| 1 | Remove CMake code for downloading and builing bundled dependencies:
|
| 2 | They are packaged separately as rapidjson, avalon-toolkit, freesasa,
|
| 3 | ringdecomposerlib and yaehmop.
|
| 4 |
|
| 5 | diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt
|
| 6 | index 0c1e9a0de..c3504e6f1 100644
|
| 7 | |
| 8 | |
| 9 | @@ -1,26 +1,3 @@
|
| 10 | -
|
| 11 | -if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
|
| 12 | - downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
|
| 13 | - "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
|
| 14 | - "badd12c511e081fec6c89c43a7027bce")
|
| 15 | - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
|
| 16 | - ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
|
| 17 | - WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
|
| 18 | - # comment out a line which causes a compilation error on some platforms
|
| 19 | - # (based on the change which has already been applied to the RapidJSON master branch, see
|
| 20 | - # https://github.com/Tencent/rapidjson/blob/ab1842a2dae061284c0a62dca1cc6d5e7e37e346/include/rapidjson/document.h#L414)
|
| 21 | - file(READ ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h RAPIDJSON_DOCUMENT_H)
|
| 22 | - string(REGEX REPLACE
|
| 23 | - "( *)(GenericStringRef& operator=\\(const GenericStringRef& rhs\\) { s = rhs\\.s. length = rhs\\.length. })" "\\1//\\2"
|
| 24 | - RAPIDJSON_DOCUMENT_H "${RAPIDJSON_DOCUMENT_H}")
|
| 25 | - file(WRITE ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h "${RAPIDJSON_DOCUMENT_H}")
|
| 26 | -else()
|
| 27 | - message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
|
| 28 | -endif()
|
| 29 | -
|
| 30 | -include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include)
|
| 31 | -
|
| 32 | -
|
| 33 | rdkit_library(MolInterchange
|
| 34 | Parser.cpp Writer.cpp
|
| 35 | LINK_LIBRARIES GraphMol)
|
| 36 | diff --git a/External/AvalonTools/AvalonTools.cpp b/External/AvalonTools/AvalonTools.cpp
|
| 37 | index f4b37ba5c..e1b25aed1 100644
|
| 38 | |
| 39 | |
| 40 | @@ -24,15 +24,15 @@
|
| 41 | #include "AvalonTools.h"
|
| 42 |
|
| 43 | extern "C" {
|
| 44 | -#include "local.h"
|
| 45 | -#include "reaccs.h"
|
| 46 | -#include "reaccsio.h"
|
| 47 | -#include "utilities.h"
|
| 48 | -#include "ssmatch.h"
|
| 49 | -#include "smi2mol.h"
|
| 50 | -#include "canonizer.h"
|
| 51 | -#include "layout.h"
|
| 52 | -#include "struchk.h"
|
| 53 | +#include <avalontoolkit/local.h>
|
| 54 | +#include <avalontoolkit/reaccs.h>
|
| 55 | +#include <avalontoolkit/reaccsio.h>
|
| 56 | +#include <avalontoolkit/utilities.h>
|
| 57 | +#include <avalontoolkit/ssmatch.h>
|
| 58 | +#include <avalontoolkit/smi2mol.h>
|
| 59 | +#include <avalontoolkit/canonizer.h>
|
| 60 | +#include <avalontoolkit/layout.h>
|
| 61 | +#include <avalontoolkit/struchk.h>
|
| 62 |
|
| 63 | extern int RunStruchk(struct reaccs_molecule_t **mpp,
|
| 64 | struct data_line_t *data_list);
|
| 65 | diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLists.txt
|
| 66 | index 30203ecdf..4e2661d7e 100644
|
| 67 | |
| 68 | |
| 69 | @@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
|
| 70 | return()
|
