def getSpecies(self):
Parser.getSpecies(self)
for k in range(0, len(self.listOfSpecies)):
if ((len(self.writer.parsedModel.speciesId) - self.comp) < 9):
self.writer.parsedModel.speciesId.append("species0" +
repr(k + 1))
else:
self.writer.parsedModel.speciesId.append("species" +
repr(k + 1))
def parse(self):
Parser.parse(self)
self.getGlobalParameters()
self.getSpecies()
self.analyseModelStructure()
self.analyseFunctions()
self.analyseRules()
self.analyseEvents()
self.renameEverything()
def getGlobalParameters(self):
Parser.getGlobalParameters(self)
for i in range(0, self.writer.parsedModel.numGlobalParameters):
if ((len(self.writer.parsedModel.parameterId) - self.comp) < 9):
self.writer.parsedModel.parameterId.append("parameter0" +
repr(i + 1))
else:
self.writer.parsedModel.parameterId.append("parameter" +
repr(i + 1))
def __init__(self,
sbmlFileName,
modelName,
integrationType,
method,
inputPath="",
outputPath=""):
self.mathPython = []
self.mathCuda = []
Parser.__init__(self, sbmlFileName, modelName, integrationType, method,
inputPath, outputPath)
def analyseModelStructure(self):
Parser.analyseModelStructure(self)
for i in range(0, len(self.listOfReactions)):
for n in range(0, self.numLocalParameters[i]):
self.parameterId.append(self.listOfReactions[i].getKineticLaw().getParameter(n).getId())
self.writer.parsedModel.parameterId.append("parameter"+repr(len(self.parameterId)-self.comp))
name = self.listOfReactions[i].getKineticLaw().getParameter(n).getId()
new_name = 'parameter' + repr(len(self.parameterId) - self.comp)
node = self.sbmlModel.getReaction(i).getKineticLaw().getMath()
new_node = self.rename(node, name, new_name)
self.writer.parsedModel.kineticLaw[i] = formulaToString(new_node)
def renameEverything(self):
Parser.renameEverything(self)
for nam in range(0, len(self.mathPython)):
for k in range(0, len(self.writer.parsedModel.kineticLaw)):
if re.search(self.mathPython[nam],
self.writer.parsedModel.kineticLaw[k]):
s = self.writer.parsedModel.kineticLaw[k]
s = re.sub(self.mathPython[nam], self.mathCuda[nam], s)
self.writer.parsedModel.kineticLaw[k] = s
for k in range(0, len(self.writer.parsedModel.ruleFormula)):
if re.search(self.mathPython[nam],
self.writer.parsedModel.ruleFormula[k]):
s = self.writer.parsedModel.ruleFormula[k]
s = re.sub(self.mathPython[nam], self.mathCuda[nam], s)
self.writer.parsedModel.ruleFormula[k] = s
for k in range(0, len(self.writer.parsedModel.eventFormula)):
for cond in range(0, len(self.listOfAssignmentRules)):
if re.search(
self.mathPython[nam],
self.writer.parsedModel.eventFormula[k][cond]):
s = self.writer.parsedModel.eventFormula[k][cond]
s = re.sub(self.mathPython[nam], self.mathCuda[nam], s)
self.writer.parsedModel.eventFormula[k][cond] = s
for k in range(0, len(self.writer.parsedModel.eventCondition)):
if re.search(self.mathPython[nam],
self.writer.parsedModel.eventCondition[k]):
s = self.writer.parsedModel.eventCondition[k]
s = re.sub(self.mathPython[nam], self.mathCuda[nam], s)
self.writer.parsedModel.eventCondition[k] = s
for k in range(0, len(self.writer.parsedModel.functionBody)):
if re.search(self.mathPython[nam],
self.writer.parsedModel.functionBody[k]):
s = self.writer.parsedModel.functionBody[k]
s = re.sub(self.mathPython[nam], self.mathCuda[nam], s)
self.writer.parsedModel.functionBody[k] = s
for fun in range(0, len(self.writer.parsedModel.listOfFunctions)):
for k in range(
0, len(self.writer.parsedModel.functionArgument[fun])):
if re.search(
self.mathPython[nam],
self.writer.parsedModel.functionArgument[fun][k]):
s = self.writer.parsedModel.functionArgument[fun][k]
s = re.sub(self.mathPython[nam], self.mathCuda[nam], s)
self.writer.parsedModel.functionArgument[fun][k] = s
def __init__(self, sbmlFileName, modelName, integrationType, method, inputPath="", outputPath=""):
Parser.__init__(self, sbmlFileName, modelName, integrationType, method, inputPath, outputPath)
def getSpecies(self):
Parser.getSpecies(self)
for k in range(0, len(self.listOfSpecies)):
self.writer.parsedModel.speciesId.append("species"+repr(k+1))
def getGlobalParameters(self):
Parser.getGlobalParameters(self)
for i in range(0,self.writer.parsedModel.numGlobalParameters):
self.writer.parsedModel.parameterId.append("parameter"+repr(i+1))