| Message ID | 20221007152226.362-2-david.elsing@posteo.net |
|---|---|
| State | Accepted |
| Headers | show |
| Series | Add rdkit. | expand |
| Context | Check | Description |
|---|---|---|
| cbaines/comparison | success | View comparision |
| cbaines/git-branch | success | View Git branch |
| cbaines/applying patch | fail | View Laminar job |
| cbaines/issue | success | View issue |
| cbaines/comparison | success | View comparision |
| cbaines/git-branch | success | View Git branch |
| cbaines/applying patch | fail | View Laminar job |
| cbaines/issue | success | View issue |
Am Freitag, dem 07.10.2022 um 15:22 +0000 schrieb David Elsing: > * gnu/packages/chemistry.scm (rdkit): New variable. > --- > gnu/packages/chemistry.scm | 178 > ++++++++++++++++++ > .../rdkit-cmake-external-dependencies.patch | 102 ++++++++++ > 2 files changed, 280 insertions(+) > create mode 100644 gnu/packages/patches/rdkit-cmake-external- > dependencies.patch > > diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm > index 43953238cd..4b34a38797 100644 > --- a/gnu/packages/chemistry.scm > +++ b/gnu/packages/chemistry.scm > @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry) > #:use-module (gnu packages algebra) > #:use-module (gnu packages autotools) > #:use-module (gnu packages backup) > + #:use-module (gnu packages base) > #:use-module (gnu packages bison) > #:use-module (gnu packages boost) > #:use-module (gnu packages check) > @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry) > #:use-module (gnu packages cpp) > #:use-module (gnu packages documentation) > #:use-module (gnu packages flex) > + #:use-module (gnu packages fonts) > #:use-module (gnu packages fontutils) > #:use-module (gnu packages gcc) > #:use-module (gnu packages gl) > #:use-module (gnu packages graphviz) > + #:use-module (gnu packages gtk) > #:use-module (gnu packages gv) > #:use-module (gnu packages image) > #:use-module (gnu packages maths) > @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry) > #:use-module (gnu packages qt) > #:use-module (gnu packages serialization) > #:use-module (gnu packages sphinx) > + #:use-module (gnu packages sqlite) > #:use-module (gnu packages stb) > #:use-module (gnu packages tex) > #:use-module (gnu packages web) > @@ -1101,3 +1105,177 @@ (define-public ringdecomposerlib > unique ring families, relevant cycles, the smallest set of smallest > rings and > other ring topology descriptions.") > (license license:bsd-3))) > + > +(define-public rdkit > + (package > + (name "rdkit") > + (version "2022.03.5") > + (source (origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/rdkit/rdkit") > + (commit > + (string-append > + "Release_" (string-replace-substring version > "." "_"))))) > + (file-name (git-file-name name version)) > + (sha256 > + (base32 > + > "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9")) > + (patches > + (search-patches "rdkit-cmake-external- > dependencies.patch")) > + (modules '((guix build utils))) > + (snippet > + #~(begin > + ;; Remove pickle files (only used in tests), > + ;; as they are compiled programs > + (for-each > + (lambda (name) > + (display (string-append name "\n")) > + (delete-file name)) > + (find-files "." "\\.pkl(\\.gz)?$")) > + ;; Remove SQLite data files (can be generated) > + (delete-file "Data/RDData.sqlt") > + (delete-file "Data/RDTests.sqlt"))))) > + (build-system cmake-build-system) > + (arguments > + (list > + #:imported-modules (append %cmake-build-system-modules > + '((guix build python-build- > system))) > + #:modules '((guix build cmake-build-system) > + (guix build utils) > + ((guix build python-build-system) > + #:select (add-installed-pythonpath))) > + #:configure-flags > + #~(list > + "-DRDK_BUILD_AVALON_SUPPORT=ON" > + "-DRDK_BUILD_CAIRO_SUPPORT=ON" > + "-DRDK_BUILD_CPP_TESTS=ON" > + "-DRDK_BUILD_FREESASA_SUPPORT=ON" > + "-DRDK_BUILD_INCHI_SUPPORT=ON" > + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON" Are any of these implied or do they have to be explicitly enabled? > + (string-append "-DCATCH_DIR=" > + #$(this-package-native-input "catch2") > + "/include/catch2") > + "-DRDK_INSTALL_DEV_COMPONENT=ON" > + "-DRDK_INSTALL_INTREE=OFF" > + "-DRDK_INSTALL_STATIC_LIBS=OFF" > + (string-append > + "-DRDK_OPTIMIZE_POPCNT=" > + #$(let ((system (or (%current-target-system) > + (%current-system)))) > + (cond > + ((string-prefix? "x86_64" system) "ON") > + ((string-prefix? "i686" system) "ON") > + (else "OFF")))) > + "-DRDK_USE_BOOST_IOSTREAMS=ON" > + "-DRDK_USE_FLEXBISON=ON") > + #:phases > + #~(modify-phases %standard-phases > + (add-after 'unpack 'copy-external-dependencies > + (lambda _ > + (symlink > + (string-append > + #$(this-package-input "font-comic-neue") > + "/share/fonts/truetype/ComicNeue-Regular.ttf") > + "Data/Fonts/ComicNeue-Regular.ttf"))) Try (search-input-file) instead. > + (add-after 'copy-external-dependencies 'patch-source > + (lambda _ > + (substitute* "External/AvalonTools/CMakeLists.txt" > + (("^if\\(NOT RDK_BUILD" orig) > + (string-append "if(0)\n" orig)) > + (("include_directories.