| 71 | endif(NOT RDK_BUILD_AVALON_SUPPORT)
|
| 72 |
|
| 73 | -set(AVALON_VERSION "2.0.5-pre.3")
|
| 74 | -if(NOT DEFINED AVALONTOOLS_DIR)
|
| 75 | - set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}")
|
| 76 | - set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c")
|
| 77 | - set(needDownload "TRUE")
|
| 78 | - if(EXISTS "${fileToCheck}")
|
| 79 | - set(needDownload "FALSE")
|
| 80 | - endif()
|
| 81 | -else()
|
| 82 | - string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR})
|
| 83 | - set(needDownload "FALSE")
|
| 84 | -endif()
|
| 85 | -
|
| 86 | -set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C")
|
| 87 | -set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common")
|
| 88 | -set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include")
|
| 89 | -set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs")
|
| 90 | -
|
| 91 | -if(needDownload)
|
| 92 | - if(NOT DEFINED AVALONTOOLS_URL)
|
| 93 | - set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz")
|
| 94 | - endif()
|
| 95 | - if(NOT DEFINED AVALONTOOLS_MD5SUM)
|
| 96 | - set(AVALONTOOLS_MD5SUM "7a20c25a7e79f3344e0f9f49afa03351")
|
| 97 | - endif()
|
| 98 | - if(NOT DEFINED AVALONTOOLS_BASE)
|
| 99 | - string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}")
|
| 100 | - endif()
|
| 101 | - downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM})
|
| 102 | - execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf
|
| 103 | - ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz
|
| 104 | - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
|
| 105 | -endif()
|
| 106 | -
|
| 107 | -if(CMAKE_C_COMPILER_ID STREQUAL "GNU")
|
| 108 | - add_compile_options(-Wno-format-security -Wformat=0 -Wstringop-overflow=0 -Wformat-overflow=0 -Wno-unused-result )
|
| 109 | -endif()
|
| 110 | -if(CMAKE_C_COMPILER_ID STREQUAL "Clang")
|
| 111 | - add_compile_options(-Wno-absolute-value -Wno-return-type -Wno-tautological-overlap-compare)
|
| 112 | -endif()
|
| 113 | -if (MSVC)
|
| 114 | - add_definitions("/D_CRT_SECURE_NO_WARNINGS")
|
| 115 | - add_compile_options(/wd4018 /wd4101 /wd4146 /wd4334 /wd4477 /wd4715 /wd4716 /wd4996 /nologo)
|
| 116 | -endif(MSVC)
|
| 117 | -
|
| 118 | -set(avalon_clib_srcs ${AVALON_COMMON_PATH}/layout.c
|
| 119 | - ${AVALON_COMMON_PATH}/symboltable.c
|
| 120 | - ${AVALON_COMMON_PATH}/patclean.c
|
| 121 | - ${AVALON_COMMON_PATH}/utilities.c
|
| 122 | - ${AVALON_COMMON_PATH}/symbol_lists.c
|
| 123 | - ${AVALON_COMMON_PATH}/stereo.c
|
| 124 | - ${AVALON_COMMON_PATH}/set.c
|
| 125 | - ${AVALON_COMMON_PATH}/perceive.c
|
| 126 | - ${AVALON_COMMON_PATH}/local.c
|
| 127 | - ${AVALON_COMMON_PATH}/graph.c
|
| 128 | - ${AVALON_COMMON_PATH}/geometry.c
|
| 129 | - ${AVALON_COMMON_PATH}/forio.c
|
| 130 | - ${AVALON_COMMON_PATH}/depictutil.c
|
| 131 | - ${AVALON_COMMON_PATH}/denormal.c
|
| 132 | - ${AVALON_COMMON_PATH}/casutils.c
|
| 133 | - ${AVALON_COMMON_PATH}/ssmatch.c
|
| 134 | - ${AVALON_COMMON_PATH}/rtutils.c
|
| 135 | - ${AVALON_COMMON_PATH}/smi2mol.c
|
| 136 | - ${AVALON_COMMON_PATH}/didepict.c
|
| 137 | - ${AVALON_COMMON_PATH}/pattern.c
|
| 138 | - ${AVALON_COMMON_PATH}/canonizer.c
|
