guix/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch

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
@@ -2,90 +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 "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}")
-  set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c")
-  set(needDownload "TRUE")
-  if(EXISTS "${fileToCheck}")
-    set(needDownload "FALSE")
-  endif()
-else()
-  string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR})
-  set(needDownload "FALSE")
-endif()
-
-set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C")
-set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common")
-set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include")
-set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs")
-
-if(needDownload)
-  if(NOT DEFINED AVALONTOOLS_URL)
-    set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz")
-  endif()
-  if(NOT DEFINED AVALONTOOLS_MD5SUM)
-    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 xzf
-    ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-endif()
-
-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_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 ${avalon_clib_srcs})
-target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
-  set_target_properties(avalon_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
-endif()
-
-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-include_directories(${AVALON_INCLUDE_PATH})
-
 rdkit_library(AvalonLib AvalonTools.cpp SHARED 
-     LINK_LIBRARIES avalon_clib 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
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 +1,7 @@
-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 "")
-
-
+rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib)
 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
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
@@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT)
 
 add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT)
 
-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)
-
-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)
 rdkit_headers(EHTTools.h DEST GraphMol)
 rdkit_catch_test(testEHTLib1 test1.cpp
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 {
@@ -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)