Bug fixes to wrapper generation. Implemented wrappers for AMOEBA.

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/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)

wrappers/generateWrappers.py

@@ -801,6 +801,8 @@ class FortranHeaderGenerator(WrapperGenerator):
         self.typeTranslations = {'int': 'integer*4',
                                  'bool': 'integer*4',
                                  'double': 'real*8',
+                                 'char *': 'character(*)',
+                                 'const char *': 'character(*)',
                                  'std::string': 'character(*)',
                                  'const std::string &': 'character(*)',
                                  'std::vector< std::string >': 'type (OpenMM_StringArray)',
@@ -811,13 +813,14 @@ class FortranHeaderGenerator(WrapperGenerator):
                                  'std::vector< double >': 'type (OpenMM_DoubleArray)',
                                  'std::vector< int >': 'type (OpenMM_IntArray)',
                                  'std::set< int >': 'type (OpenMM_IntSet)'}
+        self.enumerationTypes = set()
     
     def writeGlobalConstants(self):
         self.out.write("    ! Global Constants\n\n")
         node = next((x for x in findNodes(self.doc.getroot(), "compounddef", kind="namespace") if x.findtext("compoundname") == "OpenMM"))
         for section in findNodes(node, "sectiondef", kind="var"):
             for memberNode in findNodes(section, "memberdef", kind="variable", mutable="no", prot="public", static="yes"):
-                vDef = convertOpenMMPrefix(getText("definition", memberNode))
+                vDef = convertOpenMMPrefix(getText("name", memberNode))
                 iDef = getText("initializer", memberNode)
                 if iDef.startswith("="):
                     iDef = iDef[1:]
@@ -829,7 +832,7 @@ class FortranHeaderGenerator(WrapperGenerator):
             className = getText("compoundname", classNode)
             shortName = stripOpenMMPrefix(className)
             typeName = convertOpenMMPrefix(className)
-            self.out.write("\n    type OpenMM_%s\n" % typeName)
+            self.out.write("\n    type %s\n" % typeName)
             self.out.write("        integer*8 :: handle = 0\n")
             self.out.write("    end type\n")
             self.typesByShortName[shortName] = typeName
@@ -858,6 +861,7 @@ class FortranHeaderGenerator(WrapperGenerator):
             enumName = getText("name", enumNode)
             enumTypeName = "%s_%s" % (typeName, enumName)
             self.typesByShortName[enumName] = enumTypeName
+            self.enumerationTypes.add(enumName)
         if len(enumNodes)>0: self.out.write("\n")
 
     def writeMethods(self, classNode):
@@ -882,8 +886,8 @@ class FortranHeaderGenerator(WrapperGenerator):
                         suffix = ""
                     else:
                         suffix = "_%d" % numConstructors
-                    self.out.write("        subroutine %s_create%s(result, " % (typeName, suffix))
-                    self.writeArguments(methodNode, False)
+                    self.out.write("        subroutine %s_create%s(result" % (typeName, suffix))
+                    self.writeArguments(methodNode, True)
                     self.out.write(")\n")
                     self.out.write("            use OpenMM_Types; implicit none\n")
                     self.out.write("            type (%s) result\n" % typeName)
@@ -960,7 +964,7 @@ class FortranHeaderGenerator(WrapperGenerator):
                 continue
             name = getText('declname', node)
             self.out.write("%s%s" % (separator, name))
-            separator = ", &\n                          "
+            separator = ", &\n"
             numArgs += 1
         return numArgs
     
@@ -986,6 +990,8 @@ class FortranHeaderGenerator(WrapperGenerator):
     def getType(self, type):
         if type in self.typeTranslations:
             return self.typeTranslations[type]
+        if type in self.enumerationTypes:
+            return 'integer*4'
         if type in self.typesByShortName:
             return 'type (%s)' % self.typesByShortName[type]
         if type.startswith('const '):