| 139 | - ${AVALON_COMMON_PATH}/aacheck.c
|
| 140 | - ${AVALON_COMMON_PATH}/fixcharges.c
|
| 141 | - ${AVALON_PROGRAMS_PATH}/struchk.c
|
| 142 | - ${AVALON_COMMON_PATH}/reaccsio.c
|
| 143 | - ${AVALON_COMMON_PATH}/hashcode.c
|
| 144 | - )
|
| 145 | -
|
| 146 | -rdkit_library(avalon_clib ${avalon_clib_srcs})
|
| 147 | -target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
|
| 148 | -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
|
| 149 | - set_target_properties(avalon_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
|
| 150 | -endif()
|
| 151 | -
|
| 152 | -include_directories(${CMAKE_CURRENT_SOURCE_DIR})
|
| 153 | -include_directories(${AVALON_INCLUDE_PATH})
|
| 154 | -
|
| 155 | rdkit_library(AvalonLib AvalonTools.cpp SHARED
|
| 156 | - LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
|
| 157 | + LINK_LIBRARIES -lavalon4rdkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs )
|
| 158 | target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD)
|
| 159 | rdkit_headers(AvalonTools.h DEST GraphMol)
|
| 160 | rdkit_test(testAvalonLib1 test1.cpp
|
| 161 | diff --git a/External/AvalonTools/Wrap/pyAvalonTools.cpp b/External/AvalonTools/Wrap/pyAvalonTools.cpp
|
| 162 | index 72c7a5ee2..e7ac609ae 100644
|
| 163 | |
| 164 | |
| 165 | @@ -12,7 +12,7 @@
|
| 166 | #include <boost/cstdint.hpp>
|
| 167 |
|
| 168 | extern "C" {
|
| 169 | -#include "struchk.h"
|
| 170 | +#include <avalontoolkit/struchk.h>
|
| 171 | }
|
| 172 |
|
| 173 | namespace python = boost::python;
|
| 174 | diff --git a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt
|
| 175 | index 8baadb618..81165a143 100644
|
| 176 | |
| 177 | |
| 178 | @@ -2,174 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT)
|
| 179 | return()
|
| 180 | endif(NOT RDK_BUILD_FREESASA_SUPPORT)
|
| 181 |
|
| 182 | -if(NOT DEFINED FREESASA_DIR)
|
| 183 | - set(FREESASA_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa")
|
| 184 | - set(needDownload "TRUE")
|
| 185 | - if(EXISTS "${FREESASA_DIR}/src/freesasa.h")
|
| 186 | - set(needDownload "FALSE")
|
| 187 | - endif()
|
| 188 | -endif()
|
| 189 | -
|
| 190 | -if(needDownload)
|
| 191 | - # don't actually use the md5 here
|
| 192 | - set(FREESASA_VERSION "2.0.3")
|
| 193 | - set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-${FREESASA_VERSION}")
|
| 194 | - if(NOT EXISTS "${FREESASA_SRC_DIR}/src")
|
| 195 | - downloadAndCheckMD5("https://github.com/mittinatten/freesasa/releases/download/${FREESASA_VERSION}/freesasa-${FREESASA_VERSION}.tar.gz"
|
| 196 | - "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz"
|
| 197 | - "")
|
| 198 | - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
|
| 199 | - ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz
|
| 200 | - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
|
| 201 | - message("Copying freesasa2.c to ${FREESASA_SRC_DIR}/src/freesasa2.c")
|
| 202 | - file(COPY freesasa2.c DESTINATION ${FREESASA_SRC_DIR}/src/)
|
| 203 | - else()
|
| 204 | - message("FreeSASA found in ${FREESASA_SRC_DIR}, no download required")
|
| 205 | - endif()
|
| 206 | -endif()
|
| 207 | -
|
| 208 | -set(CMAKE_C_STANDARD 99)
|
| 209 | -
|
