Merge pull request #245 from peastman/wrappers

Reimplemented C/Fortran wrapper generation

CMakeLists.txt

@@ -73,7 +73,7 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
-SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference libraries/validate)
+SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/validate)
 IF(WIN32)
     SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads)
     ADD_CUSTOM_TARGET(PthreadsLibraries ALL)
@@ -264,18 +264,8 @@ ENDFOREACH(subdir)
 SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-DHAVE_SSE2=1")
 
 # If API wrappers are being generated, and add them to the build.
-FIND_PROGRAM(GCCXML_PATH gccxml PATH
-    /usr/local/bin
-    "C:/Program Files/gccxml 0.9/bin"
-)
-IF(GCCXML_PATH)
-    SET(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS ON CACHE BOOL "Build wrappers for C and Fortran")
-ELSE(GCCXML_PATH)
-    SET(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS OFF CACHE BOOL "Build wrappers for C and Fortran")
-ENDIF(GCCXML_PATH)
+SET(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS ON CACHE BOOL "Build wrappers for C and Fortran")
 IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
-    FIND_PACKAGE(Java)
-    MARK_AS_ADVANCED(CLEAR JAVA_RUNTIME)
     ADD_SUBDIRECTORY(wrappers)
     SET(SOURCE_FILES ${SOURCE_FILES} wrappers/OpenMMCWrapper.cpp  wrappers/OpenMMFortranWrapper.cpp)
     SET_SOURCE_FILES_PROPERTIES(wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE)
@@ -447,18 +437,14 @@ INSTALL_FILES(/include/openmm/reference FILES ${REFERENCE_HEADERS})
 
 # Serialization support
 
-SET(OPENMM_BUILD_SERIALIZATION_SUPPORT ON CACHE BOOL "Whether to build the serialization support library")
-IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
-    ADD_SUBDIRECTORY(serialization)
-ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+ADD_SUBDIRECTORY(serialization)
+FILE(GLOB serialization_files  ${CMAKE_SOURCE_DIR}/serialization/src/*.cpp)
+SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
 
 # Python wrappers
 
 SET(OPENMM_BUILD_PYTHON_WRAPPERS ON CACHE BOOL "Build wrappers for Python")
 IF(OPENMM_BUILD_PYTHON_WRAPPERS)
-    IF(NOT OPENMM_BUILD_SERIALIZATION_SUPPORT)
-        MESSAGE(SEND_ERROR "The Python wrappers require that serialization support be built.")
-    ENDIF(NOT OPENMM_BUILD_SERIALIZATION_SUPPORT)
     IF(NOT OPENMM_BUILD_AMOEBA_PLUGIN)
         MESSAGE(SEND_ERROR "The Python wrappers require that the AMOEBA plugin be built.")
     ENDIF(NOT OPENMM_BUILD_AMOEBA_PLUGIN)

examples/HelloArgonInFortran.f90

@@ -11,6 +11,8 @@
 ! other visualization tool to produce an animation of the resulting trajectory.
 ! -----------------------------------------------------------------------------
 
+INCLUDE 'OpenMMFortranModule.f90'
+
 PROGRAM HelloArgon
     use OpenMM; implicit none
     type(OpenMM_System)           system

examples/HelloSodiumChlorideInFortran.f90

@@ -17,6 +17,8 @@
 ! interface module.
 ! ------------------------------------------------------------------------------
 
+INCLUDE 'OpenMMFortranModule.f90'
+
 !-------------------------------------------------------------------------------
 !                ATOM, FORCE FIELD, AND SIMULATION PARAMETERS
 !-------------------------------------------------------------------------------

examples/Makefile

@@ -56,11 +56,11 @@ HelloSodiumChlorideInC: HelloSodiumChlorideInC.c
 
 HelloArgonInFortran: HelloArgonInFortran.f90 openmm.mod 
 	gfortran $(FFLAGS) HelloArgonInFortran.f90 \
-	    -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloArgonInFortran
+	    -I$(INCLUDE_DIR) -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloArgonInFortran
 
 HelloSodiumChlorideInFortran: HelloSodiumChlorideInFortran.f90 openmm.mod 
 	gfortran $(FFLAGS) HelloSodiumChlorideInFortran.f90 \
-	    -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloSodiumChlorideInFortran
+	    -I$(INCLUDE_DIR) -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloSodiumChlorideInFortran
 
