Update build rules for coorgen & maeparser (#2184)

2026-06-03 21:44:30 +08:00 · 2019-01-06 01:28:00 -05:00
parent cb444f21a0
commit 3cc9206a48
11 changed files with 159 additions and 49 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -46,9 +46,10 @@ __pycache__/
 /Data/templates.mae

 /External/catch/catch/
-/External/CoordGen/coordgenlibs/
+/External/CoordGen/coordgen/
 /External/CoordGen/maeparser/
-/External/CoordGen/master.tar.gz
+/External/CoordGen/maeparser-v*.tar.gz
+/External/CoordGen/coordgenlibs-v*.tar.gz
 /External/FreeSASA/freesasa-2.0.1/
 /External/FreeSASA/master.tar.gz
 /External/INCHI-API/INCHI-1-SRC.zip
--- a/Code/GraphMol/Depictor/CMakeLists.txt
+++ b/Code/GraphMol/Depictor/CMakeLists.txt
@@ -1,6 +1,18 @@

 remove_definitions(-DRDKIT_GRAPHMOL_BUILD)
 add_definitions(-DRDKIT_DEPICTOR_BUILD)
+
+if(RDK_BUILD_COORDGEN_SUPPORT)
+
+    if(MSVC AND (NOT RDK_INSTALL_DLLS_MSVC))
+      add_definitions(-DSTATIC_COORDGEN)
+    else(MSVC AND (NOT RDK_INSTALL_DLLS_MSVC))
+      add_definitions(-DIN_COORDGEN)
+    endif(MSVC AND (NOT RDK_INSTALL_DLLS_MSVC))
+
+    include_directories(${coordgen_INCLUDE_DIRS})
+endif()
+
 rdkit_library(Depictor
              RDDepictor.cpp EmbeddedFrag.cpp DepictUtils.cpp
              LINK_LIBRARIES ${RDK_COORDGEN_LIBS} SubstructMatch GraphMol)
--- a/Code/GraphMol/FileParsers/CMakeLists.txt
+++ b/Code/GraphMol/FileParsers/CMakeLists.txt
@@ -3,11 +3,8 @@ remove_definitions(-DRDKIT_GRAPHMOL_BUILD)
 add_definitions(-DRDKIT_FILEPARSERS_BUILD)

 if(RDK_BUILD_COORDGEN_SUPPORT)
+    include_directories(${maeparser_INCLUDE_DIRS})
    set (maesupplier MaeMolSupplier.cpp)
-    set (maeparser_var maeparser)
-else()
-    set (maesupplier "")
-    set (maeparser_var "")
 endif()

 if(RDK_USE_BOOST_REGEX)
@@ -28,7 +25,7 @@ rdkit_library(FileParsers
              ProximityBonds.cpp
              SequenceParsers.cpp SequenceWriters.cpp
              SVGParser.cpp
-              LINK_LIBRARIES Depictor SmilesParse GraphMol ${maeparser_var} ${regex_lib})
+              LINK_LIBRARIES Depictor SmilesParse GraphMol ${RDK_COORDGEN_LIBS} ${regex_lib})

 rdkit_headers(FileParsers.h
              FileParserUtils.h
--- a/Code/GraphMol/FileParsers/MaeMolSupplier.cpp
+++ b/Code/GraphMol/FileParsers/MaeMolSupplier.cpp
@@ -16,8 +16,7 @@
 #include <GraphMol/MolOps.h>
 #include <GraphMol/RWMol.h>
 #include <GraphMol/FileParsers/MolSupplier.h>
-#include <CoordGen/maeparser/Reader.hpp>
-
+#include <maeparser/Reader.hpp>

 namespace RDKit {

--- a/Code/GraphMol/Wrap/CMakeLists.txt
+++ b/Code/GraphMol/Wrap/CMakeLists.txt
@@ -24,8 +24,7 @@ rdkit_python_extension(rdqueries

 if(RDK_BUILD_COORDGEN_SUPPORT)
    set (maesupplier MaeMolSupplier.cpp)
-else()
-    set (maesupplier "")
+    include_directories(${maeparser_INCLUDE_DIRS})
 endif()

 if(RDK_BUILD_COMPRESSED_SUPPLIERS)
--- a/Code/GraphMol/Wrap/MaeMolSupplier.cpp
+++ b/Code/GraphMol/Wrap/MaeMolSupplier.cpp
@@ -20,7 +20,7 @@
 #include <GraphMol/RDKitBase.h>
 #include <RDBoost/python_streambuf.h>
 #include <RDBoost/iterator_next.h>
-#include <CoordGen/maeparser/Reader.hpp>
+#include <maeparser/Reader.hpp>