| 210 | -set (freesasa_clib_srcs
|
| 211 | - ${FREESASA_SRC_DIR}/src/classifier.c
|
| 212 | - ${FREESASA_SRC_DIR}/src/classifier_naccess.c
|
| 213 | - ${FREESASA_SRC_DIR}/src/classifier_oons.c
|
| 214 | - ${FREESASA_SRC_DIR}/src/classifier_protor.c
|
| 215 | - ${FREESASA_SRC_DIR}/src/coord.c
|
| 216 | - ${FREESASA_SRC_DIR}/src/freesasa2.c
|
| 217 | - ${FREESASA_SRC_DIR}/src/lexer.c
|
| 218 | - ${FREESASA_SRC_DIR}/src/log.c
|
| 219 | - ${FREESASA_SRC_DIR}/src/nb.c
|
| 220 | - ${FREESASA_SRC_DIR}/src/node.c
|
| 221 | - ${FREESASA_SRC_DIR}/src/parser.c
|
| 222 | - ${FREESASA_SRC_DIR}/src/pdb.c
|
| 223 | - ${FREESASA_SRC_DIR}/src/rsa.c
|
| 224 | - ${FREESASA_SRC_DIR}/src/sasa_lr.c
|
| 225 | - ${FREESASA_SRC_DIR}/src/sasa_sr.c
|
| 226 | - ${FREESASA_SRC_DIR}/src/selection.c
|
| 227 | - ${FREESASA_SRC_DIR}/src/structure.c
|
| 228 | - ${FREESASA_SRC_DIR}/src/util.c
|
| 229 | - )
|
| 230 | -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
|
| 231 | - set(freesasa_additional_exports ${CMAKE_CURRENT_SOURCE_DIR}/additional_exports.def)
|
| 232 | - file(WRITE ${freesasa_additional_exports}
|
| 233 | - "EXPORTS\n"
|
| 234 | - "freesasa_calc_structure\n"
|
| 235 | - "freesasa_calc_coord\n"
|
| 236 | - "freesasa_calc_tree\n"
|
| 237 | - "freesasa_result_classes\n"
|
| 238 | - "freesasa_result_free\n"
|
| 239 | - "freesasa_classifier_from_file\n"
|
| 240 | - "freesasa_classifier_free\n"
|
| 241 | - "freesasa_classifier_radius\n"
|
| 242 | - "freesasa_classifier_class\n"
|
| 243 | - "freesasa_classifier_class2str\n"
|
| 244 | - "freesasa_classifier_name\n"
|
| 245 | - "freesasa_selection_new\n"
|
| 246 | - "freesasa_selection_free\n"
|
| 247 | - "freesasa_selection_name\n"
|
| 248 | - "freesasa_selection_command\n"
|
| 249 | - "freesasa_selection_area\n"
|
| 250 | - "freesasa_set_verbosity\n"
|
| 251 | - "freesasa_get_verbosity\n"
|
| 252 | - "freesasa_set_err_out\n"
|
| 253 | - "freesasa_get_err_out\n"
|
| 254 | - "freesasa_structure_new\n"
|
| 255 | - "freesasa_structure_free\n"
|
| 256 | - "freesasa_structure_from_pdb\n"
|
| 257 | - "freesasa_structure_array\n"
|
| 258 | - "freesasa_structure_add_atom\n"
|
| 259 | - "freesasa_structure_add_atom_wopt\n"
|
| 260 | - "freesasa_structure_get_chains\n"
|
| 261 | - "freesasa_structure_chain_labels\n"
|
| 262 | - "freesasa_structure_n\n"
|
| 263 | - "freesasa_structure_n_residues\n"
|
| 264 | - "freesasa_structure_n_chains\n"
|
| 265 | - "freesasa_structure_radius\n"
|
| 266 | - "freesasa_structure_set_radius\n"
|
| 267 | - "freesasa_structure_atom_name\n"
|
| 268 | - "freesasa_structure_atom_res_name\n"
|
| 269 | - "freesasa_structure_atom_res_number\n"
|
| 270 | - "freesasa_structure_atom_chain\n"
|
| 271 | - "freesasa_structure_atom_symbol\n"
|
| 272 | - "freesasa_structure_atom_radius\n"
|
| 273 | - "freesasa_structure_atom_set_radius\n"
|
| 274 | - "freesasa_structure_residue_name\n"
|
| 275 | - "freesasa_structure_residue_number\n"
|
| 276 | - "freesasa_structure_residue_chain\n"
|
| 277 | - "freesasa_structure_model\n"
|
| 278 | - "freesasa_structure_coord_array\n"
|
| 279 | - "freesasa_structure_residue_atoms\n"
|
| 280 | - "freesasa_structure_chain_atoms\n"