 
 # Build Fortran 95 Module file

openmmapi/include/OpenMM.h

@@ -69,5 +69,6 @@
 #include "openmm/VerletIntegrator.h"
 #include "openmm/VirtualSite.h"
 #include "openmm/Platform.h"
+#include "openmm/serialization/XmlSerializer.h"
 
 #endif /*OPENMM_H_*/

plugins/amoeba/CMakeLists.txt

@@ -16,15 +16,9 @@
 
 #INCLUDE(Dart)
 
-# ----------------------------------------------------------------------------
-#SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA OFF CACHE BOOL "Build verison of OpenMMAmoeba w/ backdoor serialization capability")
-#SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA TRUE )
-SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA FALSE )
-# ----------------------------------------------------------------------------
-
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
-SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi)
+SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi serialization)
 
 # Collect up information about the version of the OpenMM library we're building
 # and make it available to the code so it can be built into the binaries.
@@ -41,17 +35,11 @@ ADD_DEFINITIONS(-DOPENMM_AMOEBA_LIBRARY_NAME=${OPENMM_AMOEBA_LIBRARY_NAME}
 
 SET(SHARED_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME})
 SET(STATIC_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}_static)
-IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
-    SET(SHARED_AMOEBA_SERIALIZABLE_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}_serializable)
-ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
 
 # But on Unix or Cygwin we have to add the suffix manually
 IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
     SET(SHARED_AMOEBA_TARGET ${SHARED_AMOEBA_TARGET}_d)
     SET(STATIC_AMOEBA_TARGET ${STATIC_AMOEBA_TARGET}_d)
-    IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
-        SET(SHARED_AMOEBA_SERIALIZABLE_TARGET ${SHARED_AMOEBA_SERIALIZABLE_TARGET}_d)
-    ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 
 # These are all the places to search for header files which are
@@ -108,11 +96,8 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 ADD_LIBRARY(${SHARED_AMOEBA_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
 SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
 
-IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
-    ADD_LIBRARY(${SHARED_AMOEBA_SERIALIZABLE_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
-    SET_TARGET_PROPERTIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_SERIALIZE")
-    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../serialization/include)
-ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
+FILE(GLOB serialization_files  ${CMAKE_CUURENT_SOURCE_DIR}/serialization/src/*.cpp)
+SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL")
 
 IF(OPENMM_BUILD_STATIC_LIB)
   ADD_LIBRARY(${STATIC_AMOEBA_TARGET} STATIC ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
@@ -121,9 +106,6 @@ ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
     ADD_DEPENDENCIES(${SHARED_AMOEBA_TARGET} AmoebaApiWrappers)
-    IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
-        ADD_DEPENDENCIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} AmoebaApiWrappers)
-    ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
     IF(OPENMM_BUILD_STATIC_LIB)
         ADD_DEPENDENCIES(${STATIC_AMOEBA_TARGET} AmoebaApiWrappers)
     ENDIF(OPENMM_BUILD_STATIC_LIB)
@@ -135,9 +117,6 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
 FIND_LIBRARY(DL_LIBRARY dl)
 IF(DL_LIBRARY)
   TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TARGET} ${DL_LIBRARY})
-  IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
-      TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} ${DL_LIBRARY})
-  ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
   IF(OPENMM_BUILD_STATIC_LIB)
     TARGET_LINK_LIBRARIES(${STATIC_AMOEBA_TARGET} ${DL_LIBRARY})
   ENDIF(OPENMM_BUILD_STATIC_LIB)
@@ -150,9 +129,6 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 
 TARGET_LINK_LIBRARIES( ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET} )
-IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
-    TARGET_LINK_LIBRARIES( ${SHARED_AMOEBA_SERIALIZABLE_TARGET} ${SHARED_TARGET} )
-ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
 IF(OPENMM_BUILD_STATIC_LIB)
     TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} )
 ENDIF(OPENMM_BUILD_STATIC_LIB)
@@ -176,9 +152,6 @@ IF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
 ENDIF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
 
 INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_AMOEBA_TARGET})
-IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
-    INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_AMOEBA_SERIALIZABLE_TARGET})
-ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
 IF(OPENMM_BUILD_STATIC_LIB)
   INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_AMOEBA_TARGET})
 ENDIF(OPENMM_BUILD_STATIC_LIB)
@@ -201,6 +174,4 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
   SET (TEST_PATH .)
 ENDIF (EXECUTABLE_OUTPUT_PATH)
 
-IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
-    ADD_SUBDIRECTORY(serialization)
-ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+ADD_SUBDIRECTORY(serialization/tests)

plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h

@@ -175,6 +175,10 @@ private:
     std::vector<AngleInfo> angles;
 };
 
+/**
+ * This is an internal class used to record information about an angle.
+ * @private
+ */
 class AmoebaAngleForce::AngleInfo {
 public:
     int particle1, particle2, particle3;

plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h

@@ -147,6 +147,10 @@ private:
     std::vector<BondInfo> bonds;
 };
 
+/**
+ * This is an internal class used to record information about a bond.
+ * @private
+ */
 class AmoebaBondForce::BondInfo {
 public:
     int particle1, particle2;

plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h

@@ -174,6 +174,10 @@ private:
     std::vector<ParticleInfo> particles;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class AmoebaGeneralizedKirkwoodForce::ParticleInfo {
 public:
     double charge, radius, scalingFactor;

plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h

@@ -180,6 +180,10 @@ private:
     std::vector<AngleInfo> angles;
 };
 
+/**
+ * This is an internal class used to record information about an angle.
+ * @private
+ */
 class AmoebaInPlaneAngleForce::AngleInfo {
 public:
     int particle1, particle2, particle3, particle4;

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -368,6 +368,10 @@ private:
     std::vector<MultipoleInfo> multipoles;
 };
 
+/**
+ * This is an internal class used to record information about a multipole.
+ * @private
+ */
 class AmoebaMultipoleForce::MultipoleInfo {
 public:
 

plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h

@@ -172,6 +172,10 @@ private:
     std::vector<OutOfPlaneBendInfo> outOfPlaneBends;
 };
 
+/**
+ * This is an internal class used to record information about a bend.
+ * @private
+ */
 class AmoebaOutOfPlaneBendForce::OutOfPlaneBendInfo {
 public:
     int particle1, particle2, particle3, particle4;

plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h

@@ -121,6 +121,10 @@ private:
     std::vector<PiTorsionInfo> piTorsions;
 };
 
+/**
+ * This is an internal class used to record information about a torsion.
+ * @private
+ */
 class AmoebaPiTorsionForce::PiTorsionInfo {
 public:
     int particle1, particle2, particle3, particle4, particle5, particle6;

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -124,6 +124,10 @@ private:
     std::vector<StretchBendInfo> stretchBends;
 };
 
+/**
+ * This is an internal class used to record information about a stretch-bend.
+ * @private
+ */
 class AmoebaStretchBendForce::StretchBendInfo {
 public:
     int particle1, particle2, particle3;

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h

@@ -145,6 +145,10 @@ private:
     std::vector<TorsionTorsionGridInfo> torsionTorsionGrids;
 };
 
+/**
+ * This is an internal class used to record information about a torsion-torsion term.
+ * @private
+ */
 class AmoebaTorsionTorsionForce::TorsionTorsionInfo {
 
 public:
@@ -163,6 +167,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a grid.
+ * @private
+ */
 class AmoebaTorsionTorsionForce::TorsionTorsionGridInfo {
 
 public:

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -230,6 +230,10 @@ private:
     std::vector< std::vector< std::vector<double> > > sigEpsTable;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class AmoebaVdwForce::VdwInfo {
 public:
     int parentIndex;