*AVALON_SRC_PATH.*") > + (string-append "endif()\ninclude_directories(" > + #$avalontoolkit > "/include/avalontoolkit)\n")) > + (("LINK_LIBRARIES avalon_clib") > + (string-append > + "LINK_LIBRARIES -L" #$avalontoolkit "/lib - > lavalontoolkit"))) > + (let ((port > + (open-file "External/RingFamilies/dummy.cpp" > "w"))) > + (display "" port) > + (close port)) > + (let ((port > + (open-file > "External/RingFamilies/CMakeLists.txt" "w"))) > + (display (string-append > + "rdkit_library(RingDecomposerLib dummy.cpp > SHARED" > + " LINK_LIBRARIES -lRingDecomposerLib)\n" > + "set(RDK_URF_LIBS RingDecomposerLib CACHE > STRING \"\" FORCE)\n") > + port) > + (close port)) > + (substitute* > "Code/GraphMol/MolInterchange/CMakeLists.txt" > + (("if\\(NOT" orig) > + (string-append "if(0)\n" orig)) > + (("^include_directories.*") "endif()\n")) > + (substitute* "External/YAeHMOP/EHTTools.cpp" > + (("<yaehmop/tightbind/bind.h>") > "<yaehmop/bind.h>")))) I think you might want to unbundle these with a patch. > + (add-after 'unpack 'fix-inchi-include > + (lambda _ > + (substitute* "Code/cmake/Modules/FindInchi.cmake" > + (("inchi_api.h.*\\)") "inchi/inchi_api.h)") > + (("INCHI_LIBRARY NAMES.*\\)") > + "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)") > + (("find_library" prev) > + (string-append > + "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n" > + prev))) > + (substitute* "External/INCHI-API/inchi.cpp" > + (("<inchi_api.h>") "<inchi/inchi_api.h>")))) > + (add-before 'build 'enable-bytecode-determinism > + (lambda _ > + (setenv "PYTHONHASHSEED" "0") > + (setenv "PYTHONDONTWRITEBYTECODE" "1"))) > + (add-after 'install 'pre-check > + (lambda* (#:key inputs outputs #:allow-other-keys) > + (with-directory-excursion "../source" > + (invoke "sqlite3" "Data/RDData.sqlt" > + ".read rdkit/Dbase/test_data/RDData.sqlite") > + (invoke "sqlite3" "Data/RDTests.sqlt" > + ".read > rdkit/Dbase/test_data/RDTests.sqlite") > + (setenv "RDBASE" (canonicalize-path "."))) > + (add-installed-pythonpath inputs outputs))) > + (delete 'check) > + (add-after 'pre-check 'check > + (lambda* (#:key tests? parallel-tests? #:allow-other- > keys) > + (when tests? > + (let ((job-count (number->string > + (if parallel-tests? (parallel-job- > count) 1)))) > + (invoke > + "ctest" "-j" job-count > + "-E" (string-append > + "(" (string-join > + '(;; need pickled data > + "(pyDiscreteValueVect" > "pySparseIntVect" > + "graphmoltestPickler" > "pyPartialCharges" > + "substructLibraryTest" "pyFeatures" > + "pythonTestDirML" > "pythonTestDirChem" > + ;; Catching Python exception fails > + "pyRanker)") "|") ")"))))))))) I think you have two layers of brackets now – delete the inner ones. > + (native-inputs > + (list bison > + boost > + catch2 > + eigen > + flex > + freesasa > + pkg-config > + rapidjson > + tar)) > + (inputs > + (list avalontoolkit > + cairo > + coordgenlibs > + font-comic-neue > + freetype > + inchi > + maeparser > + python > + ringdecomposerlib > + sqlite > + yaehmop)) > + (propagated-inputs > + (list python-numpy python-cairocffi python-pillow)) > + (home-page "https://rdkit.org/") > + (synopsis "Collection of cheminformatics software") > + (description "RDKit is a C++ and Python library for > cheminformatics, which > +includes (among other things) the analysis and modification of > molecules in 2D > +and 3D and descriptor generation for machine learning.") > + (license license:bsd-3))) > diff --git a/gnu/packages/patches/rdkit-cmake-external- > dependencies.patch b/gnu/packages/patches/rdkit-cmake-external- > dependencies.patch > new file mode 100644 > index 0000000000..5b73864f51 > --- /dev/null > +++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch > @@ -0,0 +1,102 @@ > +diff -ur a/External/FreeSASA/CMakeLists.txt > b/External/FreeSASA/CMakeLists.txt > +--- a/External/FreeSASA/CMakeLists.txt > ++++ b/External/FreeSASA/CMakeLists.txt > +@@ -10,7 +10,7 @@ > + endif() > + endif() > + > +-if(needDownload) > ++if(FALSE) > + # don't actually use the md5 here > + set(FREESASA_VERSION "2.0.3") > + set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa- > ${FREESASA_VERSION}") > +@@ -66,24 +66,24 @@ > + endif() > + > + set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h) > +-file(READ ${freesasa_h} freesasa_h_data) > ++#file(READ ${freesasa_h} freesasa_h_data) > + string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include > <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}") > + string(REGEX