_P MATCHES 4)
SET(CMAKE_SWIG_FLAGS -package "org.RDKit")
else()
if (WIN32)
SET(CMAKE_SWIG_FLAGS -package "org.RDKit" "-DSWIGWORDSIZE64" "-DSWIGWIN")
else()
SET(CMAKE_SWIG_FLAGS -package "org.RDKit" "-DSWIGWORDSIZE64")
endif()
endif()
SET(CMAKE_SWIG_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/src/org/RDKit )
if(RDK_BUILD_INCHI_SUPPORT)
SET(CMAKE_SWIG_FLAGS "-DRDK_BUILD_INCHI_SUPPORT" ${CMAKE_SWIG_FLAGS} )
endif()
if(RDK_BUILD_AVALON_SUPPORT)
SET(CMAKE_SWIG_FLAGS "-DRDK_BUILD_AVALON_SUPPORT" ${CMAKE_SWIG_FLAGS} )
endif()
# enable this line to build the ErrorGenerator class for testing handling of C++ errors in the JNI layer
#SET(CMAKE_SWIG_FLAGS ${CMAKE_SWIG_FLAGS} "-D INCLUDE_ERROR_GENERATOR" )
FILE(GLOB SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../*.i")
# we added all source files, now remove the ones that we're not supporting in this build:
if(NOT RDK_BUILD_AVALON_SUPPORT)
LIST(REMOVE_ITEM SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../AvalonLib.i")
endif()
if(NOT RDK_BUILD_INCHI_SUPPORT)
LIST(REMOVE_ITEM SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../Inchi.i")
endif()
SET(SWIG_MODULE_GraphMolWrap_EXTRA_DEPS ${SWIG_SRC_FILES} )
SWIG_ADD_LIBRARY(GraphMolWrap TYPE MODULE LANGUAGE java SOURCES GraphMolJava.i )
# it doesnt seem like the threading libs should need to be here, but
# as of Oct 2012 using boost 1.51 under at least ubuntu 12.04 we get a
# link error if they aren't there.
SWIG_LINK_LIBRARIES(GraphMolWrap ${RDKit_Wrapper_Libs}
${Boost_SERIALIZATION_LIBRARY} ${RDKit_THREAD_LIBS})
MESSAGE("serial: ${Boost_SERIALIZATION_LIBRARY}")
MESSAGE("THREAD: ${RDKit_THREAD_LIBS}")
# code adapted from the wrapper code for
# GDCM: http://gdcm.svn.sf.net/viewvc/gdcm/trunk/Wrapping/Java/CMakeLists.txt?view=markup
ADD_CUSTOM_COMMAND(
OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar
COMMAND ${CMAKE_COMMAND} -E make_directory build
COMMAND ${CMAKE_COMMAND} -E make_directory build-test
## Add in our own Java sources
# COMMAND ${COPY_CMD}
## 1. run this custom command only after swig has been run.
COMMAND ${JAVA_COMPILE} -d build "src/org/RDKit/*.java"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
## 2. now that the *.class have been generated construct the jar file.
COMMAND ${JAVA_ARCHIVE} cf
${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar -C ${CMAKE_CURRENT_SOURCE_DIR}/build
org/RDKit
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
#DEPENDS GraphMolWrap
DEPENDS "${swig_generated_file_fullname}"
COMMENT "javac *.java; jar cf -> .jar"
OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKitDoc.jar
## Run Javadoc against newly created .java files to create docs
COMMAND ${JAVADOC_EXE} ${DOCLINT_FLAGS} -tag notes -tag example -d ${CMAKE_CURRENT_SOURCE_DIR}/doc -sourcepath ${CMAKE_CURRENT_SOURCE_DIR}/src org.RDKit
