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generateWrappers.py
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from __future__ import print_function
import sys, os
import time
import getopt
import re
import xml.etree.ElementTree as etree
def trimToSingleSpace(text):
if text is None or len(text) == 0:
return ""
t = text.strip()
if len(t) == 0:
return t
if text[0].isspace():
t = " %s" % t
if text[-1].isspace():
t = "%s " % t
return t
def getNodeText(node):
if node.text is not None:
s = node.text
else:
s = ""
for n in node:
if n.tag == "para":
s = "%s%s\n\n" % (s, getNodeText(n))
elif n.tag == "ref":
s = "%s%s" % (s, getNodeText(n))
if n.tail is not None:
s = "%s%s" % (s, n.tail)
return s
def getText(subNodePath, node):
s = ""
for n in node.findall(subNodePath):
s = "%s%s" % (s, trimToSingleSpace(getNodeText(n)))
if n.tag == "para":
s = "%s\n\n" % s
return s.strip()
def convertOpenMMPrefix(name):
return name.replace('OpenMM::', 'OpenMM_')
OPENMM_RE_PATTERN=re.compile("(.*)OpenMM:[a-zA-Z0-9_:]*:(.*)")
def stripOpenMMPrefix(name, rePattern=OPENMM_RE_PATTERN):
try:
m=rePattern.search(name)
rValue = "%s%s" % m.group(1,2)
rValue.strip()
return rValue
except:
return name
def findNodes(parent, path, **args):
nodes = []
for node in parent.findall(path):
match = True
for arg in args:
if arg not in node.attrib or node.attrib[arg] != args[arg]:
match = False
if match:
nodes.append(node)
return nodes
class WrapperGenerator:
"""This is the parent class of generators for various API wrapper files. It defines functions common to all of them."""
def __init__(self, inputDirname, output):
self.skipClasses = ['OpenMM::Vec3', 'OpenMM::XmlSerializer', 'OpenMM::Kernel', 'OpenMM::KernelImpl', 'OpenMM::KernelFactory', 'OpenMM::ContextImpl', 'OpenMM::SerializationNode', 'OpenMM::SerializationProxy']
self.skipMethods = ['OpenMM::Context::getState', 'OpenMM::Platform::loadPluginsFromDirectory', 'OpenMM::Platform::getPluginLoadFailures', 'OpenMM::Context::createCheckpoint', 'OpenMM::Context::loadCheckpoint', 'OpenMM::Context::getMolecules']
self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
self.nodeByID={}
# Read all the XML files and merge them into a single document.
self.doc = etree.ElementTree(etree.Element('root'))
for file in os.listdir(inputDirname):
if file.lower().endswith('xml'):
root = etree.parse(os.path.join(inputDirname, file)).getroot()
for node in root:
self.doc.getroot().append(node)
self.out = output
self.typesByShortName = {}
self._orderedClassNodes = self.buildOrderedClassNodes()
def getNodeByID(self, id):
if id not in self.nodeByID:
for node in findNodes(self.doc.getroot(), "compounddef", id=id):
self.nodeByID[id] = node
return self.nodeByID[id]
def buildOrderedClassNodes(self):
orderedClassNodes=[]
for node in findNodes(self.doc.getroot(), "compounddef", kind="class", prot="public"):
self.findBaseNodes(node, orderedClassNodes)
return orderedClassNodes
def findBaseNodes(self, node, excludedClassNodes=[]):
if node in excludedClassNodes:
return
if node.attrib['prot'] == 'private':
return
nodeName = getText("compoundname", node)
if nodeName in self.skipClasses:
return
for baseNodePnt in findNodes(node, "basecompoundref", prot="public"):
if "refid" in baseNodePnt.attrib:
baseNodeID = baseNodePnt.attrib["refid"]
baseNode = self.getNodeByID(baseNodeID)
self.findBaseNodes(baseNode, excludedClassNodes)
excludedClassNodes.append(node)
def getClassMethods(self, classNode):
className = getText("compoundname", classNode)
shortClassName = stripOpenMMPrefix(className)
methodList = []
for section in findNodes(classNode, "sectiondef", kind="public-static-func")+findNodes(classNode, "sectiondef", kind="public-func"):
for memberNode in findNodes(section, "memberdef", kind="function", prot="public"):
methodDefinition = getText("definition", memberNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition)
methodName = shortMethodDefinition.split()[-1]
if className+'::'+methodName in self.skipMethods:
continue
methodList.append(memberNode)
return methodList
def shouldHideType(self, typeName):
if typeName.startswith('const '):
typeName = typeName[6:].strip()
if typeName.endswith('&') or typeName.endswith('*'):
typeName = typeName[:-1].strip()
return typeName in self.hideClasses
def shouldHideMethod(self, methodNode):
paramList = findNodes(methodNode, 'param')
returnType = self.getType(getText("type", methodNode))
if self.shouldHideType(returnType):
return True
for node in paramList:
try:
type = getText('type', node)
except IndexError:
type = getText('type/ref', node)
if self.shouldHideType(type):
return True
return False
class CHeaderGenerator(WrapperGenerator):
"""This class generates the header file for the C API wrappers."""