REPLACE > "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L > ][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" > "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data > "${freesasa_h_data}") > +-file(WRITE ${freesasa_h} "${freesasa_h_data}") > ++#file(WRITE ${freesasa_h} "${freesasa_h_data}") > + > + add_definitions(-DUSE_THREADS=0) > + add_definitions(-DUSE_JSON=0) > + add_definitions(-DUSE_XML=0) > +-rdkit_library(freesasa_clib ${freesasa_clib_srcs}) > +-target_compile_definitions(freesasa_clib PRIVATE > RDKIT_FREESASALIB_BUILD) > ++#rdkit_library(freesasa_clib ${freesasa_clib_srcs}) > ++#target_compile_definitions(freesasa_clib PRIVATE > RDKIT_FREESASALIB_BUILD) > + > + if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) > + set_target_properties(freesasa_clib PROPERTIES > WINDOWS_EXPORT_ALL_SYMBOLS TRUE) > + endif() > +-include_directories("${FREESASA_SRC_DIR}/src") > ++#include_directories("${FREESASA_SRC_DIR}/src") > + > + rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED > +- LINK_LIBRARIES freesasa_clib GraphMol ) > ++ LINK_LIBRARIES -lfreesasa GraphMol ) > + target_compile_definitions(FreeSASALib PRIVATE > RDKIT_FREESASALIB_BUILD) > + > + rdkit_headers(RDFreeSASA.h DEST GraphMol) > +diff -ur a/External/YAeHMOP/CMakeLists.txt > b/External/YAeHMOP/CMakeLists.txt > +--- a/External/YAeHMOP/CMakeLists.txt > ++++ b/External/YAeHMOP/CMakeLists.txt > +@@ -18,32 +18,32 @@ > + > + include_directories( ${RDKit_ExternalDir}/YAeHMOP ) > + > +-ExternalProject_Add(yaehmop_project > +- GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git > +- GIT_TAG master > +- UPDATE_COMMAND "" > +- PATCH_COMMAND "" > +- PREFIX ${CMAKE_CURRENT_SOURCE_DIR} > +- SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop" > +- SOURCE_SUBDIR "tightbind" > +- CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF - > DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} - > DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} - > DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} > +- TEST_COMMAND "") > +- > +-include_directories(${PROJECT_BINARY_DIR}/include) > +-link_directories(${PROJECT_BINARY_DIR}/lib) > +-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project- > build) > +- > +-set(EHT_PARAM_FILE > ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) > +-install(FILES ${EHT_PARAM_FILE} > +- DESTINATION ${RDKit_ShareDir}/Data > +- COMPONENT data) > ++#ExternalProject_Add(yaehmop_project > ++# GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git > ++# GIT_TAG master > ++# UPDATE_COMMAND "" > ++# PATCH_COMMAND "" > ++# PREFIX ${CMAKE_CURRENT_SOURCE_DIR} > ++# SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop" > ++# SOURCE_SUBDIR "tightbind" > ++# CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF - > DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} - > DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} - > DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} > ++# TEST_COMMAND "") > ++ > ++#include_directories(${PROJECT_BINARY_DIR}/include) > ++#link_directories(${PROJECT_BINARY_DIR}/lib) > ++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project- > build) > ++ > ++#set(EHT_PARAM_FILE > ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) > ++#install(FILES ${EHT_PARAM_FILE} > ++# DESTINATION ${RDKit_ShareDir}/Data > ++# COMPONENT data) > + > +-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") > +-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib > ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") > ++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") > ++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib > ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") > + > +-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht > GraphMol ) > ++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES - > lyaehmop_eht GraphMol ) > + target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD) > +-add_dependencies(EHTLib yaehmop_project) > ++#add_dependencies(EHTLib yaehmop_project) > + rdkit_headers(EHTTools.h DEST GraphMol) > + rdkit_catch_test(testEHTLib1 test1.cpp > + LINK_LIBRARIES EHTLib FileParsers SmilesParse ) Cheers
