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guix-play/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
David Elsing 18f95f9335
gnu: Add rdkit. 
* gnu/packages/chemistry.scm (rdkit): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-10-15 12:05:15 +02:00

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Remove CMake code for downloading and builing bundled dependencies:
They are packaged separately as rapidjson, avalon-toolkit, freesasa,
ringdecomposerlib and yaehmop.
diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt
index 1673386a4..c3504e6f1 100644
--- a/Code/GraphMol/MolInterchange/CMakeLists.txt
+++ b/Code/GraphMol/MolInterchange/CMakeLists.txt
@@ -1,18 +1,3 @@
-
-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
- "badd12c511e081fec6c89c43a7027bce")
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
-else()
- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
-endif()
-
-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include)
-
-
rdkit_library(MolInterchange
Parser.cpp Writer.cpp
LINK_LIBRARIES GraphMol)
diff --git a/External/AvalonTools/AvalonTools.cpp b/External/AvalonTools/AvalonTools.cpp
index e6c382123..d83d80668 100644
--- a/External/AvalonTools/AvalonTools.cpp
+++ b/External/AvalonTools/AvalonTools.cpp
@@ -24,15 +24,15 @@
#include "AvalonTools.h"
extern "C" {
-#include "local.h"
-#include "reaccs.h"
-#include "reaccsio.h"
-#include "utilities.h"
-#include "ssmatch.h"
-#include "smi2mol.h"
-#include "canonizer.h"
-#include "layout.h"
-#include "struchk.h"
+#include <avalontoolkit/local.h>
+#include <avalontoolkit/reaccs.h>
+#include <avalontoolkit/reaccsio.h>
+#include <avalontoolkit/utilities.h>
+#include <avalontoolkit/ssmatch.h>
+#include <avalontoolkit/smi2mol.h>
+#include <avalontoolkit/canonizer.h>
+#include <avalontoolkit/layout.h>
+#include <avalontoolkit/struchk.h>
extern int RunStruchk(struct reaccs_molecule_t **mpp,
struct data_line_t *data_list);
diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLists.txt
index 3e31195fc..314ba35b5 100644
--- a/External/AvalonTools/CMakeLists.txt
+++ b/External/AvalonTools/CMakeLists.txt
@@ -2,107 +2,14 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
return()
endif(NOT RDK_BUILD_AVALON_SUPPORT)
-if(NOT DEFINED AVALONTOOLS_DIR)
- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution")
- set(fileToPatch "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution/common/reaccsio.c")
- set(needDownload "TRUE")
- if(EXISTS "${fileToPatch}")
- file(READ "${fileToPatch}" buffer)
- if("${buffer}" MATCHES "//MyFree\\(\\(char \\*\\)tempdir\\);")
- set(needDownload "FALSE")
- endif()
- endif()
-else()
- string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR})
- set(needDownload "FALSE")
-endif()
-
-set(AVALON_SRC_PATH ${AVALONTOOLS_DIR}/common)
-
-if(needDownload)
- if(NOT DEFINED AVALONTOOLS_URL)
- set(AVALONTOOLS_URL "https://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar")
- endif()
- if(NOT DEFINED AVALONTOOLS_MD5SUM)
- set(AVALONTOOLS_MD5SUM "092a94f421873f038aa67d4a6cc8cb54")
- endif()
- if(NOT DEFINED AVALONTOOLS_BASE)
- string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${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
- 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")
-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")
-endif()
-
-
-
-rdkit_library(avalon_clib ${avalon_clib_srcs})
-target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
- set_target_properties(avalon_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
-endif()
-
-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-include_directories(${AVALON_SRC_PATH})
-
rdkit_library(AvalonLib AvalonTools.cpp SHARED
- LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
+ LINK_LIBRARIES -lavalontoolkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD)
rdkit_headers(AvalonTools.h DEST GraphMol)
rdkit_test(testAvalonLib1 test1.cpp
diff --git a/External/AvalonTools/Wrap/pyAvalonTools.cpp b/External/AvalonTools/Wrap/pyAvalonTools.cpp
index fb24c497e..31997bc0a 100644
--- a/External/AvalonTools/Wrap/pyAvalonTools.cpp
+++ b/External/AvalonTools/Wrap/pyAvalonTools.cpp
@@ -12,7 +12,7 @@
#include <boost/cstdint.hpp>
extern "C" {
-#include "struchk.h"
+#include <avalontoolkit/struchk.h>
}
namespace python = boost::python;
diff --git a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt
index 43dfbdc40..81165a143 100644
--- a/External/FreeSASA/CMakeLists.txt
+++ b/External/FreeSASA/CMakeLists.txt
@@ -2,88 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT)
return()
endif(NOT RDK_BUILD_FREESASA_SUPPORT)
-if(NOT DEFINED FREESASA_DIR)
- set(FREESASA_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa")
- set(needDownload "TRUE")
- if(EXISTS "${FREESASA_DIR}/src/freesasa.h")
- set(needDownload "FALSE")
- endif()
-endif()
-
-if(needDownload)
- # don't actually use the md5 here
- set(FREESASA_VERSION "2.0.3")
- set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-${FREESASA_VERSION}")