def __init__(self, inputDirname, output):
WrapperGenerator.__init__(self, inputDirname, output)
self.typeTranslations = {'bool': 'OpenMM_Boolean',
'Vec3': 'OpenMM_Vec3',
'std::string': 'char*',
'const std::string &': 'const char*',
'std::vector< std::string >': 'OpenMM_StringArray',
'std::vector< Vec3 >': 'OpenMM_Vec3Array',
'std::vector< std::pair< int, int > >': 'OpenMM_BondArray',
'std::map< std::string, double >': 'OpenMM_ParameterArray',
'std::map< std::string, std::string >': 'OpenMM_PropertyArray',
'std::vector< double >': 'OpenMM_DoubleArray',
'std::vector< int >': 'OpenMM_IntArray',
'std::set< int >': 'OpenMM_IntSet'}
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))
iDef = getText("initializer", memberNode)
if iDef.startswith("="):
iDef = iDef[1:]
self.out.write("static %s = %s;\n" % (vDef, iDef))
def writeTypeDeclarations(self):
self.out.write("\n/* Type Declarations */\n\n")
for classNode in self._orderedClassNodes:
className = getText("compoundname", classNode)
shortName = stripOpenMMPrefix(className)
typeName = convertOpenMMPrefix(className)
self.out.write("typedef struct %s_struct %s;\n" % (typeName, typeName))
self.typesByShortName[shortName] = typeName
def writeClasses(self):
for classNode in self._orderedClassNodes:
className = stripOpenMMPrefix(getText("compoundname", classNode))
self.out.write("\n/* %s */\n" % className)
self.writeEnumerations(classNode)
self.writeMethods(classNode)
self.out.write("\n")
def writeEnumerations(self, classNode):
enumNodes = []
for section in findNodes(classNode, "sectiondef", kind="public-type"):
for node in findNodes(section, "memberdef", kind="enum", prot="public"):
enumNodes.append(node)
className = getText("compoundname", classNode)
shortClassName = stripOpenMMPrefix(className)
typeName = convertOpenMMPrefix(className)
for enumNode in enumNodes:
enumName = getText("name", enumNode)
enumTypeName = "%s_%s" % (typeName, enumName)
self.out.write("typedef enum {\n ")
argSep=""
for valueNode in findNodes(enumNode, "enumvalue", prot="public"):
vName = convertOpenMMPrefix(getText("name", valueNode))
vInit = getText("initializer", valueNode)
if vInit.startswith("="):
vInit = vInit[1:].strip()
self.out.write("%s%s_%s = %s" % (argSep, typeName, vName, vInit))
argSep=", "
self.out.write("\n} %s;\n" % enumTypeName)
self.typesByShortName[enumName] = enumTypeName
if len(enumNodes)>0: self.out.write("\n")
def writeMethods(self, classNode):
methodList = self.getClassMethods(classNode)
className = getText("compoundname", classNode)
shortClassName = stripOpenMMPrefix(className)
typeName = convertOpenMMPrefix(className)
destructorName = '~'+shortClassName
isAbstract = any('virt' in method.attrib and method.attrib['virt'] == 'pure-virtual' for method in classNode.getiterator('memberdef'))
if not isAbstract:
# Write constructors
numConstructors = 0
for methodNode in methodList:
methodDefinition = getText("definition", methodNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition)
methodName = shortMethodDefinition.split()[-1]
if methodName == shortClassName:
if self.shouldHideMethod(methodNode):
continue
numConstructors += 1
if numConstructors == 1:
suffix = ""
else:
suffix = "_%d" % numConstructors
self.out.write("extern OPENMM_EXPORT %s* %s_create%s(" % (typeName, typeName, suffix))
self.writeArguments(methodNode, False)
self.out.write(");\n")
# Write destructor
self.out.write("extern OPENMM_EXPORT void %s_destroy(%s* target);\n" % (typeName, typeName))
# Record method names for future reference.
methodNames = {}
for methodNode in methodList:
methodDefinition = getText("definition", methodNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition)
methodNames[methodNode] = shortMethodDefinition.split()[-1]
# Write other methods
for methodNode in methodList:
methodName = methodNames[methodNode]
if methodName in (shortClassName, destructorName):
continue
if self.shouldHideMethod(methodNode):
continue
isConstMethod = (methodNode.attrib['const'] == 'yes')
if isConstMethod and any(methodNames[m] == methodName and m.attrib['const'] == 'no' for m in methodList):
