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[bug#58261] [PATCH 11/11] gnu: Add rdkit.
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From: |
David Elsing |
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Subject: |
[bug#58261] [PATCH 11/11] gnu: Add rdkit. |
|
Date: |
Mon, 3 Oct 2022 00:19:56 +0000 |
* 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"
+ (("<yaehmop/tightbind/bind.h>") "<yaehmop/bind.h>"))
+ #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"
+ (("<inchi_api.h>") "<inchi/inchi_api.h>"))
+ #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 ${freesasa_h} freesasa_h_data)
+ string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include
<RDGeneral/export.h>" freesasa_h_data "${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 )
--
2.37.0
[bug#58261] [PATCH 08/11] gnu: Add maeparser., David Elsing, 2022/10/02
[bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind., David Elsing, 2022/10/02