|
| 281 | - "freesasa_structure_chain_residues\n"
|
| 282 | - "freesasa_structure_classifier_name\n"
|
| 283 | - "freesasa_tree_new\n"
|
| 284 | - "freesasa_tree_init\n"
|
| 285 | - "freesasa_tree_add_result\n"
|
| 286 | - "freesasa_tree_join\n"
|
| 287 | - "freesasa_tree_export\n"
|
| 288 | - "freesasa_node_free\n"
|
| 289 | - "freesasa_node_area\n"
|
| 290 | - "freesasa_node_children\n"
|
| 291 | - "freesasa_node_next\n"
|
| 292 | - "freesasa_node_parent\n"
|
| 293 | - "freesasa_node_type\n"
|
| 294 | - "freesasa_node_name\n"
|
| 295 | - "freesasa_node_classified_by\n"
|
| 296 | - "freesasa_node_atom_is_polar\n"
|
| 297 | - "freesasa_node_atom_is_mainchain\n"
|
| 298 | - "freesasa_node_atom_radius\n"
|
| 299 | - "freesasa_node_atom_pdb_line\n"
|
| 300 | - "freesasa_node_residue_number\n"
|
| 301 | - "freesasa_node_residue_n_atoms\n"
|
| 302 | - "freesasa_node_residue_reference\n"
|
| 303 | - "freesasa_node_chain_n_residues\n"
|
| 304 | - "freesasa_node_structure_n_chains\n"
|
| 305 | - "freesasa_node_structure_n_atoms\n"
|
| 306 | - "freesasa_node_structure_chain_labels\n"
|
| 307 | - "freesasa_node_structure_model\n"
|
| 308 | - "freesasa_node_structure_result\n"
|
| 309 | - "freesasa_node_structure_selections\n"
|
| 310 | - "freesasa_node_structure_add_selection\n"
|
| 311 | - "freesasa_node_result_parameters\n"
|
| 312 | - "freesasa_select_area\n"
|
| 313 | - "freesasa_default_parameters DATA\n"
|
| 314 | - "freesasa_protor_classifier DATA\n"
|
| 315 | - "freesasa_naccess_classifier DATA\n"
|
| 316 | - "freesasa_oons_classifier DATA\n"
|
| 317 | - )
|
| 318 | - set (freesasa_clib_srcs
|
| 319 | - ${freesasa_clib_srcs}
|
| 320 | - ${freesasa_additional_exports}
|
| 321 | - )
|
| 322 | -endif()
|
| 323 | -
|
| 324 | -set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
|
| 325 | -file(READ ${freesasa_h} freesasa_h_data)
|
| 326 | -if (NOT freesasa_h_data MATCHES "RDGeneral/export")
|
| 327 | - string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
|
| 328 | -endif()
|
| 329 | -if (MSVC)
|
| 330 | - set (RDKIT_FREESASA_CLIB_EXPORT "RDKIT_FREESASA_CLIB_EXPORT ")
|
| 331 | -else()
|
| 332 | - set (RDKIT_FREESASA_CLIB_EXPORT "")
|
| 333 | -endif()
|
| 334 | -string(REGEX REPLACE "(RDKIT_FREESASA_CLIB_EXPORT )?(extern const)" "${RDKIT_FREESASA_CLIB_EXPORT}\\2" freesasa_h_data "${freesasa_h_data}")
|
| 335 | -file(WRITE ${freesasa_h} "${freesasa_h_data}")
|
| 336 | -
|
| 337 | -add_definitions(-DUSE_THREADS=0)
|
| 338 | -add_definitions(-DUSE_JSON=0)
|
| 339 | -add_definitions(-DUSE_XML=0)
|
| 340 | -rdkit_library(freesasa_clib ${freesasa_clib_srcs})
|
| 341 | -target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD)
|
| 342 | -
|
| 343 | -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
|
| 344 | - set_target_properties(freesasa_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
|
| 345 | -endif()
|
| 346 | -include_directories("${FREESASA_SRC_DIR}/src")
|
| 347 | -
|
| 348 | rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED
|
| 349 | - LINK_LIBRARIES freesasa_clib GraphMol )
|
| 350 | + LINK_LIBRARIES -lfreesasa GraphMol )
|
