@@ 1073,7 1073,7 @@ other ring topology descriptions.")
(define-public rdkit
(package
(name "rdkit")
- (version "2022.03.5")
+ (version "2023.09.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ 1084,7 1084,7 @@ other ring topology descriptions.")
(file-name (git-file-name name version))
(sha256
(base32
- "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
+ "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8"))
(patches
(search-patches "rdkit-unbundle-external-dependencies.patch"))
(modules '((guix build utils)))
@@ 1183,7 1183,10 @@ other ring topology descriptions.")
"substructLibraryTest" "pyFeatures"
"pythonTestDirML" "pythonTestDirChem"
;; Catching Python exception fails
- "pyRanker") "|")
+ "pyRanker"
+ ;; Flaky test depending on floating point rounding
+ "testConrec"
+ ) "|")
")")))))))))
(inputs
(list avalon-toolkit
@@ 1200,7 1203,7 @@ other ring topology descriptions.")
(native-inputs
(list bison
boost
- catch2
+ catch2-3
eigen
flex
freesasa
@@ 1214,4 1217,8 @@ other ring topology descriptions.")
(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.")
+ ;; For 32 bit systems, there is a bug in Boost.Python:
+ ;; https://github.com/boostorg/python/issues/312. Additionally, several
+ ;; other test fail.
+ (supported-systems %64bit-supported-systems)
(license license:bsd-3)))
@@ 58,99 58,82 @@ diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLis
index 3e31195fc..314ba35b5 100644
--- a/External/AvalonTools/CMakeLists.txt
+++ b/External/AvalonTools/CMakeLists.txt
-@@ -2,107 +2,14 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
+@@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
return()
endif(NOT RDK_BUILD_AVALON_SUPPORT)
+-set(AVALON_VERSION "2.0.5-pre.3")
-if(NOT DEFINED AVALONTOOLS_DIR)
-- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution")
-- set(fileToPatch "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution/common/reaccsio.c")
+- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}")
+- set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c")
- set(needDownload "TRUE")
-- if(EXISTS "${fileToPatch}")
-- file(READ "${fileToPatch}" buffer)
-- if("${buffer}" MATCHES "//MyFree\\(\\(char \\*\\)tempdir\\);")
-- set(needDownload "FALSE")
-- endif()
+- if(EXISTS "${fileToCheck}")
+- set(needDownload "FALSE")
- endif()
-else()
- string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR})
- set(needDownload "FALSE")
-endif()
-
--set(AVALON_SRC_PATH ${AVALONTOOLS_DIR}/common)
+-set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C")
+-set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common")
+-set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include")
+-set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs")
-
-if(needDownload)
- if(NOT DEFINED AVALONTOOLS_URL)
-- set(AVALONTOOLS_URL "https://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar")
+- set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz")
- endif()
- if(NOT DEFINED AVALONTOOLS_MD5SUM)
-- set(AVALONTOOLS_MD5SUM "092a94f421873f038aa67d4a6cc8cb54")
+- set(AVALONTOOLS_MD5SUM "7a20c25a7e79f3344e0f9f49afa03351")
- endif()
- if(NOT DEFINED AVALONTOOLS_BASE)
- string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}")
- endif()
- downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM})
-- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf
-- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_1.2.0.source.tar
+- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf
+- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-- # apply patch to AvalonTools
-- configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
-- file(READ "${fileToPatch}" buffer)
-- string(REGEX REPLACE "MyFree\\(\\(char \\*\\)tempdir\\);"
-- "//MyFree((char *)tempdir);" buffer "${buffer}")
-- file(WRITE "${fileToPatch}" "${buffer}")