# There are two identical methods that differ only in whether they are const. Skip the const one.
continue
returnType = self.getType(getText("type", methodNode))
self.out.write("extern OPENMM_EXPORT %s %s_%s(" % (returnType, typeName, methodName))
isInstanceMethod = (methodNode.attrib['static'] != 'yes')
if isInstanceMethod:
if isConstMethod:
self.out.write('const ')
self.out.write("%s* target" % typeName)
self.writeArguments(methodNode, isInstanceMethod)
self.out.write(");\n")
def writeArguments(self, methodNode, initialSeparator):
paramList = findNodes(methodNode, 'param')
if initialSeparator:
separator = ", "
else:
separator = ""
for node in paramList:
try:
type = getText('type', node)
except IndexError:
type = getText('type/ref', node)
if type == 'void':
continue
type = self.getType(type)
name = getText('declname', node)
self.out.write("%s%s %s" % (separator, type, name))
separator = ", "
def getType(self, type):
if type in self.typeTranslations:
return self.typeTranslations[type]
if type in self.typesByShortName:
return self.typesByShortName[type]
if type.startswith('const '):
return 'const '+self.getType(type[6:].strip())
if type.endswith('&') or type.endswith('*'):
return self.getType(type[:-1].strip())+'*'
return type
def writeOutput(self):
print("""
#ifndef OPENMM_CWRAPPER_H_
#define OPENMM_CWRAPPER_H_
#ifndef OPENMM_EXPORT
#define OPENMM_EXPORT
#endif
""", file=self.out)
self.writeGlobalConstants()
self.writeTypeDeclarations()
print("""
typedef struct OpenMM_Vec3Array_struct OpenMM_Vec3Array;
typedef struct OpenMM_StringArray_struct OpenMM_StringArray;
typedef struct OpenMM_BondArray_struct OpenMM_BondArray;
typedef struct OpenMM_ParameterArray_struct OpenMM_ParameterArray;
typedef struct OpenMM_PropertyArray_struct OpenMM_PropertyArray;
typedef struct OpenMM_DoubleArray_struct OpenMM_DoubleArray;
typedef struct OpenMM_IntArray_struct OpenMM_IntArray;
typedef struct OpenMM_IntSet_struct OpenMM_IntSet;
typedef struct {double x, y, z;} OpenMM_Vec3;
typedef enum {OpenMM_False = 0, OpenMM_True = 1} OpenMM_Boolean;
#if defined(__cplusplus)
extern "C" {
#endif
/* OpenMM_Vec3 */
extern OPENMM_EXPORT OpenMM_Vec3 OpenMM_Vec3_scale(const OpenMM_Vec3 vec, double scale);
/* OpenMM_Vec3Array */
extern OPENMM_EXPORT OpenMM_Vec3Array* OpenMM_Vec3Array_create(int size);
extern OPENMM_EXPORT void OpenMM_Vec3Array_destroy(OpenMM_Vec3Array* array);
extern OPENMM_EXPORT int OpenMM_Vec3Array_getSize(const OpenMM_Vec3Array* array);
extern OPENMM_EXPORT void OpenMM_Vec3Array_resize(OpenMM_Vec3Array* array, int size);
extern OPENMM_EXPORT void OpenMM_Vec3Array_append(OpenMM_Vec3Array* array, const OpenMM_Vec3 vec);
extern OPENMM_EXPORT void OpenMM_Vec3Array_set(OpenMM_Vec3Array* array, int index, const OpenMM_Vec3 vec);
extern OPENMM_EXPORT const OpenMM_Vec3* OpenMM_Vec3Array_get(const OpenMM_Vec3Array* array, int index);
/* OpenMM_StringArray */
extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_StringArray_create(int size);
extern OPENMM_EXPORT void OpenMM_StringArray_destroy(OpenMM_StringArray* array);
extern OPENMM_EXPORT int OpenMM_StringArray_getSize(const OpenMM_StringArray* array);
extern OPENMM_EXPORT void OpenMM_StringArray_resize(OpenMM_StringArray* array, int size);
extern OPENMM_EXPORT void OpenMM_StringArray_append(OpenMM_StringArray* array, const char* string);
extern OPENMM_EXPORT void OpenMM_StringArray_set(OpenMM_StringArray* array, int index, const char* string);
extern OPENMM_EXPORT const char* OpenMM_StringArray_get(const OpenMM_StringArray* array, int index);
/* OpenMM_BondArray */
extern OPENMM_EXPORT OpenMM_BondArray* OpenMM_BondArray_create(int size);
extern OPENMM_EXPORT void OpenMM_BondArray_destroy(OpenMM_BondArray* array);
extern OPENMM_EXPORT int OpenMM_BondArray_getSize(const OpenMM_BondArray* array);
extern OPENMM_EXPORT void OpenMM_BondArray_resize(OpenMM_BondArray* array, int size);
extern OPENMM_EXPORT void OpenMM_BondArray_append(OpenMM_BondArray* array, int particle1, int particle2);
extern OPENMM_EXPORT void OpenMM_BondArray_set(OpenMM_BondArray* array, int index, int particle1, int particle2);
extern OPENMM_EXPORT void OpenMM_BondArray_get(const OpenMM_BondArray* array, int index, int* particle1, int* particle2);
/* OpenMM_ParameterArray */
extern OPENMM_EXPORT int OpenMM_ParameterArray_getSize(const OpenMM_ParameterArray* array);
extern OPENMM_EXPORT double OpenMM_ParameterArray_get(const OpenMM_ParameterArray* array, const char* name);
/* OpenMM_PropertyArray */
extern OPENMM_EXPORT OpenMM_PropertyArray* OpenMM_PropertyArray_create();
extern OPENMM_EXPORT void OpenMM_PropertyArray_destroy(OpenMM_PropertyArray* array);
extern OPENMM_EXPORT void OpenMM_PropertyArray_add(OpenMM_PropertyArray* array, const char* name, const char* value);
extern OPENMM_EXPORT int OpenMM_PropertyArray_getSize(const OpenMM_PropertyArray* array);
extern OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyArray* array, const char* name);""", file=self.out)
for type in ('double', 'int'):
name = 'OpenMM_%sArray' % type.capitalize()
values = {'type':type, 'name':name}
print("""
/* %(name)s */
extern OPENMM_EXPORT %(name)s* %(name)s_create(int size);
extern OPENMM_EXPORT void %(name)s_destroy(%(name)s* array);
extern OPENMM_EXPORT int %(name)s_getSize(const %(name)s* array);