| 351 | target_compile_definitions(FreeSASALib PRIVATE RDKIT_FREESASALIB_BUILD)
|
| 352 |
|
| 353 | rdkit_headers(RDFreeSASA.h DEST GraphMol)
|
| 354 | diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeLists.txt
|
| 355 | index 08dd1fe04..068435506 100644
|
| 356 | |
| 357 | |
| 358 | @@ -1,47 +1,7 @@
|
| 359 | -add_custom_target(ringdecomposerlib_support ALL)
|
| 360 | -
|
| 361 | if(NOT RDK_USE_URF)
|
| 362 | return()
|
| 363 | endif(NOT RDK_USE_URF)
|
| 364 |
|
| 365 | -if(NOT DEFINED URFLIB_DIR)
|
| 366 | - set(URFLIB_DIR "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib/src/RingDecomposerLib")
|
| 367 | -endif()
|
| 368 | -
|
| 369 | -if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h")
|
| 370 | - set(RELEASE_NO "1.1.3_rdkit")
|
| 371 | - set(MD5 "e9a0bcdda8b921a35e812b9888a9a874")
|
| 372 | - downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz"
|
| 373 | - "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5})
|
| 374 | - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
|
| 375 | - ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz
|
| 376 | - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
|
| 377 | - file(RENAME "RingDecomposerLib-${RELEASE_NO}" "RingDecomposerLib")
|
| 378 | -else()
|
| 379 | - message("-- Found RingDecomposerLib source in ${URFLIB_DIR}")
|
| 380 | -endif()
|
| 381 | -
|
| 382 | -set(urflib_INCLUDE_DIRS ${URFLIB_DIR}
|
| 383 | - CACHE STRING "RingDecomposerLib Include Dir" FORCE)
|
| 384 | -file(GLOB URFSOURCES "${URFLIB_DIR}/*.c")
|
| 385 | -
|
| 386 | -#if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS)))
|
| 387 | -if(WIN32)
|
| 388 | - set (ringdecomposerlib_h ${URFLIB_DIR}/RingDecomposerLib.h)
|
| 389 | - file(READ ${ringdecomposerlib_h} ringdecomposerlib_h_data)
|
| 390 | - if (NOT "${ringdecomposerlib_h_data}" MATCHES "RDKIT_URFLIB_BUILD")
|
| 391 | - string(REGEX REPLACE "(#if[ ]+\\([ ]*defined[ ]*\\([ ]*_WIN32[ ]*\\)[ ]*&&[ ]*)(defined\\([ ]*_MSC_VER[ ]*\\))" "\\1!defined( RDL_WIN_STATIC )" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}")
|
| 392 | - string(REGEX REPLACE "([ ]*)(#define[ ]+RDL_API[ ]+__declspec)(\\([ ]*dllexport[ ]*\\))" "\\1#ifdef RDKIT_URFLIB_BUILD\n\\1\\1\\2\\3\n\\1#else\n\\1\\1\\2(dllimport)\n\\1#endif" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}")
|
| 393 | - file(WRITE ${ringdecomposerlib_h} "${ringdecomposerlib_h_data}")
|
| 394 | - endif()
|
| 395 | -endif()
|
| 396 | -rdkit_library(RingDecomposerLib ${URFSOURCES} SHARED)
|
| 397 | -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS)))
|
| 398 | - target_compile_definitions(RingDecomposerLib PRIVATE RDKIT_URFLIB_BUILD)
|
| 399 | -endif()
|
| 400 | -install(TARGETS RingDecomposerLib DESTINATION ${RDKit_LibDir})
|
| 401 | -rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "")
|
| 402 | -
|
| 403 | -
|
| 404 | +rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib)
|
| 405 | set(RDK_URF_LIBS RingDecomposerLib
|
| 406 | CACHE STRING "the libraries for the URF calculation" FORCE)
|
| 407 | diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp
|
| 408 | new file mode 100644
|
| 409 | index 000000000..e69de29bb
|
