def unstable_reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
index = np.random.randint(0, len(topology.particles))
recipe.separate_vertex(index)
recipe.change_particle_type(index, "Decay")
recipe.change_particle_position(index, [0, 0, 0])
return recipe
def dissociation_reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
edges = topology.get_graph().get_edges()
edge = edges[1 + np.random.randint(0, len(edges) - 2)]
recipe.remove_edge(edge)
recipe.change_particle_type(edge[0].get().particle_index, "Head")
recipe.change_particle_type(edge[1].get().particle_index, "Head")
return recipe
def clean_sites_reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
vertices = topology.get_graph().get_vertices()
def search_configuration():
# dfs for finding configuration core-site-site-core
for v1 in vertices:
if topology.particle_type_of_vertex(v1) == "core":
for v2_ref in v1.neighbors():
v2 = v2_ref.get()
if topology.particle_type_of_vertex(v2) == "site":
for v3_ref in v2.neighbors():
v3 = v3_ref.get()
if v3.particle_index != v1.particle_index:
if topology.particle_type_of_vertex(
v3) == "site":
for v4_ref in v3.neighbors():
v4 = v4_ref.get()
if v4.particle_index != v2.particle_index:
if topology.particle_type_of_vertex(
v4) == "core":
return v1.particle_index, v2.particle_index, v3.particle_index, v4.particle_index
core1_p_idx, site1_p_idx, site2_p_idx, core2_p_idx = search_configuration(
)
# find corresponding vertex indices from particle indices
core1_v_idx = None
site1_v_idx = None
site2_v_idx = None
core2_v_idx = None
for i, v in enumerate(vertices):
if v.particle_index == core1_p_idx and core1_v_idx is None:
core1_v_idx = i
elif v.particle_index == site1_p_idx and site1_v_idx is None:
site1_v_idx = i
elif v.particle_index == site2_p_idx and site2_v_idx is None:
site2_v_idx = i
elif v.particle_index == core2_p_idx and core2_v_idx is None:
core2_v_idx = i
else:
pass
if (core1_v_idx is not None) and (core2_v_idx is not None) and (
site1_v_idx is not None) and (site2_v_idx is not None):
recipe.add_edge(core1_v_idx, core2_v_idx)
recipe.separate_vertex(site1_v_idx)
recipe.separate_vertex(site2_v_idx)
recipe.change_particle_type(site1_v_idx, "dummy")
recipe.change_particle_type(site2_v_idx, "dummy")
else:
raise RuntimeError("core-site-site-core wasn't found")
return recipe
def intermediate_reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
for v in topology.graph.vertices:
recipe.change_particle_type(v, "unstable T")
recipe.change_topology_type("unstable")
return recipe
def reaction_fun(topology):
return readdy.StructuralReactionRecipe(topology) \
.change_particle_type(0, "foo").change_particle_position(0, [0., 0., .1])
def reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
if topology.get_n_particles() == 1:
recipe.change_particle_type(0, "B")
return recipe._get()
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 intermediate_reaction_function(topology):
recipe = readdy.StructuralReactionRecipe(topology)
for i in range(len(topology.get_graph().get_vertices())):
recipe.change_particle_type(i, "unstable T")
recipe.change_topology_type("unstable")
return recipe
def flip2(topology):
recipe = readdy.StructuralReactionRecipe(topology)
for v in topology.graph.vertices:
recipe.change_particle_type(v, "B")
recipe.change_topology_type("T1")
return recipe
