def constants(self):
"""Replacing the constantVarValues attribute of scrn.Network instances,
as it is buggy and does not update upon changing p in certain ways.
"""
return Series([var.value for var in self.constantVars],
self.constantVars.keys(),
dtype=np.float)
def get_dxdt(net):
"""Get the velocities of species dynamics, dx/dt.
(Another way of getting it is N*v.)
"""
if not hasattr(net, 'res_function'):
net.compile()
# assume it is an autonomous dynamical system
# (time-invariant, hence t=0 here)
dxdt = net.res_function(0, net.x, np.zeros(net.xdim), net.constants)
return Series(dxdt, index=net.xids)
def v(self):
return Series(OD([(rxn.id, self.evaluate_expr(rxn.kineticLaw))
for rxn in self.reactions]),
dtype=np.float)
def asgrules(self):
return Series(OD(self.assignmentRules.items()), dtype=object)
def ratelaws(self):
return Series(OD([(rxn.id, rxn.kineticLaw) for rxn in self.reactions]),
dtype=object)
def rxns(self):
return Series(OD([(rxn.id, rxn) for rxn in self.reactions]),
dtype=object)
def varvals(self):
return Series(OD([(var.id, var.value) for var in self.variables]),
dtype=np.float)
def vars(self):
return Series(OD(self.variables.items()), dtype=object)
def c(self):
return Series(OD([(sp.id, sp.value) for sp in self.species
if sp.is_constant]),
dtype=np.float)
def x(self):
return Series([var.value for var in self.dynamicVars],
self.xids, dtype=np.float)
def p0(self):
return Series([var.initialValue for var in self.optimizableVars],
self.pids, dtype=np.float)
def get_J(net, *args, **kwargs):
"""Get steady-state flux.
"""
set_ss(net, *args, **kwargs)
return Series(net.v.values, net.Jids)