def mathForFortran(self):
"""
Takes the libSBML mathNode AST tree of this Reaction's
KineticLaw and converts it into
something that is valid FORTRAN code. (e.g. "pow(x,2)" becomes
"x ** 2", etc.)
"""
if not self.kineticLaw:
return
validFortran = helpers.handleMathNode(self.kineticLaw.getMath())
# we start with replacing the longest IDs first. should help
# to minimize problems with IDs that are substrings of longer IDs
# Note: The problem still persists, it's not gone entirely. (Because
# the replacement also contains the original ID and can still overlap
# with other IDs.)
sortedLocalParamIDs = sorted(self.localParameterIDs, key=len, reverse=True)
for localParam in sortedLocalParamIDs:
if localParam in validFortran:
validFortran = validFortran.replace(localParam, "%s_%s" % (self.id, localParam))
return validFortran
def mathForFortran(self):
"""
Takes the libSBML mathNode AST tree of this Reaction's
KineticLaw and converts it into
something that is valid FORTRAN code. (e.g. "pow(x,2)" becomes
"x ** 2", etc.)
"""
if not self.kineticLaw:
return
validFortran = helpers.handleMathNode(self.kineticLaw.getMath())
# we start with replacing the longest IDs first. should help
# to minimize problems with IDs that are substrings of longer IDs
# Note: The problem still persists, it's not gone entirely. (Because
# the replacement also contains the original ID and can still overlap
# with other IDs.)
sortedLocalParamIDs = sorted(self.localParameterIDs,
key=len,
reverse=True)
for localParam in sortedLocalParamIDs:
if localParam in validFortran:
validFortran = validFortran.replace(
localParam, "%s_%s" % (self.id, localParam))
return validFortran
def mathForFortran(self):
"""
Takes the current libSBML mathNode AST tree and converts it into
something that is valid FORTRAN code. (e.g. "pow(x,2)" becomes
"x ** 2", etc.)
"""
odeString = helpers.handleMathNode(self.mathNode)
return odeString
def mathForFortran(self):
"""
Takes the current libSBML mathNode AST tree and converts it into
something that is valid FORTRAN code. (e.g. "pow(x,2)" becomes
"x ** 2", etc.)
"""
odeString = helpers.handleMathNode(self.mathNode)
return odeString
def mathForFortran(self):
"""
DEPRECATED! The FORTRAN backend is no longer... :)
Takes the current libSBML mathNode AST tree and converts it into
something that is valid FORTRAN code. (e.g. "pow(x,2)" becomes
"x ** 2", etc.)
If "formula" was given during creation of this instance it is assumed
that this formula string already is valid FORTRAN code. It will
be returned unaltered.
"""
if self.formula:
return self.formula
# else: get string from self.mathNode (libSBML ASTNode graph)
odeString = helpers.handleMathNode(self.mathNode)
return odeString
def mathForFortran(self):
"""
DEPRECATED! The FORTRAN backend is no longer... :)
Takes the current libSBML mathNode AST tree and converts it into
something that is valid FORTRAN code. (e.g. "pow(x,2)" becomes
"x ** 2", etc.)
If "formula" was given during creation of this instance it is assumed
that this formula string already is valid FORTRAN code. It will
be returned unaltered.
"""
if self.formula:
return self.formula
# else: get string from self.mathNode (libSBML ASTNode graph)
odeString = helpers.handleMathNode(self.mathNode)
return odeString