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
## Put the doc files into their own separate archive.
COMMAND ${JAVA_ARCHIVE} cf
${CMAKE_CURRENT_SOURCE_DIR}/org.RDKitDoc.jar
doc
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
#DEPENDS GraphMolWrap
DEPENDS "${swig_generated_file_fullname}"
COMMENT "jar cf org.RDKitDoc.jar -d doc"
)
ADD_CUSTOM_TARGET(GraphMolWrapJar ALL
DEPENDS GraphMolWrap ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar
COMMENT "building jar"
)
## Tests -- note that building/rebuilding them keys on the file WrapperTests.class
SET(CMAKE_JAVA_TEST_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/build-test )
FILE(GLOB JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/*.java")
# we added all source files, now remove the ones that we're not supporting in this build:
if(NOT RDK_BUILD_AVALON_SUPPORT)
LIST(REMOVE_ITEM JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/AvalonLibTests.java")
endif()
if(NOT RDK_BUILD_INCHI_SUPPORT)
LIST(REMOVE_ITEM JAVA_TEST_FILES "${CMAKE_CURRENT_SOURCE_DIR}/src-test/org/RDKit/InchiTests.java")
endif()
ADD_CUSTOM_COMMAND(
OUTPUT ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class
COMMAND ${JAVA_COMPILE} ${DOCLINT_FLAGS} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
DEPENDS GraphMolWrapJar ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKitDoc.jar ${JAVA_TEST_FILES}
)
ADD_CUSTOM_TARGET(BuildJavaWrapperTests ALL
DEPENDS ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class GraphMolWrap
COMMENT "building test classes"
)
ADD_CUSTOM_TARGET(RunJavaWrapperTests
DEPENDS BuildJavaWrapperTests
COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/runUnitTests.sh
)
# need to add boost libs for testing
SET (CTEST_ENVIRONMENT
"LD_LIBRARY_PATH=${Boost_LIBRARY_DIRS}"
"DYLD_LIBRARY_PATH=${Boost_LIBRARY_DIRS}"
)
ADD_TEST(JavaAromaticTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AromaticTests)
ADD_TEST(JavaAtomPairsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AtomPairsTests)
ADD_TEST(JavaBasicMoleculeTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.BasicMoleculeTests)
ADD_TEST(JavaBasicMolecule2Tests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.BasicMolecule2Tests)
ADD_TEST(JavaChemAtomTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemAtomTests)
ADD_TEST(JavaChemBondTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemBondTests)
ADD_TEST(JavaChemReactionTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemReactionTests)
ADD_TEST(JavaChemSmartsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemSmartsTests)
ADD_TEST(JavaChemTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemTests)
ADD_TEST(JavaChemv2Tests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.Chemv2Tests)
ADD_TEST(JavaConformerTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ConformerTests)
ADD_TEST(JavaDescriptorTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.DescriptorTests)
ADD_TEST(JavaDistanceGeometryTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.DistanceGeometryTests)
ADD_TEST(JavaErrorHandlingTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ErrorHandlingTests)
ADD_TEST(JavaFingerprintsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.FingerprintsTests)
ADD_TEST(JavaForceFieldsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ForceFieldsTests)
ADD_TEST(JavaHManipulationsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.HManipulationsTests)
ADD_TEST(JavaLipinskiTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.LipinskiTests)
ADD_TEST(JavaPicklingTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.PicklingTests)
ADD_TEST(JavaSmilesCreationTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SmilesCreationTests)
ADD_TEST(JavaSmilesDetailsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SmilesDetailsTests)
ADD_TEST(JavaSmilesTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SmilesTests)
ADD_TEST(JavaSuppliersTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SuppliersTests)
ADD_TEST(JavaTrajectoryTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.TrajectoryTests)
ADD_TEST(JavaWrapperTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.WrapperTests)
if(RDK_BUILD_AVALON_SUPPORT)
ADD_TEST(JavaAvalonTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AvalonLibTests)
endif(RDK_BUILD_AVALON_SUPPORT)
if (RDK_BUILD_INCHI_SUPPORT)
ADD_TEST(JavaInchiTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.InchiTests)
endif (RDK_BUILD_INCHI_SUPPORT)
#ADD_TEST(JavaMemoryTests
# java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
# -cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
# org.RDKit.MemoryTests)
ADD_TEST(JavaChemTransformsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.ChemTransformsTests)
ADD_TEST(JavaFMCSTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.FMCSTests)
ADD_TEST(JavaPDBTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.PDBTests)
ADD_TEST(JavaSequenceTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.SequenceTests)
ADD_TEST(JavaAlignTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.AlignTests)
ADD_TEST(JavaMolQueryTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.MolQueryTests)
ADD_TEST(JavaFilterCatalogTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.FilterCatalogTests)
ADD_TEST(JavaDiversityPickerTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.DiversityPickerTests)
ADD_TEST(JavaBitOpsTests
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.BitOpsTests)
ADD_TEST(MolStandardizeTest
java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
org.RDKit.MolStandardizeTest)
INSTALL(TARGETS GraphMolWrap
DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} )
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