Liliana Marie Prikler <liliana.prikler@gmail.com> writes: > Am Freitag, dem 07.10.2022 um 15:22 +0000 schrieb David Elsing: >> * gnu/packages/chemistry.scm (rdkit): New variable. >> --- >> gnu/packages/chemistry.scm | 178 >> ++++++++++++++++++ >> .../rdkit-cmake-external-dependencies.patch | 102 ++++++++++ >> 2 files changed, 280 insertions(+) >> create mode 100644 gnu/packages/patches/rdkit-cmake-external- >> dependencies.patch >> >> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm >> index 43953238cd..4b34a38797 100644 >> --- a/gnu/packages/chemistry.scm >> +++ b/gnu/packages/chemistry.scm >> @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry) >> #:use-module (gnu packages algebra) >> #:use-module (gnu packages autotools) >> #:use-module (gnu packages backup) >> + #:use-module (gnu packages base) >> #:use-module (gnu packages bison) >> #:use-module (gnu packages boost) >> #:use-module (gnu packages check) >> @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry) >> #:use-module (gnu packages cpp) >> #:use-module (gnu packages documentation) >> #:use-module (gnu packages flex) >> + #:use-module (gnu packages fonts) >> #:use-module (gnu packages fontutils) >> #:use-module (gnu packages gcc) >> #:use-module (gnu packages gl) >> #:use-module (gnu packages graphviz) >> + #:use-module (gnu packages gtk) >> #:use-module (gnu packages gv) >> #:use-module (gnu packages image) >> #:use-module (gnu packages maths) >> @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry) >> #:use-module (gnu packages qt) >> #:use-module (gnu packages serialization) >> #:use-module (gnu packages sphinx) >> + #:use-module (gnu packages sqlite) >> #:use-module (gnu packages stb) >> #:use-module (gnu packages tex) >> #:use-module (gnu packages web) >> @@ -1101,3 +1105,177 @@ (define-public ringdecomposerlib >> unique ring families, relevant cycles, the smallest set of smallest >> rings and >> other ring topology descriptions.") >> (license license:bsd-3))) >> + >> +(define-public rdkit >> + (package >> + (name "rdkit") >> + (version "2022.03.5") >> + (source (origin >> + (method git-fetch) >> + (uri (git-reference >> + (url "https://github.com/rdkit/rdkit") >> + (commit >> + (string-append >> + "Release_" (string-replace-substring version >> "." "_"))))) >> + (file-name (git-file-name name version)) >> + (sha256 >> + (base32 >> + >> "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9")) >> + (patches >> + (search-patches "rdkit-cmake-external- >> dependencies.patch")) >> + (modules '((guix build utils))) >> + (snippet >> + #~(begin >> + ;; Remove pickle files (only used in tests), >> + ;; as they are compiled programs >> + (for-each >> + (lambda (name) >> + (display (string-append name "\n")) >> + (delete-file name)) >> + (find-files "." "\\.pkl(\\.gz)?$")) >> + ;; Remove SQLite data files (can be generated) >> + (delete-file "Data/RDData.sqlt") >> + (delete-file "Data/RDTests.sqlt"))))) >> + (build-system cmake-build-system) >> + (arguments >> + (list >> + #:imported-modules (append %cmake-build-system-modules >> + '((guix build python-build- >> system))) >> + #:modules '((guix build cmake-build-system) >> + (guix build utils) >> + ((guix build python-build-system) >> + #:select (add-installed-pythonpath))) >> + #:configure-flags >> + #~(list >> + "-DRDK_BUILD_AVALON_SUPPORT=ON" >> + "-DRDK_BUILD_CAIRO_SUPPORT=ON" >> + "-DRDK_BUILD_CPP_TESTS=ON" >> + "-DRDK_BUILD_FREESASA_SUPPORT=ON" >> + "-DRDK_BUILD_INCHI_SUPPORT=ON" >> + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON" > Are any of these implied or do they have to be explicitly enabled? Oops, I overlooked some, now only flags changing the default are specified. >> + (string-append "-DCATCH_DIR=" >> + #$(this-package-native-input "catch2") >> + "/include/catch2") >> + "-DRDK_INSTALL_DEV_COMPONENT=ON" >> + "-DRDK_INSTALL_INTREE=OFF" >> + "-DRDK_INSTALL_STATIC_LIBS=OFF" >> + (string-append >> + "-DRDK_OPTIMIZE_POPCNT=" >> + #$(let ((system (or (%current-target-system) >> + (%current-system)))) >> + (cond >> + ((string-prefix? "x86_64" system) "ON") >> + ((string-prefix? "i686" system) "ON") >> + (else "OFF")))) >> + "-DRDK_USE_BOOST_IOSTREAMS=ON" >> + "-DRDK_USE_FLEXBISON=ON") >> + #:phases >> + #~(modify-phases %standard-phases >> + (add-after 'unpack 'copy-external-dependencies >> + (lambda _ >> + (symlink >> + (string-append >> + #$(this-package-input "font-comic-neue") >> + "/share/fonts/truetype/ComicNeue-Regular.ttf") >> + "Data/Fonts/ComicNeue-Regular.ttf"))) > Try (search-input-file) instead. >> + (add-after 'copy-external-dependencies 'patch-source >> + (lambda _ >> + (substitute* "External/AvalonTools/CMakeLists.txt" >> + (("^if\\(NOT RDK_BUILD" orig) >> + (string-append "if(0)\n" orig)) >> + (("include_directories.*AVALON_SRC_PATH.*") >> + (string-append "endif()\ninclude_directories(" >> + #$avalontoolkit >> "/include/avalontoolkit)\n")) >> + (("LINK_LIBRARIES avalon_clib") >> + (string-append >> + "LINK_LIBRARIES -L" #$avalontoolkit "/lib - >> lavalontoolkit"))) >> + (let ((port >> + (open-file "External/RingFamilies/dummy.cpp" >> "w"))) >> + (display "" port) >> + (close port)) >> + (let ((port >> + (open-file >> "External/RingFamilies/CMakeLists.txt" "w"))) >> + (display (string-append >> + "rdkit_library(RingDecomposerLib dummy.cpp >> SHARED" >> + " LINK_LIBRARIES -lRingDecomposerLib)\n" >> + "set(RDK_URF_LIBS RingDecomposerLib CACHE >> STRING \"\" FORCE)\n") >> + port) >> + (close port)) >> + (substitute* >> "Code/GraphMol/MolInterchange/CMakeLists.txt" >> + (("if\\(NOT" orig) >> + (string-append "if(0)\n" orig)) >> + (("^include_directories.