def add_structural_reaction(self,
name,
topology_type,
reaction_function,
rate_function,
expect_connected=False):
"""
Adds a spatially independent structural topology reaction for a certain topology type. It basically consists
out of two functions:
* the reaction function, taking a topology object as input and returning a reaction recipe describing what
the structural changes are to be applied to the topology
* the rate function, which takes a topology object as input and returns a corresponding fixed rate
It should be noted that the rate function will only be evaluated upon changes of the topology, i.e., as rarely
as possible. The reaction function is evaluated when the actual reaction takes place. Also the rate is expected
to be returned in terms of the magnitude w.r.t. the default units.
:param name: name of the structural reaction, has to be unique; otherwise an exception is raised
:param topology_type: the topology type for which this reaction is evaluated
:param reaction_function: the reaction function, as described above
:param rate_function: the rate function, as described above
:param expect_connected: can trigger a raise if set to true and the topology's connectivity graph decayed into
two or more independent components.
"""
fun1, fun2 = _top.ReactionFunction(lambda x: reaction_function(x)._get(
)), _top.RateFunction(rate_function)
reaction = _top.StructuralTopologyReaction(name, fun1, fun2)
if expect_connected:
reaction.expect_connected_after_reaction()
else:
reaction.create_child_topologies_after_reaction()
self._registry.add_structural_reaction(topology_type, reaction)
def _get_decay_reaction(self):
def reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
if topology.get_n_particles() == 1:
recipe.change_particle_type(0, "B")
return recipe._get()
def rate_function(topology):
return 1.0 if topology.get_n_particles() == 1 else 0
fun1, fun2 = top.ReactionFunction(reaction_function), top.RateFunction(rate_function)
reaction = top.StructuralTopologyReaction(fun1, fun2)
reaction.raise_if_invalid()
reaction.create_child_topologies_after_reaction()
return reaction
def _get_decay_reaction(self, typeidb):
def reaction_function(topology):
recipe = top.Recipe(topology)
if topology.get_n_particles() == 1:
recipe.change_particle_type(0, typeidb)
return recipe
def rate_function(topology):
return 1. / self.time_step if topology.get_n_particles(
) == 1 else 0
fun1, fun2 = top.ReactionFunction(reaction_function), top.RateFunction(
rate_function)
reaction = top.TopologyReaction(fun1, fun2)
reaction.raise_if_invalid()
reaction.create_child_topologies_after_reaction()
return reaction
def _get_split_reaction(self):
def reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
if topology.get_n_particles() > 1:
edge = np.random.randint(0, topology.get_n_particles() - 1)
recipe.remove_edge(edge, edge + 1)
return recipe._get()
def rate_function(topology):
if topology.get_n_particles() > 1:
return topology.get_n_particles() / 20.
else:
return .0
fun1 = top.ReactionFunction(reaction_function)
fun2 = top.RateFunction(rate_function)
reaction = top.StructuralTopologyReaction("split", fun1, fun2)
reaction.create_child_topologies_after_reaction()
return reaction
def _get_split_reaction(self):
def reaction_function(topology):
recipe = top.Recipe(topology)
if topology.get_n_particles() > 1:
edge = np.random.randint(0, topology.get_n_particles() - 1)
recipe.remove_edge(edge, edge + 1)
return recipe
def rate_function(topology):
if topology.get_n_particles() > 1:
return topology.get_n_particles() / 20.
else:
return .0
fun1 = top.ReactionFunction(reaction_function)
fun2 = top.RateFunction(rate_function)
reaction = top.TopologyReaction(fun1, fun2)
reaction.roll_back_if_invalid()
reaction.create_child_topologies_after_reaction()
return reaction
def add_structural_reaction(self,
topology_type,
reaction_function,
rate_function,
raise_if_invalid=True,
expect_connected=False):
"""
Adds a spatially independent structural topology reaction for a certain topology type. It basically consists
out of two functions:
* the reaction function, taking a topology object as input and returning a reaction recipe describing what
the structural changes are to be applied to the topology
* the rate function, which takes a topology object as input and returns a corresponding fixed rate
It should be noted that the rate function will only be evaluated upon changes of the topology, i.e., as rarely
as possible. The reaction function is evaluated when the actual reaction takes place. Also the rate is expected
to be returned in terms of the magnitude w.r.t. the default units.
:param topology_type: the topology type for which this reaction is evaluated
:param reaction_function: the reaction function, as described above
:param rate_function: the rate function, as described above
:param raise_if_invalid: raises an error if the outcome of the reaction function is invalid and set to True,
otherwise it will just roll back to the state of before the reaction and print a
warning into the log
:param expect_connected: can trigger a raise if set to true and the topology's connectivity graph decayed into
two or more independent components, depending on the value of `raise_if_invalid`.
"""
fun1, fun2 = _top.ReactionFunction(
reaction_function), _top.RateFunction(rate_function)
reaction = _top.StructuralTopologyReaction(fun1, fun2)
if raise_if_invalid:
reaction.raise_if_invalid()
else:
reaction.roll_back_if_invalid()
if expect_connected:
reaction.expect_connected_after_reaction()
else:
reaction.create_child_topologies_after_reaction()
self._registry.add_structural_reaction(topology_type, reaction)