| 410 | diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
|
| 411 | index c8daef9a5..01eaddac6 100644
|
| 412 | |
| 413 | |
| 414 | @@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT)
|
| 415 |
|
| 416 | add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT)
|
| 417 |
|
| 418 | -if(NOT DEFINED YAEHMOP_DIR)
|
| 419 | - set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop")
|
| 420 | -endif()
|
| 421 | -
|
| 422 | -if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h")
|
| 423 | - set(RELEASE_NO "2024.03.1")
|
| 424 | - set(MD5 "ebbddca4f79ab71544cb1fef9a7eca8a")
|
| 425 | - downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz"
|
| 426 | - "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5})
|
| 427 | - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
|
| 428 | - ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz
|
| 429 | - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
|
| 430 | -
|
| 431 | - file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}")
|
| 432 | -else()
|
| 433 | - message("-- Found YAeHMOP source in ${YAEHMOP_DIR}")
|
| 434 | -endif()
|
| 435 | -
|
| 436 | -set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/..
|
| 437 | - CACHE STRING "yaehmop Include File" FORCE)
|
| 438 | -include_directories(${yaehmop_INCLUDE_DIRS})
|
| 439 | -
|
| 440 | -if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN)
|
| 441 | - SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
|
| 442 | -endif()
|
| 443 | -if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
|
| 444 | - SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
|
| 445 | -endif()
|
| 446 | -
|
| 447 | -# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency)
|
| 448 | -add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True)
|
| 449 | -
|
| 450 | -# set install dir for the yaehmop library:
|
| 451 | -INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets
|
| 452 | - DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
|
| 453 | - COMPONENT runtime )
|
| 454 | -
|
| 455 | -
|
| 456 | -
|
| 457 | -
|
| 458 | -set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
|
| 459 | -install(FILES ${EHT_PARAM_FILE}
|
| 460 | - DESTINATION ${RDKit_ShareDir}/Data
|
| 461 | - COMPONENT data)
|
| 462 | -
|
| 463 | -rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol )
|
| 464 | +rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol )
|
| 465 | target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
|
| 466 | rdkit_headers(EHTTools.h DEST GraphMol)
|
| 467 | rdkit_catch_test(testEHTLib1 test1.cpp
|
| 468 | diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp
|
| 469 | index 021c548f1..43afdca57 100644
|
| 470 | |
| 471 | |
| 472 | @@ -13,7 +13,7 @@
|
| 473 | #include <filesystem>
|
| 474 |
|
| 475 | extern "C" {
|
| 476 | -#include <yaehmop/tightbind/bind.h>
|
| 477 | +#include <yaehmop/bind.h>
|
| 478 | }
|
| 479 |
|
| 480 | namespace RDKit {
|
| 481 | @@ -211,4 +211,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId,
|
| 482 | }
|
| 483 |
|
| 484 | } // end of namespace EHTTools
|
| 485 | -} // end of namespace RDKit
|
| 486 | \ No newline at end of file
|