extern OPENMM_EXPORT void %(name)s_resize(%(name)s* array, int size);
extern OPENMM_EXPORT void %(name)s_append(%(name)s* array, %(type)s value);
extern OPENMM_EXPORT void %(name)s_set(%(name)s* array, int index, %(type)s value);
extern OPENMM_EXPORT %(type)s %(name)s_get(const %(name)s* array, int index);""" % values, file=self.out)
for type in ('int',):
name = 'OpenMM_%sSet' % type.capitalize()
values = {'type':type, 'name':name}
print("""
/* %(name)s */
extern OPENMM_EXPORT %(name)s* %(name)s_create();
extern OPENMM_EXPORT void %(name)s_destroy(%(name)s* set);
extern OPENMM_EXPORT int %(name)s_getSize(const %(name)s* set);
extern OPENMM_EXPORT void %(name)s_insert(%(name)s* set, %(type)s value);""" % values, file=self.out)
print("""
/* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox);
extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState_2(const OpenMM_Context* target, int types, int enforcePeriodicBox, int groups);
extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const char* directory);
extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_getPluginLoadFailures();
extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeSystem(const OpenMM_System* system);
extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeState(const OpenMM_State* state);
extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeIntegrator(const OpenMM_Integrator* integrator);
extern OPENMM_EXPORT OpenMM_System* OpenMM_XmlSerializer_deserializeSystem(const char* xml);
extern OPENMM_EXPORT OpenMM_State* OpenMM_XmlSerializer_deserializeState(const char* xml);
extern OPENMM_EXPORT OpenMM_Integrator* OpenMM_XmlSerializer_deserializeIntegrator(const char* xml);""", file=self.out)
self.writeClasses()
print("""
#if defined(__cplusplus)
}
#endif
#endif /*OPENMM_CWRAPPER_H_*/""", file=self.out)
class CSourceGenerator(WrapperGenerator):
"""This class generates the source file for the C API wrappers."""
def __init__(self, inputDirname, output):
WrapperGenerator.__init__(self, inputDirname, output)
self.typeTranslations = {'bool': 'OpenMM_Boolean',
'Vec3': 'OpenMM_Vec3',
'std::string': 'char*',
'const std::string &': 'const char*',
'std::vector< std::string >': 'OpenMM_StringArray',
'std::vector< Vec3 >': 'OpenMM_Vec3Array',
'std::vector< std::pair< int, int > >': 'OpenMM_BondArray',
'std::map< std::string, double >': 'OpenMM_ParameterArray',
'std::map< std::string, std::string >': 'OpenMM_PropertyArray',
'std::vector< double >': 'OpenMM_DoubleArray',
'std::vector< int >': 'OpenMM_IntArray',
'std::set< int >': 'OpenMM_IntSet'}
self.inverseTranslations = dict((self.typeTranslations[key], key) for key in self.typeTranslations)
self.classesByShortName = {}
self.enumerationTypes = {}
self.findTypes()
def findTypes(self):
for classNode in self._orderedClassNodes:
className = getText("compoundname", classNode)
shortName = stripOpenMMPrefix(className)
typeName = convertOpenMMPrefix(className)
self.typesByShortName[shortName] = typeName
self.classesByShortName[shortName] = className
def findEnumerations(self, classNode):
enumNodes = []
for section in findNodes(classNode, "sectiondef", kind="public-type"):
for node in findNodes(section, "memberdef", kind="enum", prot="public"):
enumNodes.append(node)
className = getText("compoundname", classNode)
typeName = convertOpenMMPrefix(className)
for enumNode in enumNodes:
enumName = getText("name", enumNode)
enumTypeName = "%s_%s" % (typeName, enumName)
enumClassName = "%s::%s" % (className, enumName)
self.typesByShortName[enumName] = enumTypeName
self.classesByShortName[enumName] = enumClassName
self.enumerationTypes[enumClassName] = enumTypeName
def writeClasses(self):
for classNode in self._orderedClassNodes:
className = stripOpenMMPrefix(getText("compoundname", classNode))
self.out.write("\n/* OpenMM::%s */\n" % className)
self.findEnumerations(classNode)
self.writeMethods(classNode)
self.out.write("\n")
def writeMethods(self, classNode):
methodList = self.getClassMethods(classNode)
className = getText("compoundname", classNode)
shortClassName = stripOpenMMPrefix(className)
typeName = convertOpenMMPrefix(className)
destructorName = '~'+shortClassName
isAbstract = any('virt' in method.attrib and method.attrib['virt'] == 'pure-virtual' for method in classNode.getiterator('memberdef'))
if not isAbstract:
# Write constructors
numConstructors = 0
for methodNode in methodList:
methodDefinition = getText("definition", methodNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition)
methodName = shortMethodDefinition.split()[-1]
if methodName == shortClassName:
if self.shouldHideMethod(methodNode):
continue
numConstructors += 1
if numConstructors == 1:
suffix = ""
else:
suffix = "_%d" % numConstructors
self.out.write("OPENMM_EXPORT %s* %s_create%s(" % (typeName, typeName, suffix))
self.writeArguments(methodNode, False)
self.out.write(") {\n")
self.out.write(" return reinterpret_cast<%s*>(new %s(" % (typeName, className))
self.writeInvocationArguments(methodNode, False)
self.out.write("));\n")
self.out.write("}\n")
# Write destructor
self.out.write("OPENMM_EXPORT void %s_destroy(%s* target) {\n" % (typeName, typeName))
self.out.write(" delete reinterpret_cast<%s*>(target);\n" % className)
self.out.write("}\n")
