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Update embedded InChI to v1.05 (#1684)

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* Update download-inchi.sh for InChI 1.05

* Fix downloadAndCheckMD5

* Update FindInchi.cmake for InChI 1.05

* Update CMakeLists.txt for InChI 1.05
This commit is contained in:
Matt Swain
2017-12-20 05:36:16 +00:00
committed by Greg Landrum
parent c8deb705e7
commit 15c31e1f88
4 changed files with 78 additions and 41 deletions
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20
Code/cmake/Modules/FindInchi.cmake
View File

@@ -27,38 +27,38 @@ else()
endif()
set(CUSTOM_INCHI_PATH "${CMAKE_CURRENT_SOURCE_DIR}/External/INCHI-API")
# check whether we have custom InChI source
if(EXISTS ${CUSTOM_INCHI_PATH}/src/ichican2.c)
if(EXISTS ${CUSTOM_INCHI_PATH}/src/INCHI_BASE/src/ichican2.c)
message("CUSTOM_INCHI_PATH = ${CUSTOM_INCHI_PATH}")
message(STATUS "Found InChI software locally")
if(INCHI_FOUND)
message(WARNING "** Local InChI software takes precedence when both system InChI and local InChI are found")
endif(INCHI_FOUND)
else(EXISTS ${CUSTOM_INCHI_PATH}/src/ichican2.c)
else(EXISTS ${CUSTOM_INCHI_PATH}/src/INCHI_BASE/src/ichican2.c)
if (INCHI_FOUND)
include_directories(${INCHI_INCLUDE_DIR})
else (INCHI_FOUND)
# system InChI is missing, download it
if(NOT DEFINED INCHI_URL)
set(INCHI_URL "http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip")
set(INCHI_URL "http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip")
endif()
if(NOT DEFINED INCHI_MD5SUM)
set(INCHI_MD5SUM "8447bf108af12fe66eecba41bbc89918")
set(INCHI_MD5SUM "ccc497c7e6ced1521a6953d859e49af4")
endif()
if(NOT DEFINED INCHI_BASE)
string(REGEX REPLACE "^.*/" "" INCHI_BASE "${INCHI_URL}")
endif()
downloadAndCheckMD5(${INCHI_URL} "${CUSTOM_INCHI_PATH}/${INCHI_BASE}" ${INCHI_MD5SUM})
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf
${CUSTOM_INCHI_PATH}/INCHI-1-API.zip
${CUSTOM_INCHI_PATH}/INCHI-1-SRC.zip
WORKING_DIRECTORY ${CUSTOM_INCHI_PATH})
execute_process(COMMAND "${CMAKE_COMMAND}" -E copy_directory
"${CUSTOM_INCHI_PATH}/INCHI-1-API/INCHI_API/inchi_dll" "${CUSTOM_INCHI_PATH}/src")
"${CUSTOM_INCHI_PATH}/INCHI-1-SRC" "${CUSTOM_INCHI_PATH}/src")
endif(INCHI_FOUND)
endif(EXISTS ${CUSTOM_INCHI_PATH}/src/ichican2.c)
if(EXISTS ${CUSTOM_INCHI_PATH}/src/ichican2.c)
endif(EXISTS ${CUSTOM_INCHI_PATH}/src/INCHI_BASE/src/ichican2.c)
if(EXISTS ${CUSTOM_INCHI_PATH}/src/INCHI_BASE/src/ichican2.c)
set(INCHI_LIBRARIES Inchi)
endif(EXISTS ${CUSTOM_INCHI_PATH}/src/ichican2.c)
if((NOT EXISTS ${CUSTOM_INCHI_PATH}/src/ichican2.c)
endif(EXISTS ${CUSTOM_INCHI_PATH}/src/INCHI_BASE/src/ichican2.c)
if((NOT EXISTS ${CUSTOM_INCHI_PATH}/src/INCHI_BASE/src/ichican2.c)
AND (NOT INCHI_FOUND))
message(WARNING "** NO INCHI SOFTWARE FOUND\n"
"InChI support will be turned off. If you want to add InChI support, please follow the instructions inside $RDBASE/External/INCHI-API/README to download a copy of InChI software and then rerun cmake.")

4
Code/cmake/Modules/RDKitUtils.cmake
View File

@@ -171,9 +171,9 @@ function(downloadAndCheckMD5 url target md5chksum)
endif()
if (NOT ${md5chksum} EQUAL "")
execute_process(COMMAND ${CMAKE_COMMAND} -E md5sum ${target} OUTPUT_VARIABLE md5list)
string(REGEX REPLACE ":" ";" md5list "${md5list}")
string(REGEX REPLACE "([a-z0-9]+)" "\\1;" md5list "${md5list}")
list(GET md5list 0 md5)
if (NOT md5 EQUAL ${md5chksum})
if (NOT md5 STREQUAL ${md5chksum})
MESSAGE(FATAL_ERROR "The md5 checksum for ${target} is incorrect; expected: ${md5chksum}, found: ${md5}")
endif()
endif()

