def get_model(is_netfree=False, without_reset=False, seeds=None):
if any([
not isinstance(rr, ecell4.core.ReactionRule)
for rr in REACTION_RULES
]):
from ecell4.ode import ODENetworkModel
m = ODENetworkModel()
elif seeds is not None or is_netfree:
m = ecell4.core.NetfreeModel()
else:
m = ecell4.core.NetworkModel()
for sp in SPECIES_ATTRIBUTES:
m.add_species_attribute(sp)
for rr in REACTION_RULES:
m.add_reaction_rule(rr)
for param in PARAMETERS:
m.add_parameter(param)
if not without_reset:
reset_model()
if seeds is not None:
return m.expand(seeds)
return m
def get_model(is_netfree=False, without_reset=False, seeds=None, effective=False):
"""
Generate a model with parameters in the global scope, ``SPECIES_ATTRIBUTES``
and ``REACTIONRULES``.
Parameters
----------
is_netfree : bool, optional
Return ``NetfreeModel`` if True, and ``NetworkModel`` if else.
Default is False.
without_reset : bool, optional
Do not reset the global variables after the generation if True.
Default is False.
seeds : list, optional
A list of seed ``Species`` for expanding the model.
If this is not None, generate a ``NetfreeModel`` once, and return a
``NetworkModel``, which is an expanded form of that with the given seeds.
Default is None.
effective : bool, optional
See ``NetfreeModel.effective`` and ``Netfree.set_effective``.
Only meaningfull with option ``is_netfree=True``.
Default is False
Returns
-------
model : NetworkModel, NetfreeModel, or ODENetworkModel
"""
try:
if any([not isinstance(rr, ecell4.core.ReactionRule) for rr in REACTION_RULES]):
from ecell4.ode import ODENetworkModel
m = ODENetworkModel()
elif seeds is not None or is_netfree:
m = ecell4.core.NetfreeModel()
else:
m = ecell4.core.NetworkModel()
for sp in SPECIES_ATTRIBUTES:
m.add_species_attribute(sp)
for rr in REACTION_RULES:
m.add_reaction_rule(rr)
if not without_reset:
reset_model()
if seeds is not None:
return m.expand(seeds)
if isinstance(m, ecell4.core.NetfreeModel):
m.set_effective(effective)
except Exception as e:
reset_model()
raise e
return m
def get_model(is_netfree=False, without_reset=False, seeds=None, effective=False):
"""
Generate a model with parameters in the global scope, ``SPECIES_ATTRIBUTES``
and ``REACTIONRULES``.
Parameters
----------
is_netfree : bool, optional
Return ``NetfreeModel`` if True, and ``NetworkModel`` if else.
Default is False.
without_reset : bool, optional
Do not reset the global variables after the generation if True.
Default is False.
seeds : list, optional
A list of seed ``Species`` for expanding the model.
If this is not None, generate a ``NetfreeModel`` once, and return a
``NetworkModel``, which is an expanded form of that with the given seeds.
Default is None.
effective : bool, optional
See ``NetfreeModel.effective`` and ``Netfree.set_effective``.
Only meaningfull with option ``is_netfree=True``.
Default is False
Returns
-------
model : NetworkModel, NetfreeModel, or ODENetworkModel
"""
if any([not isinstance(rr, ecell4.core.ReactionRule) for rr in REACTION_RULES]):
from ecell4.ode import ODENetworkModel
m = ODENetworkModel()
elif seeds is not None or is_netfree:
m = ecell4.core.NetfreeModel()
else:
m = ecell4.core.NetworkModel()
for sp in SPECIES_ATTRIBUTES:
m.add_species_attribute(sp)
for rr in REACTION_RULES:
m.add_reaction_rule(rr)
if not without_reset:
reset_model()
if seeds is not None:
return m.expand(seeds)
if isinstance(m, ecell4.core.NetfreeModel):
m.set_effective(effective)
return m
def get_model(is_netfree=False, without_reset=False, seeds=None):
if any([not isinstance(rr, ecell4.core.ReactionRule) for rr in REACTION_RULES]):
from ecell4.ode import ODENetworkModel
m = ODENetworkModel()
elif seeds is not None or is_netfree:
m = ecell4.core.NetfreeModel()
else:
m = ecell4.core.NetworkModel()
for sp in SPECIES_ATTRIBUTES:
m.add_species_attribute(sp)
for rr in REACTION_RULES:
m.add_reaction_rule(rr)
for param in PARAMETERS:
m.add_parameter(param)
if not without_reset:
reset_model()
if seeds is not None:
return m.expand(seeds)
return m