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -137,6 +137,10 @@ private:
     std::vector<WcaDispersionInfo> parameters;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class AmoebaWcaDispersionForce::WcaDispersionInfo {
 public:
     double radius, epsilon;

plugins/amoeba/serialization/CMakeLists.txt

-#---------------------------------------------------
-# OpenMMAmoeba Serialization Library
-#
-# Creates OpenMMAmoeba serializatin library, base name=OpenMMAmoebaSerialization.
-# Default libraries are shared & optimized. Variants
-# are created for static (_static) and debug (_d).
-#
-# Windows:
-#   OpenMMAmoebaSerialization[_d].dll
-#   OpenMMAmoebaSerialization[_d].lib
-# Unix:
-#   libOpenMMAmoebaSerialization[_d].so
-#----------------------------------------------------
-
-# The source is organized into subdirectories, but we handle them all from
-# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
-SET(OPENMM_SOURCE_SUBDIRS . ../../../serialization)
-SET(OPENMM_AMOEBA_SOURCE_SUBDIRS . )
-
-# Collect up information about the version of the OpenMM library we're building
-# and make it available to the code so it can be built into the binaries.
-
-SET(OPENMM_AMOEBA_LIBRARY_NAME OpenMMAmoeba)
-SET(OPENMM_SERIALIZATION_LIBRARY_NAME OpenMMSerialization)
-SET(OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME OpenMMAmoebaSerialization)
-
-# Ensure that debug libraries have "_d" appended to their names.
-# CMake gets this right on Windows automatically with this definition.
-IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
-    SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
-ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
-
-# But on Unix or Cygwin we have to add the suffix manually
-IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-    SET(OPENMM_AMOEBA_LIBRARY_NAME ${OPENMM_AMOEBA_LIBRARY_NAME}_d)
-    SET(OPENMM_SERIALIZATION_LIBRARY_NAME ${OPENMM_SERIALIZATION_LIBRARY_NAME}_d)
-    SET(OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME}_d)
-ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-
-# These are all the places to search for header files which are
-# to be part of the API.
-SET(API_INCLUDE_DIRS) # start empty
-FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
-    # append
-    SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
-                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
-                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
-ENDFOREACH(subdir)
-
-# We'll need both *relative* path names, starting with their API_INCLUDE_DIRS,
-# and absolute pathnames.
-SET(API_REL_INCLUDE_FILES)   # start these out empty
-SET(API_ABS_INCLUDE_FILES)
-
-FOREACH(dir ${API_INCLUDE_DIRS})
-    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
-    SET(API_ABS_INCLUDE_FILES ${API_ABS_INCLUDE_FILES} ${fullpaths})
-
-    FOREACH(pathname ${fullpaths})
-        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
-        SET(API_REL_INCLUDE_FILES ${API_REL_INCLUDE_FILES} ${dir}/${filename})
-    ENDFOREACH(pathname)
-ENDFOREACH(dir)
-
-# collect up source files
-SET(SOURCE_FILES) # empty
-SET(SOURCE_INCLUDE_FILES)
-
-FOREACH(subdir ${OPENMM_AMOEBA_SOURCE_SUBDIRS})
-    FILE(GLOB_RECURSE src_files   ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.c)
-    FILE(GLOB incl_files  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.hpp)
-    SET(SOURCE_FILES         ${SOURCE_FILES}         ${src_files})   #append
-    SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
-    INCLUDE_DIRECTORIES(BEFORE  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
-    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../../serialization/${subdir}/include)
-ENDFOREACH(subdir)
-#Message( "API_REL_INCLUDE_FILES=${API_REL_INCLUDE_FILES}\n" )
-
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src )
-
-# Create the library
-ADD_LIBRARY(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-TARGET_LINK_LIBRARIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_LIBRARY_NAME} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${SHARED_TARGET})
-SET_TARGET_PROPERTIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_SERIALIZATION_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
-INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME})
-
-ADD_SUBDIRECTORY(tests)

plugins/amoeba/serialization/tests/CMakeLists.txt

@@ -11,7 +11,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
 
     # All tests use shared libraries
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_LIBRARY_NAME})
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET})
     SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 