--endif()
-
- if (MSVC)
- add_definitions("/D_CRT_SECURE_NO_WARNINGS")
- add_compile_options(/wd4224 /wd4101 /wd4018 /wd4996 /wd4244 /wd4305 /wd4013 /wd4146 /wd4334 /wd4715 /wd4715 /nologo)
- endif(MSVC)
-
--set(avalon_clib_srcs ${AVALON_SRC_PATH}/layout.c
-- ${AVALON_SRC_PATH}/symboltable.c
-- ${AVALON_SRC_PATH}/patclean.c
-- ${AVALON_SRC_PATH}/utilities.c
-- ${AVALON_SRC_PATH}/symbol_lists.c
-- ${AVALON_SRC_PATH}/stereo.c
-- ${AVALON_SRC_PATH}/set.c
-- ${AVALON_SRC_PATH}/perceive.c
-- ${AVALON_SRC_PATH}/local.c
-- ${AVALON_SRC_PATH}/graph.c
-- ${AVALON_SRC_PATH}/geometry.c
-- ${AVALON_SRC_PATH}/forio.c
-- ${AVALON_SRC_PATH}/depictutil.c
-- ${AVALON_SRC_PATH}/denormal.c
-- ${AVALON_SRC_PATH}/casutils.c
-- ${AVALON_SRC_PATH}/ssmatch.c
-- ${AVALON_SRC_PATH}/rtutils.c
-- ${AVALON_SRC_PATH}/smi2mol.c
-- ${AVALON_SRC_PATH}/didepict.c
-- ${AVALON_SRC_PATH}/pattern.c
-- ${AVALON_SRC_PATH}/canonizer.c
-- ${AVALON_SRC_PATH}/aacheck.c
-- ${AVALON_SRC_PATH}/fixcharges.c
-- ${AVALON_SRC_PATH}/struchk.c
-- ${AVALON_SRC_PATH}/reaccsio.c
-- ${AVALON_SRC_PATH}/hashcode.c
-- )
--
--# we need this to ensure that builds continue
--# to work on linux systems with older versions
--# of glibc when we're building with gcc-4.1.
--# Without this flag, we'll endup requiring
--# glibc 2.7.
--if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
-- add_definitions(-D_GNU_SOURCE=1)
-endif()
-
--if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
-- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-return-type -Wno-implicit-function-declaration -Wno-absolute-value -Wno-parentheses -Wno-logical-op-parentheses -Wno-dangling-else -Wno-format")
+-if(CMAKE_C_COMPILER_ID STREQUAL "GNU")
+- add_compile_options(-Wno-format-security -Wformat=0 -Wstringop-overflow=0 -Wformat-overflow=0 -Wno-unused-result )
-endif()
--if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-result -Wformat-overflow=0 -Wformat=0 -Wno-format-security -Wno-implicit-function-declaration")
+-if(CMAKE_C_COMPILER_ID STREQUAL "Clang")
+- add_compile_options(-Wno-absolute-value -Wno-return-type -Wno-tautological-overlap-compare)
-endif()
+-if (MSVC)
+- add_definitions("/D_CRT_SECURE_NO_WARNINGS")
+- add_compile_options(/wd4018 /wd4101 /wd4146 /wd4334 /wd4477 /wd4715 /wd4716 /wd4996 /nologo)
+-endif(MSVC)
-
--
+-set(avalon_clib_srcs ${AVALON_COMMON_PATH}/layout.c
+- ${AVALON_COMMON_PATH}/symboltable.c
+- ${AVALON_COMMON_PATH}/patclean.c
+- ${AVALON_COMMON_PATH}/utilities.c
+- ${AVALON_COMMON_PATH}/symbol_lists.c
+- ${AVALON_COMMON_PATH}/stereo.c
+- ${AVALON_COMMON_PATH}/set.c
+- ${AVALON_COMMON_PATH}/perceive.c
+- ${AVALON_COMMON_PATH}/local.c
+- ${AVALON_COMMON_PATH}/graph.c
+- ${AVALON_COMMON_PATH}/geometry.c
+- ${AVALON_COMMON_PATH}/forio.c
+- ${AVALON_COMMON_PATH}/depictutil.c
+- ${AVALON_COMMON_PATH}/denormal.c
+- ${AVALON_COMMON_PATH}/casutils.c
+- ${AVALON_COMMON_PATH}/ssmatch.c
+- ${AVALON_COMMON_PATH}/rtutils.c
+- ${AVALON_COMMON_PATH}/smi2mol.c
+- ${AVALON_COMMON_PATH}/didepict.c
+- ${AVALON_COMMON_PATH}/pattern.c
+- ${AVALON_COMMON_PATH}/canonizer.c
+- ${AVALON_COMMON_PATH}/aacheck.c
+- ${AVALON_COMMON_PATH}/fixcharges.c
+- ${AVALON_PROGRAMS_PATH}/struchk.c
+- ${AVALON_COMMON_PATH}/reaccsio.c
+- ${AVALON_COMMON_PATH}/hashcode.c
+- )
-
-rdkit_library(avalon_clib ${avalon_clib_srcs})
-target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
@@ 159,11 142,11 @@ index 3e31195fc..314ba35b5 100644
-endif()
-
-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
--include_directories(${AVALON_SRC_PATH})
+-include_directories(${AVALON_INCLUDE_PATH})
-
rdkit_library(AvalonLib AvalonTools.cpp SHARED
- LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
-+ LINK_LIBRARIES -lavalontoolkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
++ LINK_LIBRARIES -lavalon4rdkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD)