| 487 | +} // end of namespace RDKit
|
| 488 | diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt
|
| 489 | index 759a9f360..114d24532 100644
|
| 490 | |
| 491 | |
| 492 | @@ -4,6 +4,8 @@ rdkit_python_extension(rdEHTTools
|
| 493 | DEST Chem
|
| 494 | LINK_LIBRARIES
|
| 495 | EHTLib )
|
| 496 | +
|
| 497 | +target_include_directories(rdEHTTools PRIVATE ${RDKit_ExternalDir}/YAeHMOP)
|
| 498 |
|
| 499 | add_pytest(pyEHTTools
|
| 500 | ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)
|
| 501 | diff --git a/External/pubchem_shape/CMakeLists.txt b/External/pubchem_shape/CMakeLists.txt
|
| 502 | index a0f16eadb..463a9e31e 100644
|
| 503 | |
| 504 | |
| 505 | @@ -2,47 +2,8 @@ if(NOT RDK_BUILD_PUBCHEMSHAPE_SUPPORT)
|
| 506 | return()
|
| 507 | endif()
|
| 508 |
|
| 509 | -if(NOT DEFINED PUBCHEMSHAPE_DIR)
|
| 510 | - set(PUBCHEMSHAPE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/pubchem-align3d")
|
| 511 | - set(fileToCheck "${PUBCHEMSHAPE_DIR}/shape_functions1.cpp")
|
| 512 | - set(needDownload "TRUE")
|
| 513 | - if(EXISTS "${fileToCheck}")
|
| 514 | - set(needDownload "FALSE")
|
| 515 | - endif()
|
| 516 | -else()
|
| 517 | - set(needDownload "FALSE")
|
| 518 | -endif()
|
| 519 | -
|
| 520 | -if(needDownload)
|
| 521 | - set(PUBCHEM_COMMIT_SHA daefab3)
|
| 522 | - if(NOT DEFINED PUBCHEMSHAPE_URL)
|
| 523 | - set(PUBCHEMSHAPE_URL "https://github.com/ncbi/pubchem-align3d/archive/${PUBCHEM_COMMIT_SHA}.tar.gz")
|
| 524 | - endif()
|
| 525 | - if(NOT DEFINED PUBCHEMSHAPE_MD5SUM)
|
| 526 | - set(PUBCHEMSHAPE_MD5SUM "a78a6273851709083ac3803d62cb5ae6")
|
| 527 | - endif()
|
| 528 | - if(NOT DEFINED PUBCHEMSHAPE_BASE)
|
| 529 | - string(REGEX REPLACE "^.*/" "" PUBCHEMSHAPE_BASE "${PUBCHEMSHAPE_URL}")
|
| 530 | - endif()
|
| 531 | - downloadAndCheckMD5(${PUBCHEMSHAPE_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${PUBCHEMSHAPE_BASE}" ${PUBCHEMSHAPE_MD5SUM})
|
| 532 | - execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf
|
| 533 | - ${CMAKE_CURRENT_SOURCE_DIR}/${PUBCHEM_COMMIT_SHA}.tar.gz
|
| 534 | - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
|
| 535 | -
|
| 536 | - file(GLOB tar_dirname ${CMAKE_CURRENT_SOURCE_DIR}/pubchem-align3d-${PUBCHEM_COMMIT_SHA}*)
|
| 537 | - execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${tar_dirname}
|
| 538 | - ${PUBCHEMSHAPE_DIR}
|
| 539 | - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
|
| 540 | -endif()
|
| 541 | -
|
| 542 | -rdkit_library(pubchem_align3d ./pubchem-align3d/shape_functions1.cpp
|
| 543 | - ./pubchem-align3d/shape_functions2.cpp ./pubchem-align3d/shape_neighbor.cpp SHARED)
|
| 544 | -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
|
| 545 | - set_target_properties(pubchem_align3d PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
|
| 546 | -endif()
|
| 547 | -
|
| 548 | rdkit_library(PubChemShape PubChemShape.cpp SHARED
|
| 549 | - LINK_LIBRARIES pubchem_align3d SmilesParse SubstructMatch)
|
| 550 | + LINK_LIBRARIES -lpubchem-align3d SmilesParse SubstructMatch)
|
| 551 | target_compile_definitions(PubChemShape PRIVATE RDKIT_PUBCHEMSHAPE_BUILD)
|
| 552 |
|
| 553 | rdkit_headers(PubChemShape.hpp DEST GraphMol)
|