# Record method names for future reference.
methodNames = {}
for methodNode in methodList:
methodDefinition = getText("definition", methodNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition)
methodNames[methodNode] = shortMethodDefinition.split()[-1]
# Write other methods
for methodNode in methodList:
methodName = methodNames[methodNode]
if methodName in (shortClassName, destructorName):
continue
if self.shouldHideMethod(methodNode):
continue
isConstMethod = (methodNode.attrib['const'] == 'yes')
if isConstMethod and any(methodNames[m] == methodName and m.attrib['const'] == 'no' for m in methodList):
# There are two identical methods that differ only in whether they are const. Skip the const one.
continue
methodType = getText("type", methodNode)
returnType = self.getType(methodType)
if methodType in self.classesByShortName:
methodType = self.classesByShortName[methodType]
self.out.write("OPENMM_EXPORT %s %s_%s(" % (returnType, typeName, methodName))
isInstanceMethod = (methodNode.attrib['static'] != 'yes')
if isInstanceMethod:
if isConstMethod:
self.out.write('const ')
self.out.write("%s* target" % typeName)
self.writeArguments(methodNode, isInstanceMethod)
self.out.write(") {\n")
self.out.write(" ")
if returnType != 'void':
if methodType.endswith('&'):
# Convert references to pointers
self.out.write('%s* result = &' % methodType[:-1].strip())
else:
self.out.write('%s result = ' % methodType)
if isInstanceMethod:
self.out.write('reinterpret_cast<')
if isConstMethod:
self.out.write('const ')
self.out.write('%s*>(target)->' % className)
else:
self.out.write('%s::' % className)
self.out.write('%s(' % methodName)
self.writeInvocationArguments(methodNode, False)
self.out.write(');\n')
if returnType != 'void':
self.out.write(' return %s;\n' % self.wrapValue(methodType, 'result'))
self.out.write("}\n")
def writeArguments(self, methodNode, initialSeparator):
paramList = findNodes(methodNode, 'param')
if initialSeparator:
separator = ", "
else:
separator = ""
for node in paramList:
try:
type = getText('type', node)
except IndexError:
type = getText('type/ref', node)
if type == 'void':
continue
type = self.getType(type)
name = getText('declname', node)
self.out.write("%s%s %s" % (separator, type, name))
separator = ", "
def writeInvocationArguments(self, methodNode, initialSeparator):
paramList = findNodes(methodNode, 'param')
if initialSeparator:
separator = ", "
else:
separator = ""
for node in paramList:
try:
type = getText('type', node)
except IndexError:
type = getText('type/ref', node)
if type == 'void':
continue
name = getText('declname', node)
if self.getType(type) != type:
name = self.unwrapValue(type, name)
self.out.write("%s%s" % (separator, name))
separator = ", "
def getType(self, type):
if type in self.typeTranslations:
return self.typeTranslations[type]
if type in self.typesByShortName:
return self.typesByShortName[type]
if type.startswith('const '):
return 'const '+self.getType(type[6:].strip())
if type.endswith('&') or type.endswith('*'):
return self.getType(type[:-1].strip())+'*'
return type
def wrapValue(self, type, value):
if type == 'bool':
return '(%s ? OpenMM_True : OpenMM_False)' % value
if type == 'std::string':
return '%s.c_str()' % value
if type == 'const std::string &':
return '%s->c_str()' % value
if type in self.enumerationTypes:
return 'static_cast<%s>(%s)' % (self.enumerationTypes[type], value)
wrappedType = self.getType(type)
if wrappedType == type:
return value;
if type.endswith('*') or type.endswith('&'):
return 'reinterpret_cast<%s>(%s)' % (wrappedType, value)
return 'static_cast<%s>(%s)' % (wrappedType, value)
def unwrapValue(self, type, value):
if type.endswith('&'):
unwrappedType = type[:-1].strip()
if unwrappedType in self.classesByShortName:
unwrappedType = self.classesByShortName[unwrappedType]
if unwrappedType == 'const std::string':
return 'std::string(%s)' % value
return '*'+self.unwrapValue(unwrappedType+'*', value)
if type in self.classesByShortName:
return 'static_cast<%s>(%s)' % (self.classesByShortName[type], value)
if type == 'bool':
return value
return 'reinterpret_cast<%s>(%s)' % (type, value)
def writeOutput(self):
print("""
#include "OpenMM.h"
#include "OpenMMCWrapper.h"
#include <cstdlib>
#include <cstring>
#include <sstream>
#include <vector>
#include <stdio.h>
#include <stdlib.h>
using namespace OpenMM;
using namespace std;
extern "C" {
/* OpenMM_Vec3 */
OPENMM_EXPORT OpenMM_Vec3 OpenMM_Vec3_scale(const OpenMM_Vec3 vec, double scale) {
OpenMM_Vec3 result = {vec.x*scale, vec.y*scale, vec.z*scale};
return result;
}
/* OpenMM_Vec3Array */
OPENMM_EXPORT OpenMM_Vec3Array* OpenMM_Vec3Array_create(int size) {
return reinterpret_cast<OpenMM_Vec3Array*>(new vector<Vec3>(size));
}
OPENMM_EXPORT void OpenMM_Vec3Array_destroy(OpenMM_Vec3Array* array) {