*") "endif()\n")) >> + (substitute* "External/YAeHMOP/EHTTools.cpp" >> + (("<yaehmop/tightbind/bind.h>") >> "<yaehmop/bind.h>")))) > I think you might want to unbundle these with a patch. Is the patch ok? >> + (add-after 'unpack 'fix-inchi-include >> + (lambda _ >> + (substitute* "Code/cmake/Modules/FindInchi.cmake" >> + (("inchi_api.h.*\\)") "inchi/inchi_api.h)") >> + (("INCHI_LIBRARY NAMES.*\\)") >> + "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)") >> + (("find_library" prev) >> + (string-append >> + "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n" >> + prev))) >> + (substitute* "External/INCHI-API/inchi.cpp" >> + (("<inchi_api.h>") "<inchi/inchi_api.h>")))) >> + (add-before 'build 'enable-bytecode-determinism >> + (lambda _ >> + (setenv "PYTHONHASHSEED" "0") >> + (setenv "PYTHONDONTWRITEBYTECODE" "1"))) >> + (add-after 'install 'pre-check >> + (lambda* (#:key inputs outputs #:allow-other-keys) >> + (with-directory-excursion "../source" >> + (invoke "sqlite3" "Data/RDData.sqlt" >> + ".read rdkit/Dbase/test_data/RDData.sqlite") >> + (invoke "sqlite3" "Data/RDTests.sqlt" >> + ".read >> rdkit/Dbase/test_data/RDTests.sqlite") >> + (setenv "RDBASE" (canonicalize-path "."))) >> + (add-installed-pythonpath inputs outputs))) >> + (delete 'check) >> + (add-after 'pre-check 'check >> + (lambda* (#:key tests? parallel-tests? #:allow-other- >> keys) >> + (when tests? >> + (let ((job-count (number->string >> + (if parallel-tests? (parallel-job- >> count) 1)))) >> + (invoke >> + "ctest" "-j" job-count >> + "-E" (string-append >> + "(" (string-join >> + '(;; need pickled data >> + "(pyDiscreteValueVect" >> "pySparseIntVect" >> + "graphmoltestPickler" >> "pyPartialCharges" >> + "substructLibraryTest" "pyFeatures" >> + "pythonTestDirML" >> "pythonTestDirChem" >> + ;; Catching Python exception fails >> + "pyRanker)") "|") ")"))))))))) > I think you have two layers of brackets now – delete the inner ones. Oh thanks! >> + (native-inputs >> + (list bison >> + boost >> + catch2 >> + eigen >> + flex >> + freesasa >> + pkg-config >> + rapidjson >> + tar)) >> + (inputs >> + (list avalontoolkit >> + cairo >> + coordgenlibs >> + font-comic-neue >> + freetype >> + inchi >> + maeparser >> + python >> + ringdecomposerlib >> + sqlite >> + yaehmop)) >> + (propagated-inputs >> + (list python-numpy python-cairocffi python-pillow)) >> + (home-page "https://rdkit.org/") >> + (synopsis "Collection of cheminformatics software") >> + (description "RDKit is a C++ and Python library for >> cheminformatics, which >> +includes (among other things) the analysis and modification of >> molecules in 2D >> +and 3D and descriptor generation for machine learning.") >> + (license license:bsd-3))) >> diff --git a/gnu/packages/patches/rdkit-cmake-external- >> dependencies.patch b/gnu/packages/patches/rdkit-cmake-external- >> dependencies.patch >> new file mode 100644 >> index 0000000000..5b73864f51 >> --- /dev/null >> +++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch >> @@ -0,0 +1,102 @@ >> +diff -ur a/External/FreeSASA/CMakeLists.txt >> b/External/FreeSASA/CMakeLists.txt >> +--- a/External/FreeSASA/CMakeLists.txt >> ++++ b/External/FreeSASA/CMakeLists.txt >> +@@ -10,7 +10,7 @@ >> + endif() >> + endif() >> + >> +-if(needDownload) >> ++if(FALSE) >> + # don't actually use the md5 here >> + set(FREESASA_VERSION "2.0.3") >> + set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa- >> ${FREESASA_VERSION}") >> +@@ -66,24 +66,24 @@ >> + endif() >> + >> + set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h) >> +-file(READ ${freesasa_h} freesasa_h_data) >> ++#file(READ ${freesasa_h} freesasa_h_data) >> + string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include >> <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}") >> + string(REGEX REPLACE >> "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L >> ][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" >> "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data >> "${freesasa_h_data}") >> +-file(WRITE ${freesasa_h} "${freesasa_h_data}") >> ++#file(WRITE ${freesasa_h} "${freesasa_h_data}") >> + >> + add_definitions(-DUSE_THREADS=0) >> + add_definitions(-DUSE_JSON=0) >> + add_definitions(-DUSE_XML=0) >> +-rdkit_library(freesasa_clib ${freesasa_clib_srcs}) >> +-target_compile_definitions(freesasa_clib PRIVATE >> RDKIT_FREESASALIB_BUILD) >> ++#rdkit_library(freesasa_clib ${freesasa_clib_srcs}) >> ++#target_compile_definitions(freesasa_clib PRIVATE >> RDKIT_FREESASALIB_BUILD) >> + >> + if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) >> + set_target_properties(freesasa_clib PROPERTIES >> WINDOWS_EXPORT_ALL_SYMBOLS TRUE) >> + endif() >> +-include_directories("${FREESASA_SRC_DIR}/src") >> ++#include_directories("${FREESASA_SRC_DIR}/src") >> + >> + rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED >> +- LINK_LIBRARIES freesasa_clib GraphMol ) >> ++ LINK_LIBRARIES -lfreesasa GraphMol ) >> + target_compile_definitions(FreeSASALib PRIVATE >> RDKIT_FREESASALIB_BUILD) >> + >> + rdkit_headers(RDFreeSASA.h DEST GraphMol) >> +diff -ur a/External/YAeHMOP/CMakeLists.txt >> b/External/YAeHMOP/CMakeLists.txt >> +--- a/External/YAeHMOP/CMakeLists.txt >> ++++ b/External/YAeHMOP/CMakeLists.txt >> +@@ -18,32 +18,32 @@ >> + >> + include_directories( ${RDKit_ExternalDir}/YAeHMOP ) >> + >> +-ExternalProject_Add(yaehmop_project >> +- GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git >> +- GIT_TAG master >> +- UPDATE_COMMAND "" >> +- PATCH_COMMAND "" >> +- PREFIX ${CMAKE_CURRENT_SOURCE_DIR} >> +- SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop" >> +- SOURCE_SUBDIR "tightbind" >> +- CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF - >> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} - >> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} - >> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} >> +- TEST_COMMAND "") >> +- >> +-include_directories(${PROJECT_BINARY_DIR}/include) >> +-link_directories(${PROJECT_BINARY_DIR}/lib) >> +-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project- >> build) >> +- >> +-set(EHT_PARAM_FILE >> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) >> +-install(FILES ${EHT_PARAM_FILE} >> +- DESTINATION ${RDKit_ShareDir}/Data >> +- COMPONENT data) >> ++#ExternalProject_Add(yaehmop_project >> ++# GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git >> ++# GIT_TAG master >> ++# UPDATE_COMMAND "" >> ++# PATCH_COMMAND "" >> ++# PREFIX ${CMAKE_CURRENT_SOURCE_DIR} >> ++# SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop" >> ++# SOURCE_SUBDIR "tightbind" >> ++# CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF - >> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} - >> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} - >> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} >> ++# TEST_COMMAND "") >> ++ >> ++#include_directories(${PROJECT_BINARY_DIR}/include) >> ++#link_directories(${PROJECT_BINARY_DIR}/lib) >> ++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project- >> build) >> ++ >> ++#set(EHT_PARAM_FILE >> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) >> ++#install(FILES ${EHT_PARAM_FILE} >> ++# DESTINATION ${RDKit_ShareDir}/Data >> ++# COMPONENT data) >> + >> +-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") >> +-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib >> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") >> ++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") >> ++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib >> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") >> + >> +-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht >> GraphMol ) >> ++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES - >> lyaehmop_eht GraphMol ) >> + target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD) >> +-add_dependencies(EHTLib yaehmop_project) >> ++#add_dependencies(EHTLib yaehmop_project) >> + rdkit_headers(EHTTools.h DEST GraphMol) >> + rdkit_catch_test(testEHTLib1 test1.cpp >> + LINK_LIBRARIES EHTLib FileParsers SmilesParse ) > Cheers
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 43953238cd..4b34a38797 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages backup) + #:use-module (gnu packages base) #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry) #:use-module (gnu packages cpp) #:use-module (gnu packages documentation) #:use-module (gnu packages flex) + #:use-module (gnu packages fonts) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages gl) #:use-module (gnu packages graphviz) + #:use-module (gnu packages gtk) #:use-module (gnu packages gv) #:use-module (gnu packages image) #:use-module (gnu packages maths) @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry) #:use-module (gnu packages qt) #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) + #:use-module (gnu packages sqlite) #:use-module (gnu packages stb) #:use-module (gnu packages tex) #:use-module (gnu packages web) @@ -1101,3 +1105,177 @@ (define-public ringdecomposerlib unique ring families, relevant cycles, the smallest set of smallest rings and other ring topology descriptions.") (license license:bsd-3))) + +(define-public rdkit + (package + (name "rdkit") + (version "2022.03.