class ParameterValues(object):
"""
Parameters set for kinetic models wich can be indexed with symbols or
"""
def __init__(self, parameter_values, kmodel=None):
"""
:param kmodel: KineticModel class
:param parameter_values: a dict contaning parameter names and values
"""
if parameter_values.__class__ is Series:
parameter_values = parameter_values.to_dict()
self._parameter_values = TabDict([
(str(p), v) for p, v in parameter_values.items()
])
# Check if this is a good solution
if kmodel is not None:
model_params = kmodel.parameters
self._str_to_sym = {
p: model_params[p].symbol
for p in model_params
}
else:
self._str_to_sym = {p: Symbol(p) for p in parameter_values}
self._sym_to_str = {
self._str_to_sym[p]: p
for p in self._parameter_values
}
#self._str_to_param = {p:model_params[p] for p in self._parameter_values}
def __getitem__(self, item):
if item.__class__ is str:
return self._parameter_values[item]
if item.__class__ is Symbol:
return self._parameter_values[self._sym_to_str[item]]
def __setitem__(self, item, value):
if item.__class__ is str:
self._parameter_values[item] = value
if item.__class__ is Symbol:
self._parameter_values[self._sym_to_str[item]] = value
def items(self):
return self._parameter_values.items()
def keys(self):
return self._parameter_values.keys()
def values(self):
return self._parameter_values.values()
def reactant_stoichiometry(self):
reactant_stoichiometry = TabDict([])
for k, v in self.mechanism.reactant_stoichiometry.items():
if self.mechanism.reactants[k].type == VARIABLE:
this_reactant = self.mechanism.reactants[k]
if this_reactant in reactant_stoichiometry.keys():
reactant_stoichiometry[this_reactant] += v
else:
reactant_stoichiometry[this_reactant] = v
for this_modifier in self.modifiers.values():
for k, v in this_modifier.reactants.items():
if v.type == VARIABLE and this_modifier.reactant_stoichiometry[
k] != 0:
reactant_stoichiometry[
v] = this_modifier.reactant_stoichiometry[k]
return reactant_stoichiometry