delete reinterpret_cast<vector<Vec3>*>(array);
}
OPENMM_EXPORT int OpenMM_Vec3Array_getSize(const OpenMM_Vec3Array* array) {
return reinterpret_cast<const vector<Vec3>*>(array)->size();
}
OPENMM_EXPORT void OpenMM_Vec3Array_resize(OpenMM_Vec3Array* array, int size) {
reinterpret_cast<vector<Vec3>*>(array)->resize(size);
}
OPENMM_EXPORT void OpenMM_Vec3Array_append(OpenMM_Vec3Array* array, const OpenMM_Vec3 vec) {
reinterpret_cast<vector<Vec3>*>(array)->push_back(Vec3(vec.x, vec.y, vec.z));
}
OPENMM_EXPORT void OpenMM_Vec3Array_set(OpenMM_Vec3Array* array, int index, const OpenMM_Vec3 vec) {
(*reinterpret_cast<vector<Vec3>*>(array))[index] = Vec3(vec.x, vec.y, vec.z);
}
OPENMM_EXPORT const OpenMM_Vec3* OpenMM_Vec3Array_get(const OpenMM_Vec3Array* array, int index) {
return reinterpret_cast<const OpenMM_Vec3*>((&(*reinterpret_cast<const vector<Vec3>*>(array))[index]));
}
/* OpenMM_StringArray */
OPENMM_EXPORT OpenMM_StringArray* OpenMM_StringArray_create(int size) {
return reinterpret_cast<OpenMM_StringArray*>(new vector<string>(size));
}
OPENMM_EXPORT void OpenMM_StringArray_destroy(OpenMM_StringArray* array) {
delete reinterpret_cast<vector<string>*>(array);
}
OPENMM_EXPORT int OpenMM_StringArray_getSize(const OpenMM_StringArray* array) {
return reinterpret_cast<const vector<string>*>(array)->size();
}
OPENMM_EXPORT void OpenMM_StringArray_resize(OpenMM_StringArray* array, int size) {
reinterpret_cast<vector<string>*>(array)->resize(size);
}
OPENMM_EXPORT void OpenMM_StringArray_append(OpenMM_StringArray* array, const char* str) {
reinterpret_cast<vector<string>*>(array)->push_back(string(str));
}
OPENMM_EXPORT void OpenMM_StringArray_set(OpenMM_StringArray* array, int index, const char* str) {
(*reinterpret_cast<vector<string>*>(array))[index] = string(str);
}
OPENMM_EXPORT const char* OpenMM_StringArray_get(const OpenMM_StringArray* array, int index) {
return (*reinterpret_cast<const vector<string>*>(array))[index].c_str();
}
/* OpenMM_BondArray */
OPENMM_EXPORT OpenMM_BondArray* OpenMM_BondArray_create(int size) {
return reinterpret_cast<OpenMM_BondArray*>(new vector<pair<int, int> >(size));
}
OPENMM_EXPORT void OpenMM_BondArray_destroy(OpenMM_BondArray* array) {
delete reinterpret_cast<vector<pair<int, int> >*>(array);
}
OPENMM_EXPORT int OpenMM_BondArray_getSize(const OpenMM_BondArray* array) {
return reinterpret_cast<const vector<pair<int, int> >*>(array)->size();
}
OPENMM_EXPORT void OpenMM_BondArray_resize(OpenMM_BondArray* array, int size) {
reinterpret_cast<vector<pair<int, int> >*>(array)->resize(size);
}
OPENMM_EXPORT void OpenMM_BondArray_append(OpenMM_BondArray* array, int particle1, int particle2) {
reinterpret_cast<vector<pair<int, int> >*>(array)->push_back(pair<int, int>(particle1, particle2));
}
OPENMM_EXPORT void OpenMM_BondArray_set(OpenMM_BondArray* array, int index, int particle1, int particle2) {
(*reinterpret_cast<vector<pair<int, int> >*>(array))[index] = pair<int, int>(particle1, particle2);
}
OPENMM_EXPORT void OpenMM_BondArray_get(const OpenMM_BondArray* array, int index, int* particle1, int* particle2) {
pair<int, int> particles = (*reinterpret_cast<const vector<pair<int, int> >*>(array))[index];
*particle1 = particles.first;
*particle2 = particles.second;
}
/* OpenMM_ParameterArray */
OPENMM_EXPORT int OpenMM_ParameterArray_getSize(const OpenMM_ParameterArray* array) {
return reinterpret_cast<const map<string, double>*>(array)->size();
}
OPENMM_EXPORT double OpenMM_ParameterArray_get(const OpenMM_ParameterArray* array, const char* name) {
const map<string, double>* params = reinterpret_cast<const map<string, double>*>(array);
const map<string, double>::const_iterator iter = params->find(string(name));
if (iter == params->end())
throw OpenMMException("OpenMM_ParameterArray_get: No such parameter");
return iter->second;
}
/* OpenMM_PropertyArray */
OPENMM_EXPORT OpenMM_PropertyArray* OpenMM_PropertyArray_create() {
return reinterpret_cast<OpenMM_PropertyArray*>(new map<string, string>);
}
OPENMM_EXPORT void OpenMM_PropertyArray_destroy(OpenMM_PropertyArray* array) {
delete reinterpret_cast<map<string, string>*>(array);
}
OPENMM_EXPORT void OpenMM_PropertyArray_add(OpenMM_PropertyArray* array, const char* name, const char* value) {
reinterpret_cast<map<string, string>*>(array)->operator[](string(name)) = string(value);
}
OPENMM_EXPORT int OpenMM_PropertyArray_getSize(const OpenMM_PropertyArray* array) {
return reinterpret_cast<const map<string, double>*>(array)->size();
}
OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyArray* array, const char* name) {
const map<string, string>* params = reinterpret_cast<const map<string, string>*>(array);
const map<string, string>::const_iterator iter = params->find(string(name));