plugins/amoeba/wrappers/CMakeLists.txt

-#set(GCCXML_EXTRA_ARGS "" CACHE STRING "Additional arguments to gccxml, such as '--gccxml-compiler;msvc8'")
-#SET(GCCXML_ARGS) # start empty
-#FOREACH(subdir ${API_INCLUDE_DIRS})
-#    SET(GCCXML_ARGS ${GCCXML_ARGS} -I${subdir})
-#ENDFOREACH(subdir)
-#SET(GCCXML_ARGS ${GCCXML_ARGS} ${GCCXML_EXTRA_ARGS})
-
-SET(SAXON_JAR ${CMAKE_SOURCE_DIR}/wrappers/saxonb9-1-0-7j/saxon9.jar)
-
-# OpenMMAmoeba
-
-ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMApi.xml COMMAND ${GCCXML_PATH} ${GCCXML_ARGS} -I${CMAKE_SOURCE_DIR}/openmmapi/include -I${CMAKE_SOURCE_DIR}/olla/include ${CMAKE_SOURCE_DIR}/plugins/amoeba/openmmapi/include/OpenMMAmoeba.h -fxml=AmoebaOpenMMApi.xml)
-
-ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMCWrapper.h COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-     -xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/CWrapper_Header.xslt -o:AmoebaOpenMMCWrapper.h DEPENDS AmoebaOpenMMApi.xml)
-#
-ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMCWrapper.cpp COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-     -xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/CWrapper_Source.xslt -o:AmoebaOpenMMCWrapper.cpp DEPENDS AmoebaOpenMMApi.xml)
-
-ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMFortranModule.f90 COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-     -xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/FortranWrapper_Header.xslt -o:AmoebaOpenMMFortranModule.f90 DEPENDS AmoebaOpenMMApi.xml ${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/FortranWrapper_Header.xslt)
-
-ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMFortranWrapper.cpp COMMAND ${JAVA_RUNTIME} -jar ${SAXON_JAR} -t -s:AmoebaOpenMMApi.xml
-     -xsl:${CMAKE_SOURCE_DIR}/plugins/amoeba/wrappers/FortranWrapper_Source.xslt -o:AmoebaOpenMMFortranWrapper.cpp DEPENDS AmoebaOpenMMApi.xml)
-
-ADD_CUSTOM_TARGET(AmoebaApiWrappers DEPENDS AmoebaOpenMMCWrapper.h AmoebaOpenMMCWrapper.cpp  AmoebaOpenMMFortranModule.f90 AmoebaOpenMMFortranWrapper.cpp)
-
-INSTALL_FILES(/include FILES AmoebaOpenMMCWrapper.h AmoebaOpenMMFortranModule.f90 )
+# WRAPPER_DOXYGEN_DIR is a workspace directory where wrapper files will be created
+set(WRAPPER_DOXYGEN_DIR "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
+file(MAKE_DIRECTORY "${WRAPPER_DOXYGEN_DIR}")
+
+# Step 1 - Create Doxyfile to point to OpenMM headers
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+    ${WRAPPER_DOXYGEN_DIR}/Doxyfile
+    @ONLY
+)
+
+# Step 2 - Run doxygen to analyze the headers
+add_custom_command(
+    OUTPUT "${WRAPPER_DOXYGEN_DIR}/xml/index.xml"
+    COMMAND "${DOXYGEN_EXECUTABLE}"
+    DEPENDS "${WRAPPER_DOXYGEN_DIR}/Doxyfile"
+    WORKING_DIRECTORY "${WRAPPER_DOXYGEN_DIR}"
+    COMMENT "Parsing OpenMM header files with Doxygen..."
+)
+
+# Step 3 - Generate the wrappers
+ADD_CUSTOM_COMMAND(OUTPUT AmoebaOpenMMCWrapper.h AmoebaOpenMMCWrapper.cpp AmoebaOpenMMFortranModule.f90 AmoebaOpenMMFortranWrapper.cpp
+     COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/generateAmoebaWrappers.py" "${WRAPPER_DOXYGEN_DIR}/xml" "${CMAKE_CURRENT_BINARY_DIR}"
+     DEPENDS "${WRAPPER_DOXYGEN_DIR}/xml/index.xml" "${CMAKE_CURRENT_SOURCE_DIR}/generateAmoebaWrappers.py")
+
+ADD_CUSTOM_TARGET(AmoebaApiWrappers DEPENDS AmoebaOpenMMCWrapper.h AmoebaOpenMMCWrapper.cpp AmoebaOpenMMFortranModule.f90 AmoebaOpenMMFortranWrapper.cpp)
+
+INSTALL_FILES(/include FILES AmoebaOpenMMCWrapper.h AmoebaOpenMMFortranModule.f90)