rdkit_headers(AvalonTools.h DEST GraphMol)
rdkit_test(testAvalonLib1 test1.cpp
@@ 278,7 261,7 @@ diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeL
index 08dd1fe04..66ecd5834 100644
--- a/External/RingFamilies/CMakeLists.txt
+++ b/External/RingFamilies/CMakeLists.txt
-@@ -1,47 +1,6 @@
+@@ -1,47 +1,7 @@
-add_custom_target(ringdecomposerlib_support ALL)
-
if(NOT RDK_USE_URF)
@@ 324,10 307,9 @@ index 08dd1fe04..66ecd5834 100644
-rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "")
-
-
--set(RDK_URF_LIBS RingDecomposerLib
-- CACHE STRING "the libraries for the URF calculation" FORCE)
+rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib)
-+set(RDK_URF_LIBS RingDecomposerLib CACHE STRING "" FORCE)
+ set(RDK_URF_LIBS RingDecomposerLib
+ CACHE STRING "the libraries for the URF calculation" FORCE)
diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp
new file mode 100644
index 000000000..e69de29bb
@@ 335,40 317,60 @@ diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
index f1027b3bd..8bee2f910 100644
--- a/External/YAeHMOP/CMakeLists.txt
+++ b/External/YAeHMOP/CMakeLists.txt
-@@ -18,32 +18,8 @@ endif()
+@@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT)
- include_directories( ${RDKit_ExternalDir}/YAeHMOP )
+ add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT)
--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)
+-if(NOT DEFINED YAEHMOP_DIR)
+- set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop")
+-endif()
+-
+-if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h")
+- set(RELEASE_NO "2023.03.1")
+- set(MD5 "e6450f13e02c54d024233b993c3c7ff6")
+- downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz"
+- "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5})
+- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+- ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz
+- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-
+- file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}")
+-else()
+- message("-- Found YAeHMOP source in ${YAEHMOP_DIR}")
+-endif()
+-
+-set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/..
+- CACHE STRING "yaehmop Include File" FORCE)
+-include_directories(${yaehmop_INCLUDE_DIRS})
+-
+-if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN)
+- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+-endif()
+-if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+-endif()
+-
+-# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency)
+-add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True)
+-
+-# set install dir for the yaehmop library:
+-INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets
+- DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
+- COMPONENT runtime )
+-
+-
+-
-
-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")
--
-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)
rdkit_headers(EHTTools.h DEST GraphMol)
rdkit_catch_test(testEHTLib1 test1.cpp
- LINK_LIBRARIES EHTLib FileParsers SmilesParse )
diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp
index 7a229f51f..71033dc5c 100644
--- a/External/YAeHMOP/EHTTools.cpp
@@ 382,3 384,23 @@ index 7a229f51f..71033dc5c 100644
}
namespace RDKit {
+@@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId,
+ }
+
+ } // end of namespace EHTTools
+-} // end of namespace RDKit
+\ No newline at end of file
++} // end of namespace RDKit
+diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt
+index 759a9f360..114d24532 100644
+--- a/External/YAeHMOP/Wrap/CMakeLists.txt
++++ b/External/YAeHMOP/Wrap/CMakeLists.txt
+@@ -4,6 +4,8 @@ rdkit_python_extension(rdEHTTools
+ DEST Chem
+ LINK_LIBRARIES
+ EHTLib )
++
++target_include_directories(rdEHTTools PRIVATE ${RDKit_ExternalDir}/YAeHMOP)
+
+ add_pytest(pyEHTTools
+ ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)