 #include "MolSupplier.h"

--- a/Code/cmake/Modules/Findcoordgen.cmake
+++ b/Code/cmake/Modules/Findcoordgen.cmake
@@ -0,0 +1,46 @@
+# Try to find Schrodinger's CoorgGen libraries.
+#
+# Different version handling is not yet supported
+#
+# Once found, this will find and define the following variables:
+#
+# coordgen_INCLUDE_DIRS   - CoordGen's includes directory
+# coordgen_LIBRARIES      - CoordGen's shared libraries
+# coordgen_TEMPLATE_FILE  - CoordGen templates file
+#
+#
+
+include(FindPackageHandleStandardArgs)
+
+find_path(coordgen_INCLUDE_DIRS
+    NAMES "coordgen/sketcherMinimizer.h"
+    HINTS ${COORDGEN_DIR} ${coordgen_DIR}
+    PATH_SUFFIXES "include"
+    DOC "include path for coordgen"
+)
+message("-- coordgen include dir set as ${coordgen_INCLUDE_DIRS}")
+
+find_library(coordgen_LIBRARIES
+    NAMES coordgen coordgenlibs
+    HINTS ${COORDGEN_DIR} ${coordgen_DIR}
+    PATH_SUFFIXES "lib"
+    DOC "libraries for coordgen"
+)
+message("-- coordgen libraries set as '${coordgen_LIBRARIES}'")
+
+# Just in case, add parent directory above libraries to templates search hints
+get_filename_component(libs_parent_dir ${coordgen_LIBRARIES} PATH)
+find_file(coordgen_TEMPLATE_FILE
+    NAMES templates.mae
+    HINTS ${COORDGEN_DIR} ${coordgen_DIR} ${libs_parent_dir}
+    PATH_SUFFIXES "share" "share/coordgen"
+    DOC "templates file for coordgen"
+)
+message("-- coordgen templates file set as '${coordgen_TEMPLATE_FILE}'")
+
+find_package_handle_standard_args(coordgen FOUND_VAR coordgen_FOUND
+                                  REQUIRED_VARS coordgen_INCLUDE_DIRS
+                                  coordgen_LIBRARIES coordgen_TEMPLATE_FILE)
+
+
+
--- a/Code/cmake/Modules/Findmaeparser.cmake
+++ b/Code/cmake/Modules/Findmaeparser.cmake
@@ -0,0 +1,32 @@
+# Try to find Schrodinger's MAEParser libraries.
+#
+# Different version handling is not yet supported
+#
+# Once found, this will find and define the following variables:
+#
+# maeparser_INCLUDE_DIRS  - maeparser's includes directory
+# maeparser_LIBRARIES     - maeparser's shared libraries
+#
+#
+
+include(FindPackageHandleStandardArgs)
+
+find_path(maeparser_INCLUDE_DIRS
+    NAMES "maeparser/Reader.hpp"
+    HINTS ${MAEPARSER_DIR} ${maeparser_DIR}
+    PATH_SUFFIXES "include"
+    DOC "include path for maeparser"
+)
+message("-- maeparser include dir set as '${maeparser_INCLUDE_DIRS}'")
+
+find_library(maeparser_LIBRARIES
+    NAMES maeparser
+    HINTS ${MAEPARSER_DIR} ${maeparser_DIR}
+    PATH_SUFFIXES "lib"
+    DOC "libraries for maeparser"
+)
+message("-- maeparser libraries set as '${maeparser_LIBRARIES}'")
+
+find_package_handle_standard_args(maeparser FOUND_VAR maeparser_FOUND
+                                  REQUIRED_VARS maeparser_INCLUDE_DIRS
+                                  maeparser_LIBRARIES)
--- a/External/CoordGen/CMakeLists.txt
+++ b/External/CoordGen/CMakeLists.txt
@@ -1,77 +1,101 @@
 add_custom_target(coordgen_support ALL)

