Subject: [bug#58261] [PATCH 11/11] gnu: Add rdkit.

From: David Elsing <[email-masked]>
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