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rdkit/rdkit") + (commit + (string-append + "Release_" (string-replace-substring version "." "_"))))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9")) + (patches + (search-patches "rdkit-cmake-external-dependencies.patch")) + (modules '((guix build utils))) + (snippet + #~(begin + ;; Remove pickle files (only used in tests), + ;; as they are compiled programs + (for-each + (lambda (name) + (display (string-append name "\n")) + (delete-file name)) + (find-files "." "\\.pkl(\\.gz)?$")) + ;; Remove SQLite data files (can be generated) + (delete-file "Data/RDData.sqlt") + (delete-file "Data/RDTests.sqlt"))))) + (build-system cmake-build-system) + (arguments + (list + #:imported-modules (append %cmake-build-system-modules + '((guix build python-build-system))) + #:modules '((guix build cmake-build-system) + (guix build utils) + ((guix build python-build-system) + #:select (add-installed-pythonpath))) + #:configure-flags + #~(list + "-DRDK_BUILD_AVALON_SUPPORT=ON" + "-DRDK_BUILD_CAIRO_SUPPORT=ON" + "-DRDK_BUILD_CPP_TESTS=ON" + "-DRDK_BUILD_FREESASA_SUPPORT=ON" + "-DRDK_BUILD_INCHI_SUPPORT=ON" + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON" + (string-append "-DCATCH_DIR=" + #$(this-package-native-input "catch2") + "/include/catch2") + "-DRDK_INSTALL_DEV_COMPONENT=ON" + "-DRDK_INSTALL_INTREE=OFF" + "-DRDK_INSTALL_STATIC_LIBS=OFF" + (string-append + "-DRDK_OPTIMIZE_POPCNT=" + #$(let ((system (or (%current-target-system) + (%current-system)))) + (cond + ((string-prefix? "x86_64" system) "ON") + ((string-prefix? "i686" system) "ON") + (else "OFF")))) + "-DRDK_USE_BOOST_IOSTREAMS=ON" + "-DRDK_USE_FLEXBISON=ON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'copy-external-dependencies + (lambda _ + (symlink + (string-append + #$(this-package-input "font-comic-neue") + "/share/fonts/truetype/ComicNeue-Regular.ttf") + "Data/Fonts/ComicNeue-Regular.ttf"))) + (add-after 'copy-external-dependencies 'patch-source + (lambda _ + (substitute* "External/AvalonTools/CMakeLists.txt" + (("^if\\(NOT RDK_BUILD" orig) + (string-append "if(0)\n" orig)) + (("include_directories.*AVALON_SRC_PATH.*") + (string-append "endif()\ninclude_directories(" + #$avalontoolkit "/include/avalontoolkit)\n")) + (("LINK_LIBRARIES avalon_clib") + (string-append + "LINK_LIBRARIES -L" #$avalontoolkit "/lib -lavalontoolkit"))) + (let ((port + (open-file "External/RingFamilies/dummy.cpp" "w"))) + (display "" port) + (close port)) + (let ((port + (open-file "External/RingFamilies/CMakeLists.txt" "w"))) + (display (string-append + "rdkit_library(RingDecomposerLib dummy.cpp SHARED" + " LINK_LIBRARIES -lRingDecomposerLib)\n" + "set(RDK_URF_LIBS RingDecomposerLib CACHE STRING \"\" FORCE)\n") + port) + (close port)) + (substitute* "Code/GraphMol/MolInterchange/CMakeLists.txt" + (("if\\(NOT" orig) + (string-append "if(0)\n" orig)) + (("^include_directories.*") "endif()\n")) + (substitute* "External/YAeHMOP/EHTTools.cpp" + (("<yaehmop/tightbind/bind.h>") "<yaehmop/bind.h>")))) + (add-after 'unpack 'fix-inchi-include + (lambda _ + (substitute* "Code/cmake/Modules/FindInchi.cmake" + (("inchi_api.h.*\\)") "inchi/inchi_api.h)") + (("INCHI_LIBRARY NAMES.*\\)") + "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)") + (("find_library" prev) + (string-append + "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n" + prev))) + (substitute* "External/INCHI-API/inchi.cpp" + (("<inchi_api.h>") "<inchi/inchi_api.h>")))) + (add-before 'build 'enable-bytecode-determinism + (lambda _ + (setenv "PYTHONHASHSEED" "0") + (setenv "PYTHONDONTWRITEBYTECODE" "1"))) + (add-after 'install 'pre-check + (lambda* (#:key inputs outputs #:allow-other-keys) + (with-directory-excursion "../source" + (invoke "sqlite3" "Data/RDData.sqlt" + ".read rdkit/Dbase/test_data/RDData.sqlite") + (invoke "sqlite3" "Data/RDTests.sqlt" + ".read rdkit/Dbase/test_data/RDTests.sqlite") + (setenv "RDBASE" (canonicalize-path "."))) + (add-installed-pythonpath inputs outputs))) + (delete 'check) + (add-after 'pre-check 'check + (lambda* (#:key tests? parallel-tests? #:allow-other-keys) + (when tests? + (let ((job-count (number->string + (if parallel-tests? (parallel-job-count) 1)))) + (invoke + "ctest" "-j" job-count + "-E" (string-append + "(" (string-join + '(;; need pickled data + "(pyDiscreteValueVect" "pySparseIntVect" + "graphmoltestPickler" "pyPartialCharges" + "substructLibraryTest" "pyFeatures" + "pythonTestDirML" "pythonTestDirChem" + ;; Catching Python exception fails + "pyRanker)") "|") ")"))))))))) + (native-inputs + (list bison + boost + catch2 + eigen + flex + freesasa + pkg-config + rapidjson + tar)) + (inputs + (list avalontoolkit + cairo + coordgenlibs + font-comic-neue + freetype + inchi + maeparser + python + ringdecomposerlib + sqlite + yaehmop)) + (propagated-inputs + (list python-numpy python-cairocffi python-pillow)) + (home-page "https://rdkit.org/") + (synopsis "Collection of cheminformatics software") + (description "RDKit is a C++ and Python library for cheminformatics, which +includes (among other things) the analysis and modification of molecules in 2D +and 3D and descriptor generation for machine learning.") + (license license:bsd-3))) diff --git a/gnu/packages/patches/rdkit-cmake-external-dependencies.patch b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch new file mode 100644 index 0000000000..5b73864f51 --- /dev/null +++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch @@ -0,0 +1,102 @@ +diff -ur a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt +--- a/External/FreeSASA/CMakeLists.txt ++++ b/External/FreeSASA/CMakeLists.txt +@@ -10,7 +10,7 @@ + endif() + endif() + +-if(needDownload) ++if(FALSE) + # don't actually use the md5 here + set(FREESASA_VERSION "2.0.3") + set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-${FREESASA_VERSION}") +@@ -66,24 +66,24 @@ + endif() + + set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h) +-file(READ ${freesasa_h} freesasa_h_data) ++#file(READ ${freesasa_h} freesasa_h_data) + string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}") + string(REGEX REPLACE "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data "${freesasa_h_data}") +-file(WRITE ${freesasa_h} "${freesasa_h_data}") ++#file(WRITE ${freesasa_h} "${freesasa_h_data}") + + add_definitions(-DUSE_THREADS=0) + add_definitions(-DUSE_JSON=0) + add_definitions(-DUSE_XML=0) +-rdkit_library(freesasa_clib ${freesasa_clib_srcs}) +-target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD) ++#rdkit_library(freesasa_clib ${freesasa_clib_srcs}) ++#target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD) + + if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) + set_target_properties(freesasa_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + endif() +-include_directories("${FREESASA_SRC_DIR}/src") ++#include_directories("${FREESASA_SRC_DIR}/src") + + rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED +- LINK_LIBRARIES freesasa_clib GraphMol ) ++ LINK_LIBRARIES -lfreesasa GraphMol ) + target_compile_definitions(FreeSASALib PRIVATE RDKIT_FREESASALIB_BUILD) + + rdkit_headers(RDFreeSASA.h DEST GraphMol) +diff -ur a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt +--- a/External/YAeHMOP/CMakeLists.txt ++++ b/External/YAeHMOP/CMakeLists.txt +@@ -18,32 +18,32 @@ + + include_directories( ${RDKit_ExternalDir}/YAeHMOP ) + +-ExternalProject_Add(yaehmop_project +- GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git +- GIT_TAG master +- UPDATE_COMMAND "" +- PATCH_COMMAND "" +- PREFIX ${CMAKE_CURRENT_SOURCE_DIR} +- SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop" +- SOURCE_SUBDIR "tightbind" +- CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} +- TEST_COMMAND "") +- +-include_directories(${PROJECT_BINARY_DIR}/include) +-link_directories(${PROJECT_BINARY_DIR}/lib) +-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build) +- +-set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) +-install(FILES ${EHT_PARAM_FILE} +- DESTINATION ${RDKit_ShareDir}/Data +- COMPONENT data) ++#ExternalProject_Add(yaehmop_project ++# GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git ++# GIT_TAG master ++# UPDATE_COMMAND "" ++# PATCH_COMMAND "" ++# PREFIX ${CMAKE_CURRENT_SOURCE_DIR} ++# SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop" ++# SOURCE_SUBDIR "tightbind" ++# CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} ++# TEST_COMMAND "") ++ ++#include_directories(${PROJECT_BINARY_DIR}/include) ++#link_directories(${PROJECT_BINARY_DIR}/lib) ++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build) ++ ++#set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) ++#install(FILES ${EHT_PARAM_FILE} ++# DESTINATION ${RDKit_ShareDir}/Data ++# COMPONENT data) + +-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") +-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") ++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") ++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") + +-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol ) ++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol ) + target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD) +-add_dependencies(EHTLib yaehmop_project) ++#add_dependencies(EHTLib yaehmop_project) + rdkit_headers(EHTTools.h DEST GraphMol) + rdkit_catch_test(testEHTLib1 test1.cpp + LINK_LIBRARIES EHTLib FileParsers SmilesParse )