 if(RDK_BUILD_COORDGEN_SUPPORT)
+  include(RDKitUtils)
+
+  if(MSVC AND (NOT RDK_INSTALL_DLLS_MSVC))
+    add_definitions(-DSTATIC_COORDGEN)
+  else(MSVC AND (NOT RDK_INSTALL_DLLS_MSVC))
    add_definitions(-DIN_MAEPARSER)
    add_definitions(-DIN_COORDGEN)
-    include(RDKitUtils)
+  endif(MSVC AND (NOT RDK_INSTALL_DLLS_MSVC))
+
+  find_package(maeparser MODULE)
+
+  if(MAEPARSER_FORCE_BUILD OR (NOT maeparser_FOUND))
    if(NOT DEFINED MAEPARSER_DIR)
      set(MAEPARSER_DIR "${CMAKE_CURRENT_SOURCE_DIR}/maeparser")
    endif()
+
    if(NOT EXISTS "${MAEPARSER_DIR}/MaeParser.hpp")
        set(RELEASE_NO "1.0.1")
+        set(MD5 "1292494df756e95fd1cce722286f28fe")
        downloadAndCheckMD5("https://github.com/schrodinger/maeparser/archive/v${RELEASE_NO}.tar.gz"
-              "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz"
-              "1292494df756e95fd1cce722286f28fe")
+              "${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz" ${MD5})
        execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
-          ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz
+          ${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz
          WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
        file(RENAME "maeparser-${RELEASE_NO}" "${MAEPARSER_DIR}")
        patchCoordGenMaeExportHeaders("MAEPARSER" "${MAEPARSER_DIR}/MaeParserConfig.hpp")

-        # patch a bug in the 1.0.0 release of maeparser
-        #file(READ "${MAEPARSER_DIR}/Buffer.cpp" buffer)
-        #string(REPLACE "m_data->reserve(m_size + 1);"
-        #       "m_data->resize(m_size + 1);" buffer "${buffer}")
-        #file(WRITE "${MAEPARSER_DIR}/Buffer.cpp" "${buffer}")
    else()
      message("-- Found MAEParser source in ${MAEPARSER_DIR}")
    endif()

+    set(maeparser_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}
+        CACHE STRING "MaeParser Include Dir" FORCE)
    file(GLOB MAESOURCES "${MAEPARSER_DIR}/*.cpp")
    rdkit_library(maeparser ${MAESOURCES} SHARED )
    install(TARGETS maeparser DESTINATION ${RDKit_LibDir})
+    set(maeparser_LIBRARIES maeparser)
+
+  endif(MAEPARSER_FORCE_BUILD OR (NOT maeparser_FOUND))
+
+  find_package(coordgen MODULE)
+  if(COORDGEN_FORCE_BUILD OR (NOT coordgen_FOUND))

    if(NOT DEFINED COORDGEN_DIR)
-      set(COORDGEN_DIR "${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs")
+      set(COORDGEN_DIR "${CMAKE_CURRENT_SOURCE_DIR}/coordgen")
    endif()
+
    if(NOT EXISTS "${COORDGEN_DIR}/sketcherMinimizer.h")
-        set(RELEASE_NO "1.1")
-        set(SHA "ede3191bf1c1dde53f70ca086014ff9ec7768c55")
+        set(RELEASE_NO "1.2")
+        set(MD5 "cc132a4655e194143d760239f69dd265")
        downloadAndCheckMD5("https://github.com/schrodinger/coordgenlibs/archive/v${RELEASE_NO}.tar.gz"
-              "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz"
-              "493cf2eab7d4ab6242e25da112831798")
+              "${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz" ${MD5})
        execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
-          ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz
+          ${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz
          WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
        file(RENAME "coordgenlibs-${RELEASE_NO}" "${COORDGEN_DIR}")
-        patchCoordGenMaeExportHeaders("COORDGEN" "${COORDGEN_DIR}/CoordgenConfig.hpp")
+
    else()
      message("-- Found coordgenlibs source in ${COORDGEN_DIR}")
    endif()

