diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/chemistry.scm | 150 | ||||
| -rw-r--r-- | gnu/packages/patches/rdkit-unbundle-external-dependencies.patch | 384 |
2 files changed, 534 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index da65c90152..d0582c4b6f 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -34,6 +34,7 @@ #: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) @@ -42,10 +43,12 @@ #: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) @@ -57,6 +60,7 @@ #: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 tex) #:use-module (gnu packages web) @@ -1079,3 +1083,149 @@ and rendering molecules.") unique ring families, relevant cycles, the smallest set of smallest rings and other ring topology descriptions.") (license license:bsd-3))) + +(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-unbundle-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)?$")) + ;; Remove SQLite data files (can be generated) + (delete-file "Data/RDData.sqlt") + (delete-file "Data/RDTests.sqlt"))))) + (build-system cmake-build-system) + (arguments + (list + #:imported-modules (append %cmake-build-system-modules + '((guix build python-build-system))) + #:modules '((guix build cmake-build-system) + (guix build utils) + ((guix build python-build-system) + #:select (add-installed-pythonpath))) + #:configure-flags + #~(list "-DRDK_BUILD_AVALON_SUPPORT=ON" + "-DRDK_BUILD_CAIRO_SUPPORT=ON" + "-DRDK_BUILD_FREESASA_SUPPORT=ON" + "-DRDK_BUILD_INCHI_SUPPORT=ON" + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON" + (string-append "-DCATCH_DIR=" + (search-input-directory %build-inputs + "/include/catch2")) + "-DRDK_INSTALL_INTREE=OFF" + "-DRDK_INSTALL_STATIC_LIBS=OFF" + (string-append + "-DRDK_OPTIMIZE_POPCNT=" + #$(let ((system (or (%current-target-system) + (%current-system)))) + (cond + ((string-prefix? "x86_64" system) "ON") + ((string-prefix? "i686" system) "ON") + (else "OFF")))) + "-DRDK_USE_FLEXBISON=ON" + (string-append + "-DCMAKE_INCLUDE_PATH=" + (search-input-directory %build-inputs "/include/avalontoolkit"))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'copy-external-dependencies + (lambda _ + (symlink + (string-append + (search-input-file + %build-inputs "/share/fonts/truetype/ComicNeue-Regular.ttf")) + "Data/Fonts/ComicNeue-Regular.ttf"))) + (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>")))) + (add-before 'build 'enable-bytecode-determinism + (lambda _ + (setenv "PYTHONHASHSEED" "0") + (setenv "PYTHONDONTWRITEBYTECODE" "1"))) + (add-after 'install 'pre-check + (lambda* (#:key inputs outputs #:allow-other-keys) + (with-directory-excursion "../source" + (invoke "sqlite3" "Data/RDData.sqlt" + ".read rdkit/Dbase/test_data/RDData.sqlite") + (invoke "sqlite3" "Data/RDTests.sqlt" + ".read rdkit/Dbase/test_data/RDTests.sqlite") + (setenv "RDBASE" (canonicalize-path "."))) + (add-installed-pythonpath inputs outputs))) + (delete 'check) + (add-after 'pre-check 'check + (lambda* (#:key tests? parallel-tests? #:allow-other-keys) + (when tests? + (let ((job-count (number->string + (if parallel-tests? (parallel-job-count) 1)))) + (invoke + "ctest" "-j" job-count + "-E" (string-append + "(" + (string-join + '(;; need pickled data + "pyDiscreteValueVect" "pySparseIntVect" + "graphmoltestPickler" "pyPartialCharges" + "substructLibraryTest" "pyFeatures" + "pythonTestDirML" "pythonTestDirChem" + ;; Catching Python exception fails + "pyRanker") "|") + ")"))))))))) + (inputs + (list avalon-toolkit + cairo + coordgenlibs + font-comic-neue + freetype + inchi + maeparser + python + ringdecomposerlib + sqlite + yaehmop)) + (native-inputs + (list bison + boost + catch2 + eigen + flex + freesasa + pkg-config + rapidjson + tar)) + (propagated-inputs + (list python-numpy python-cairocffi python-pillow)) + (home-page "https://rdkit.org/") + (synopsis "Collection of cheminformatics software") + (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.") + (license license:bsd-3))) diff --git a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch new file mode 100644 index 0000000000..8ee0611d3b --- /dev/null +++ b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch @@ -0,0 +1,384 @@ +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 { |