if (iter == params->end())
throw OpenMMException("OpenMM_PropertyArray_get: No such property");
return iter->second.c_str();
}""", file=self.out)
for type in ('double', 'int'):
name = 'OpenMM_%sArray' % type.capitalize()
values = {'type':type, 'name':name}
print("""
/* %(name)s */
OPENMM_EXPORT %(name)s* %(name)s_create(int size) {
return reinterpret_cast<%(name)s*>(new vector<%(type)s>(size));
}
OPENMM_EXPORT void %(name)s_destroy(%(name)s* array) {
delete reinterpret_cast<vector<%(type)s>*>(array);
}
OPENMM_EXPORT int %(name)s_getSize(const %(name)s* array) {
return reinterpret_cast<const vector<%(type)s>*>(array)->size();
}
OPENMM_EXPORT void %(name)s_resize(%(name)s* array, int size) {
reinterpret_cast<vector<%(type)s>*>(array)->resize(size);
}
OPENMM_EXPORT void %(name)s_append(%(name)s* array, %(type)s value) {
reinterpret_cast<vector<%(type)s>*>(array)->push_back(value);
}
OPENMM_EXPORT void %(name)s_set(%(name)s* array, int index, %(type)s value) {
(*reinterpret_cast<vector<%(type)s>*>(array))[index] = value;
}
OPENMM_EXPORT %(type)s %(name)s_get(const %(name)s* array, int index) {
return (*reinterpret_cast<const vector<%(type)s>*>(array))[index];
}""" % values, file=self.out)
for type in ('int',):
name = 'OpenMM_%sSet' % type.capitalize()
values = {'type':type, 'name':name}
print("""
/* %(name)s */
OPENMM_EXPORT %(name)s* %(name)s_create() {
return reinterpret_cast<%(name)s*>(new set<%(type)s>());
}
OPENMM_EXPORT void %(name)s_destroy(%(name)s* s) {
delete reinterpret_cast<set<%(type)s>*>(s);
}
OPENMM_EXPORT int %(name)s_getSize(const %(name)s* s) {
return reinterpret_cast<const set<%(type)s>*>(s)->size();
}
OPENMM_EXPORT void %(name)s_insert(%(name)s* s, %(type)s value) {
reinterpret_cast<set<%(type)s>*>(s)->insert(value);
}""" % values, file=self.out)
print("""
/* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox) {
State result = reinterpret_cast<const Context*>(target)->getState(types, enforcePeriodicBox);
return reinterpret_cast<OpenMM_State*>(new State(result));
}
OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState_2(const OpenMM_Context* target, int types, int enforcePeriodicBox, int groups) {
State result = reinterpret_cast<const Context*>(target)->getState(types, enforcePeriodicBox, groups);
return reinterpret_cast<OpenMM_State*>(new State(result));
}
OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const char* directory) {
vector<string> result = Platform::loadPluginsFromDirectory(string(directory));
return reinterpret_cast<OpenMM_StringArray*>(new vector<string>(result));
}
OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_getPluginLoadFailures() {
vector<string> result = Platform::getPluginLoadFailures();
return reinterpret_cast<OpenMM_StringArray*>(new vector<string>(result));
}
static char* createStringFromStream(stringstream& stream) {
int length = stream.str().size();
char* result = (char*) malloc(length+1);
stream.str().copy(result, length);
result[length] = 0;
return result;
}
OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeSystem(const OpenMM_System* system) {
stringstream stream;
OpenMM::XmlSerializer::serialize<OpenMM::System>(reinterpret_cast<const OpenMM::System*>(system), "System", stream);
return createStringFromStream(stream);
}
OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeState(const OpenMM_State* state) {
stringstream stream;
OpenMM::XmlSerializer::serialize<OpenMM::State>(reinterpret_cast<const OpenMM::State*>(state), "State", stream);
return createStringFromStream(stream);
}
OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeIntegrator(const OpenMM_Integrator* integrator) {
stringstream stream;
OpenMM::XmlSerializer::serialize<OpenMM::Integrator>(reinterpret_cast<const OpenMM::Integrator*>(integrator), "Integrator", stream);
return createStringFromStream(stream);
}
OPENMM_EXPORT OpenMM_System* OpenMM_XmlSerializer_deserializeSystem(const char* xml) {
string input(xml);
stringstream stream(input);
return reinterpret_cast<OpenMM_System*>(OpenMM::XmlSerializer::deserialize<OpenMM::System>(stream));
}
OPENMM_EXPORT OpenMM_State* OpenMM_XmlSerializer_deserializeState(const char* xml) {
string input(xml);
stringstream stream(input);
return reinterpret_cast<OpenMM_State*>(OpenMM::XmlSerializer::deserialize<OpenMM::State>(stream));
}
OPENMM_EXPORT OpenMM_Integrator* OpenMM_XmlSerializer_deserializeIntegrator(const char* xml) {
string input(xml);
stringstream stream(input);
return reinterpret_cast<OpenMM_Integrator*>(OpenMM::XmlSerializer::deserialize<OpenMM::Integrator>(stream));
}""", file=self.out)
self.writeClasses()
print("}\n", file=self.out)
class FortranHeaderGenerator(WrapperGenerator):
"""This class generates the header file for the Fortran API wrappers."""