+    set(coordgen_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}
+        CACHE STRING "CoordGen Include File" FORCE)
    file(GLOB CGSOURCES "${COORDGEN_DIR}/*.cpp")
-    rdkit_library(coordgenlib ${CGSOURCES} SHARED LINK_LIBRARIES maeparser)
-    install(TARGETS coordgenlib DESTINATION ${RDKit_LibDir})
+    rdkit_library(coordgen ${CGSOURCES} SHARED LINK_LIBRARIES maeparser)
+    install(TARGETS coordgen DESTINATION ${RDKit_LibDir})
+    set(coordgen_LIBRARIES coordgen)
+    set(coordgen_TEMPLATE_FILE ${COORDGEN_DIR}/templates.mae )

-    set(MAE_FILES ${COORDGEN_DIR}/templates.mae )
-    install(FILES ${MAE_FILES}
-            DESTINATION ${RDKit_ShareDir}/Data
-            COMPONENT data )
+  endif(COORDGEN_FORCE_BUILD OR (NOT coordgen_FOUND))

-    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-    set(RDK_COORDGEN_LIBS MolAlign coordgenlib maeparser CACHE STRING "the external libraries" FORCE)
-    rdkit_headers(CoordGen.h DEST GraphMol)
+  include_directories(${maeparser_INCLUDE_DIRS})
+  include_directories(${coordgen_INCLUDE_DIRS})

-    if(RDK_BUILD_PYTHON_WRAPPERS)
-      add_subdirectory(Wrap)
-    endif(RDK_BUILD_PYTHON_WRAPPERS)
+  install(FILES ${coordgen_TEMPLATE_FILE}
+          DESTINATION ${RDKit_ShareDir}/Data
+          COMPONENT data)
+
+  set(RDK_COORDGEN_LIBS MolAlign ${coordgen_LIBRARIES} ${maeparser_LIBRARIES}
+      CACHE STRING "the external libraries" FORCE)
+  rdkit_headers(CoordGen.h DEST GraphMol)
+
+  if(RDK_BUILD_PYTHON_WRAPPERS)
+    add_subdirectory(Wrap)
+  endif(RDK_BUILD_PYTHON_WRAPPERS)
+
+  rdkit_test(testCoordGen test.cpp
+    LINK_LIBRARIES
+    ${RDK_COORDGEN_LIBS} Depictor
+    FileParsers SmilesParse SubstructMatch GraphMol
+    RDGeneral DataStructs RDGeneral RDGeometryLib
+    ${RDKit_THREAD_LIBS})

-    rdkit_test(testCoordGen test.cpp
-      LINK_LIBRARIES
-      ${RDK_COORDGEN_LIBS} Depictor
-      FileParsers SmilesParse SubstructMatch GraphMol
-      RDGeneral DataStructs RDGeneral RDGeometryLib
-      ${RDKit_THREAD_LIBS})
 else (RDK_BUILD_COORDGEN_SUPPORT)
-    set(RDK_COORDGEN_LIBS  CACHE STRING "the external libraries" FORCE)
+
+  set(RDK_COORDGEN_LIBS CACHE STRING "the external libraries" FORCE)
+
 endif(RDK_BUILD_COORDGEN_SUPPORT)
--- a/External/CoordGen/CoordGen.h
+++ b/External/CoordGen/CoordGen.h
@@ -13,7 +13,7 @@
 #include <GraphMol/Substruct/SubstructMatch.h>
 #include <cstdlib>

-#include "coordgenlibs/sketcherMinimizer.h"
+#include "coordgen/sketcherMinimizer.h"

 namespace RDKit {
 namespace CoordGen {
--- a/External/CoordGen/test.cpp
+++ b/External/CoordGen/test.cpp
@@ -18,7 +18,7 @@

 #include <RDGeneral/RDLog.h>

-#include "coordgenlibs/sketcherMinimizer.h"
+#include "coordgen/sketcherMinimizer.h"
 #include <CoordGen/CoordGen.h>

 using namespace RDKit;