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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=posteo.net header.s=2017 header.b=L2N56gwQ; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.95 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=posteo.net header.s=2017 header.b=L2N56gwQ; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 6A36D138B5 X-Spam-Score: 6.95 X-Migadu-Scanner: scn1.migadu.com X-TUID: mB5VHDiuMxLK * gnu/packages/chemistry.scm (rdkit): New variable. --- gnu/packages/chemistry.scm | 198 ++++++++++++++++++ .../rdkit-cmake-external-dependencies.patch | 102 +++++++++ 2 files changed, 300 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 a39deff4bf..869cf264e3 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 web) #:use-module (gnu packages xml) @@ -899,3 +903,197 @@ (define-public yaehmop-tightbind (description "@code{YAeHMOP} contains a program and library for performing extended Hückel calculations.") (license license:bsd-2))) + +(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)?$")) + ;; Remove SQLite data files (can be generated) + (delete-file "Data/RDData.sqlt") + (delete-file "Data/RDTests.sqlt") + #t)))) + (build-system cmake-build-system) + (native-inputs + `(("bison" ,bison) + ("boost" ,boost) + ("catch2" ,catch2) + ("eigen" ,eigen) + ("flex" ,flex) + ("freesasa" ,freesasa) + ("pkg-config" ,pkg-config) + ("rapidjson" ,rapidjson) + ("tar" ,tar) + ("avalontoolkit-src" + ,(let ((version "1.2.0")) + (origin + (method url-fetch) + (uri (string-append + "http://sourceforge.net/projects/avalontoolkit/files/" + "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_" + version ".source.tar")) + (sha256 + (base32 + "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv")) + (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26))) + (snippet + #~(begin + (chdir "..") + (delete-file-recursively "StandardFiles") + (delete-file-recursively "SourceDistribution/java") + #t))))) + ("ringdecomposerlib-src" + ,(let ((version "1.1.3")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rareylab/RingDecomposerLib") + (commit (string-append "v" version "_rdkit")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi"))))))) + (inputs + (list cairo + coordgenlibs + font-comic-neue + freetype + inchi + maeparser + python + sqlite + yaehmop-tightbind)) + (propagated-inputs + (list python-numpy python-cairocffi python-pillow)) + (arguments + (list + #:imported-modules (append %cmake-build-system-modules + '((guix build python-build-system))) + #:modules '((guix build cmake-build-system) + (guix build utils) + ((guix build python-build-system) + #:select (add-installed-pythonpath))) + #:configure-flags + #~(list + "-DRDK_BUILD_AVALON_SUPPORT=ON" + "-DRDK_BUILD_CAIRO_SUPPORT=ON" + "-DRDK_BUILD_CPP_TESTS=ON" + "-DRDK_BUILD_FREESASA_SUPPORT=ON" + "-DRDK_BUILD_INCHI_SUPPORT=ON" + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON" + (string-append "-DCATCH_DIR=" + #$(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") + (symlink #$(this-package-native-input "rapidjson") + "External/rapidjson-1.1.0") + (invoke "tar" "xvf" + #$(this-package-native-input "avalontoolkit-src") + "-C" "External/AvalonTools") + (symlink #$(this-package-native-input "ringdecomposerlib-src") + "External/RingFamilies/RingDecomposerLib") + #t)) + (add-after 'copy-external-dependencies 'patch-source + (lambda _ + (with-directory-excursion "External/AvalonTools" + (invoke "patch" "-p0" "-i" + "AvalonToolkit_1.2_patch.txt")) + (substitute* "External/YAeHMOP/EHTTools.cpp" + (("") "")) + #t)) + (add-after 'unpack 'create-sqlite-data-files + (lambda _ + (invoke "sqlite3" "Data/RDData.sqlt" + ".read rdkit/Dbase/test_data/RDData.sqlite") + (invoke "sqlite3" "Data/RDTests.sqlt" + ".read rdkit/Dbase/test_data/RDTests.sqlite") + #t)) + (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" + (("") "")) + #t)) + (add-before 'build 'enable-bytecode-determinism + (lambda _ + (setenv "PYTHONHASHSEED" "0") + (setenv "PYTHONDONTWRITEBYTECODE" "1") + #t)) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs tests? parallel-tests? + #:allow-other-keys) + (when tests? + (let + ((job-count (number->string + (or (and parallel-tests? + (parallel-job-count)) + 1)))) + (setenv "RDBASE" (canonicalize-path "../source")) + (add-installed-pythonpath inputs outputs) + (invoke "ctest" + "-j" job-count + "-E" (string-append + ;; need pickled data + "(pyDiscreteValueVect" "|pySparseIntVect" + "|graphmoltestPickler" "|pyPartialCharges" + "|substructLibraryTest" "|pyFeatures" + "|pythonTestDirML" "|pythonTestDirChem" + ;; Catching Python exception fails + "|pyRanker)")))) + #t))))) + (home-page "https://rdkit.org/") + (synopsis "Open-Source Cheminformatics Software") + (description "RDKit is a collection of cheminformatics and +machine-learning software written in C++ and Python.") + (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 ${freesasa_h} freesasa_h_data) + string(REGEX REPLACE "(#include )" "\\1\n#include " freesasa_h_data "${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 ) -- 2.37.0