- if(NOT EXISTS "${FREESASA_SRC_DIR}/src")
- downloadAndCheckMD5("https://github.com/mittinatten/freesasa/releases/download/${FREESASA_VERSION}/freesasa-${FREESASA_VERSION}.tar.gz"
- "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz"
- "")
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
- message("Copying freesasa2.c to ${FREESASA_SRC_DIR}/src/freesasa2.c")
- file(COPY freesasa2.c DESTINATION ${FREESASA_SRC_DIR}/src/)
- else()
- message("FreeSASA found in ${FREESASA_SRC_DIR}, no download required")
- endif()
-endif()
-
-set(CMAKE_C_STANDARD 99)
-
-set (freesasa_clib_srcs
- ${FREESASA_SRC_DIR}/src/classifier.c
- ${FREESASA_SRC_DIR}/src/classifier_naccess.c
- ${FREESASA_SRC_DIR}/src/classifier_oons.c
- ${FREESASA_SRC_DIR}/src/classifier_protor.c
- ${FREESASA_SRC_DIR}/src/coord.c
- ${FREESASA_SRC_DIR}/src/freesasa2.c
- ${FREESASA_SRC_DIR}/src/lexer.c
- ${FREESASA_SRC_DIR}/src/log.c
- ${FREESASA_SRC_DIR}/src/nb.c
- ${FREESASA_SRC_DIR}/src/node.c
- ${FREESASA_SRC_DIR}/src/parser.c
- ${FREESASA_SRC_DIR}/src/pdb.c
- ${FREESASA_SRC_DIR}/src/rsa.c
- ${FREESASA_SRC_DIR}/src/sasa_lr.c
- ${FREESASA_SRC_DIR}/src/sasa_sr.c
- ${FREESASA_SRC_DIR}/src/selection.c
- ${FREESASA_SRC_DIR}/src/structure.c
- ${FREESASA_SRC_DIR}/src/util.c
- )
-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
- set(freesasa_additional_exports ${CMAKE_CURRENT_SOURCE_DIR}/additional_exports.def)
- file(WRITE ${freesasa_additional_exports}
- "EXPORTS\n"
- "freesasa_default_parameters DATA\n"
- "freesasa_protor_classifier DATA\n"
- "freesasa_naccess_classifier DATA\n"
- "freesasa_oons_classifier DATA\n"
- )
- set (freesasa_clib_srcs
- ${freesasa_clib_srcs}
- ${freesasa_additional_exports}
- )
-endif()
-
-set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
-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}")
-
-add_definitions(-DUSE_THREADS=0)
-add_definitions(-DUSE_JSON=0)
-add_definitions(-DUSE_XML=0)
-rdkit_library(freesasa_clib ${freesasa_clib_srcs})
-target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD)
-
-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
- set_target_properties(freesasa_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
-endif()
-include_directories("${FREESASA_SRC_DIR}/src")
-
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 --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeLists.txt
index 08dd1fe04..66ecd5834 100644
--- a/External/RingFamilies/CMakeLists.txt
+++ b/External/RingFamilies/CMakeLists.txt
@@ -1,47 +1,6 @@
-add_custom_target(ringdecomposerlib_support ALL)
-
if(NOT RDK_USE_URF)
return()
endif(NOT RDK_USE_URF)
-if(NOT DEFINED URFLIB_DIR)
- set(URFLIB_DIR "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib/src/RingDecomposerLib")
-endif()
-
-if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h")
- set(RELEASE_NO "1.1.3_rdkit")
- set(MD5 "e9a0bcdda8b921a35e812b9888a9a874")
- downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz"
- "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5})
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
- file(RENAME "RingDecomposerLib-${RELEASE_NO}" "RingDecomposerLib")
-else()
- message("-- Found RingDecomposerLib source in ${URFLIB_DIR}")
-endif()
-
-set(urflib_INCLUDE_DIRS ${URFLIB_DIR}
- CACHE STRING "RingDecomposerLib Include Dir" FORCE)
-file(GLOB URFSOURCES "${URFLIB_DIR}/*.c")
-
-#if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS)))
-if(WIN32)
- set (ringdecomposerlib_h ${URFLIB_DIR}/RingDecomposerLib.h)
- file(READ ${ringdecomposerlib_h} ringdecomposerlib_h_data)
- if (NOT "${ringdecomposerlib_h_data}" MATCHES "RDKIT_URFLIB_BUILD")
- string(REGEX REPLACE "(#if[ ]+\\([ ]*defined[ ]*\\([ ]*_WIN32[ ]*\\)[ ]*&&[ ]*)(defined\\([ ]*_MSC_VER[ ]*\\))" "\\1!defined( RDL_WIN_STATIC )" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}")
- string(REGEX REPLACE "([ ]*)(#define[ ]+RDL_API[ ]+__declspec)(\\([ ]*dllexport[ ]*\\))" "\\1#ifdef RDKIT_URFLIB_BUILD\n\\1\\1\\2\\3\n\\1#else\n\\1\\1\\2(dllimport)\n\\1#endif" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}")
- file(WRITE ${ringdecomposerlib_h} "${ringdecomposerlib_h_data}")
- endif()
-endif()
-rdkit_library(RingDecomposerLib ${URFSOURCES} SHARED)
-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS)))
- target_compile_definitions(RingDecomposerLib PRIVATE RDKIT_URFLIB_BUILD)
-endif()
-install(TARGETS RingDecomposerLib DESTINATION ${RDKit_LibDir})
-rdkit_headers(${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)
diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp
new file mode 100644
index 000000000..e69de29bb
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()
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)
-
-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
+++ b/External/YAeHMOP/EHTTools.cpp
@@ -10,7 +10,7 @@
#include <fstream>
extern "C" {
-#include <yaehmop/tightbind/bind.h>
+#include <yaehmop/bind.h>
}
namespace RDKit {
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