84
External/INCHI-API/CMakeLists.txt vendored
View File

@@ -1,30 +1,68 @@
add_custom_target(inchi_support ALL)
if(RDK_BUILD_INCHI_SUPPORT)
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/ichican2.c)
rdkit_library(Inchi src/ichican2.c src/ichicano.c
src/ichicans.c src/ichiisot.c
src/ichilnct.c src/ichimak2.c
src/ichimake.c src/ichimap1.c
src/ichimap2.c src/ichimap4.c
src/ichinorm.c src/ichiparm.c
src/ichiprt1.c src/ichiprt2.c
src/ichiprt3.c src/ichiqueu.c
src/ichiring.c src/ichisort.c
src/ichister.c src/ichitaut.c
src/ichi_bns.c src/inchi_dll.c
src/ichiread.c src/ichirvr1.c
src/ichirvr2.c src/ichirvr3.c
src/ichirvr4.c src/ichirvr5.c
src/ichirvr6.c src/ichirvr7.c
src/inchi_dll_main.c src/runichi.c
src/inchi_dll_a.c src/inchi_dll_a2.c
src/ikey_dll.c src/ikey_base26.c
src/ichi_io.c
src/sha2.c src/strutil.c
src/util.c SHARED)
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/INCHI_BASE/src/ichican2.c)
rdkit_library(Inchi
src/INCHI_BASE/src/ichi_bns.c
src/INCHI_BASE/src/ichi_io.c
src/INCHI_BASE/src/ichican2.c
src/INCHI_BASE/src/ichicano.c
src/INCHI_BASE/src/ichicans.c
src/INCHI_BASE/src/ichierr.c
src/INCHI_BASE/src/ichiisot.c
src/INCHI_BASE/src/ichimak2.c
src/INCHI_BASE/src/ichimake.c
src/INCHI_BASE/src/ichimap1.c
src/INCHI_BASE/src/ichimap2.c
src/INCHI_BASE/src/ichimap4.c
src/INCHI_BASE/src/ichinorm.c
src/INCHI_BASE/src/ichiparm.c
src/INCHI_BASE/src/ichiprt1.c
src/INCHI_BASE/src/ichiprt2.c
src/INCHI_BASE/src/ichiprt3.c
src/INCHI_BASE/src/ichiqueu.c
src/INCHI_BASE/src/ichiread.c
src/INCHI_BASE/src/ichiring.c
src/INCHI_BASE/src/ichirvr1.c
src/INCHI_BASE/src/ichirvr2.c
src/INCHI_BASE/src/ichirvr3.c
src/INCHI_BASE/src/ichirvr4.c
src/INCHI_BASE/src/ichirvr5.c
src/INCHI_BASE/src/ichirvr6.c
src/INCHI_BASE/src/ichirvr7.c
src/INCHI_BASE/src/ichisort.c
src/INCHI_BASE/src/ichister.c
src/INCHI_BASE/src/ichitaut.c
src/INCHI_BASE/src/ikey_base26.c
src/INCHI_BASE/src/ikey_dll.c
src/INCHI_BASE/src/mol2atom.c
src/INCHI_BASE/src/mol_fmt1.c
src/INCHI_BASE/src/mol_fmt2.c
src/INCHI_BASE/src/mol_fmt3.c
src/INCHI_BASE/src/mol_fmt4.c
src/INCHI_BASE/src/readinch.c
src/INCHI_BASE/src/runichi.c
src/INCHI_BASE/src/runichi2.c
src/INCHI_BASE/src/runichi3.c
src/INCHI_BASE/src/runichi4.c
src/INCHI_BASE/src/sha2.c
src/INCHI_BASE/src/strutil.c
src/INCHI_BASE/src/util.c
src/INCHI_API/libinchi/src/ichilnct.c
src/INCHI_API/libinchi/src/inchi_dll.c
src/INCHI_API/libinchi/src/inchi_dll_a.c
src/INCHI_API/libinchi/src/inchi_dll_a2.c
src/INCHI_API/libinchi/src/inchi_dll_b.c
src/INCHI_API/libinchi/src/inchi_dll_main.c
src/INCHI_API/libinchi/src/ixa/ixa_builder.c
src/INCHI_API/libinchi/src/ixa/ixa_inchikey_builder.c
src/INCHI_API/libinchi/src/ixa/ixa_mol.c
src/INCHI_API/libinchi/src/ixa/ixa_read_inchi.c
src/INCHI_API/libinchi/src/ixa/ixa_read_mol.c
src/INCHI_API/libinchi/src/ixa/ixa_status.c SHARED)
install(TARGETS Inchi DESTINATION ${RDKit_LibDir})
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src)
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/INCHI_BASE/src/)
ADD_DEFINITIONS("-DTARGET_API_LIB")
endif()
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")

11
External/INCHI-API/download-inchi.sh vendored
View File

@@ -46,22 +46,21 @@ if [[ $DIR =~ External/INCHI-API$ ]]
then
mkdir -p src
echo "================================================================"
echo "Downloading InChI software distribution version 1.04"
echo " http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip"
echo "Downloading InChI software distribution version 1.05"
echo " http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip"
echo " ====>"
echo " $TEMPDIR"
echo "================================================================"
cd $TEMPDIR
wget http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip
wget http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip
echo "================================================================"
echo "Unarchiving"
echo "================================================================"
unzip INCHI-1-API
unzip INCHI-1-SRC
echo "================================================================"
echo "Copying files"
echo "================================================================"
cp INCHI-1-API/INCHI_API/inchi_dll/* "$DIR/src"
cp -a INCHI-1-SRC/* "$DIR/src"
echo "================================================================"
echo "Removing temporary files"
echo "================================================================"