def __init__(self, inputDirname, output):
WrapperGenerator.__init__(self, inputDirname, output)
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)',
'std::vector< Vec3 >': 'type (OpenMM_Vec3Array)',
'std::vector< std::pair< int, int > >': 'type (OpenMM_BondArray)',
'std::map< std::string, double >': 'type (OpenMM_ParameterArray)',
'std::map< std::string, std::string >': 'type (OpenMM_PropertyArray)',
'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("name", memberNode))
iDef = getText("initializer", memberNode)
if iDef.startswith("="):
iDef = iDef[1:]
self.out.write(" real*8, parameter :: OpenMM_%s = %s\n" % (vDef, iDef))
def writeTypeDeclarations(self):
self.out.write("\n ! Type Declarations\n")
for classNode in self._orderedClassNodes:
className = getText("compoundname", classNode)
shortName = stripOpenMMPrefix(className)
typeName = convertOpenMMPrefix(className)
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
def writeClasses(self):
for classNode in self._orderedClassNodes:
className = getText("compoundname", classNode)
self.out.write("\n ! %s\n" % className)
self.writeMethods(classNode)
self.out.write("\n")
def writeEnumerations(self, classNode):
enumNodes = []
for section in findNodes(classNode, "sectiondef", kind="public-type"):
for node in findNodes(section, "memberdef", kind="enum", prot="public"):
enumNodes.append(node)
className = getText("compoundname", classNode)
typeName = convertOpenMMPrefix(className)
for enumNode in enumNodes:
for valueNode in findNodes(enumNode, "enumvalue", prot="public"):
vName = convertOpenMMPrefix(getText("name", valueNode))
vInit = getText("initializer", valueNode)
if vInit.startswith("="):
vInit = vInit[1:].strip()
self.out.write(" integer*4, parameter :: %s_%s = %s\n" % (typeName, vName, vInit))
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):
methodList = self.getClassMethods(classNode)
className = getText("compoundname", classNode)
shortClassName = stripOpenMMPrefix(className)
typeName = convertOpenMMPrefix(className)
destructorName = '~'+shortClassName
isAbstract = any('virt' in method.attrib and method.attrib['virt'] == 'pure-virtual' for method in classNode.getiterator('memberdef'))
if not isAbstract:
# Write constructors
numConstructors = 0
for methodNode in methodList:
methodDefinition = getText("definition", methodNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition)
methodName = shortMethodDefinition.split()[-1]
if methodName == shortClassName:
if self.shouldHideMethod(methodNode):
continue
numConstructors += 1
if numConstructors == 1:
suffix = ""
else:
suffix = "_%d" % numConstructors
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)
self.declareArguments(methodNode)
self.out.write(" end subroutine\n")
# Write destructor
self.out.write(" subroutine %s_destroy(destroy)\n" % typeName)
self.out.write(" use OpenMM_Types; implicit none\n")
self.out.write(" type (%s) destroy\n" % typeName)
self.out.write(" end subroutine\n")
# Record method names for future reference.
methodNames = {}
for methodNode in methodList:
methodDefinition = getText("definition", methodNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition)
methodNames[methodNode] = shortMethodDefinition.split()[-1]
# Write other methods
for methodNode in methodList:
methodName = methodNames[methodNode]
if methodName in (shortClassName, destructorName):
continue
if self.shouldHideMethod(methodNode):
continue
isConstMethod = (methodNode.attrib['const'] == 'yes')
if isConstMethod and any(methodNames[m] == methodName and m.attrib['const'] == 'no' for m in methodList):
# There are two identical methods that differ only in whether they are const. Skip the const one.
continue
returnType = self.getType(getText("type", methodNode))
hasReturnValue = (returnType in ('integer*4', 'real*8'))
hasReturnArg = not (hasReturnValue or returnType == 'void')
functionName = "%s_%s" % (typeName, methodName)
functionName = functionName[:63]