me/guix
Archived
1
0
Fork 0
Code Activity

gnu: Add rdkit.

Browse source 
* gnu/packages/chemistry.scm (rdkit): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
This commit is contained in:
David Elsing 2022-10-13 21:04:24 +00:00 • committed by Liliana Marie Prikler
parent 175d1a0151
commit 18f95f9335
No known key found for this signature in database
GPG key ID: 442A84B8C70E2F87
2 changed files with 534 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

150
gnu/packages/chemistry.scm
View file

@ -34,6 +34,7 @@
#:use-module (gnu packages algebra) #:use-module (gnu packages algebra)
#:use-module (gnu packages autotools) #:use-module (gnu packages autotools)
#:use-module (gnu packages backup) #:use-module (gnu packages backup)
#:use-module (gnu packages base)
#:use-module (gnu packages bison) #:use-module (gnu packages bison)
#:use-module (gnu packages boost) #:use-module (gnu packages boost)
#:use-module (gnu packages check) #:use-module (gnu packages check)
@ -42,10 +43,12 @@
#:use-module (gnu packages cpp) #:use-module (gnu packages cpp)
#:use-module (gnu packages documentation) #:use-module (gnu packages documentation)
#:use-module (gnu packages flex) #:use-module (gnu packages flex)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils) #:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc) #:use-module (gnu packages gcc)
#:use-module (gnu packages gl) #:use-module (gnu packages gl)
#:use-module (gnu packages graphviz) #:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages gv) #:use-module (gnu packages gv)
#:use-module (gnu packages image) #:use-module (gnu packages image)
#:use-module (gnu packages maths) #:use-module (gnu packages maths)
@ -57,6 +60,7 @@
#:use-module (gnu packages qt) #:use-module (gnu packages qt)
#:use-module (gnu packages serialization) #:use-module (gnu packages serialization)
#:use-module (gnu packages sphinx) #:use-module (gnu packages sphinx)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages stb) #:use-module (gnu packages stb)
#:use-module (gnu packages tex) #:use-module (gnu packages tex)
#:use-module (gnu packages web) #:use-module (gnu packages web)
@ -1079,3 +1083,149 @@ and rendering molecules.")
unique ring families, relevant cycles, the smallest set of smallest rings and unique ring families, relevant cycles, the smallest set of smallest rings and
other ring topology descriptions.") other ring topology descriptions.")
(license license:bsd-3))) (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)))

384
gnu/packages/patches/rdkit-unbundle-external-dependencies.patch Normal file
View file

@ -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 {