def _color_by_committor(self, min1, min2, T=1.):
print("coloring by the probability that a trajectory gets to minimum",
min1._id, "before", min2._id)
# get a list of transition states in the same cluster as min1
edges = nx.bfs_edges(self.graph, min1)
transition_states = [
self.graph.get_edge_data(u, v)["ts"] for u, v in edges
]
if not check_thermodynamic_info(transition_states):
raise Exception(
"The thermodynamic information is not yet computed. Use the main menu of the gui under 'Actions'"
)
A = [min2]
B = [min1]
committors = compute_committors(transition_states, A, B, T=T)
self._minima_color_value = committors
def get_committor(m):
try:
return committors[m]
except KeyError:
return 1.
self._minima_color_value = get_committor
self.show_graph()
def _layout_by_committor(self, min1, min2, T=1.):
print("coloring by the probability that a trajectory gets to minimum",
min1._id, "before", min2._id)
# get a list of transition states in the same cluster as min1
edges = nx.bfs_edges(self.graph, min1)
transition_states = [
self.graph.get_edge_data(u, v)["ts"] for u, v in edges
]
if not check_thermodynamic_info(transition_states):
raise Exception(
"The thermodynamic information is not yet computed")
A = [min2]
B = [min1]
committors = compute_committors(transition_states, A, B, T=T)
print("maximum committor", max(committors.values()))
print("minimum committor", min(committors.values()))
print("number of committors near 1",
len([v for v in committors.values() if v > 1. - 1e-4]))
print("number of committors equal to 1",
len([v for v in committors.values() if v == 1.]))
def get_committor(m):
try:
return committors[m]
except KeyError:
return 1.
self.dg.get_value = get_committor
self.dg._layout_x_axis(self.dg.tree_graph)
self.dg.color_by_value(get_committor)
self.redraw_disconnectivity_graph()
def _color_by_committor(self, min1, min2, T=1.):
print "coloring by the probability that a trajectory gets to minimum", min1._id, "before", min2._id
# get a list of transition states in the same cluster as min1
edges = nx.bfs_edges(self.graph, min1)
transition_states = [ self.graph.get_edge_data(u, v)["ts"] for u, v in edges ]
if not check_thermodynamic_info(transition_states):
raise Exception("The thermodynamic information is not yet computed")
A = [min2]
B = [min1]
committors = compute_committors(transition_states, A, B, T=T)
def get_committor(m):
try:
return committors[m]
except KeyError:
return 1.
self.dg.color_by_value(get_committor)
self.redraw_disconnectivity_graph()
def _color_by_committor(self, min1, min2, T=1.):
print("coloring by the probability that a trajectory gets to minimum", min1._id, "before", min2._id)
# get a list of transition states in the same cluster as min1
edges = nx.bfs_edges(self.graph, min1)
transition_states = [ self.graph.get_edge_data(u, v)["ts"] for u, v in edges ]
if not check_thermodynamic_info(transition_states):
raise Exception("The thermodynamic information is not yet computed. Use the main menu of the gui under 'Actions'")
A = [min2]
B = [min1]
committors = compute_committors(transition_states, A, B, T=T)
self._minima_color_value = committors
def get_committor(m):
try:
return committors[m]
except KeyError:
return 1.
self._minima_color_value = get_committor
self.show_graph()
def _color_by_committor(self, min1, min2, T=1.):
print "coloring by the probability that a trajectory gets to minimum", min1._id, "before", min2._id
# get a list of transition states in the same cluster as min1
edges = nx.bfs_edges(self.graph, min1)
transition_states = [
self.graph.get_edge_data(u, v)["ts"] for u, v in edges
]
if not check_thermodynamic_info(transition_states):
raise Exception(
"The thermodynamic information is not yet computed")
A = [min2]
B = [min1]
committors = compute_committors(transition_states, A, B, T=T)
def get_committor(m):
try:
return committors[m]
except KeyError:
return 1.
self.dg.color_by_value(get_committor)
self.redraw_disconnectivity_graph()
def _layout_by_committor(self, min1, min2, T=1.):
print "coloring by the probability that a trajectory gets to minimum", min1._id, "before", min2._id
# get a list of transition states in the same cluster as min1
edges = nx.bfs_edges(self.graph, min1)
transition_states = [ self.graph.get_edge_data(u, v)["ts"] for u, v in edges ]
if not check_thermodynamic_info(transition_states):
raise Exception("The thermodynamic information is not yet computed")
A = [min2]
B = [min1]
committors = compute_committors(transition_states, A, B, T=T)
print "maximum committor", max(committors.values())
print "minimum committor", min(committors.values())
print "number of committors near 1", len([v for v in committors.values() if v > 1.-1e-4])
print "number of committors equal to 1", len([v for v in committors.values() if v == 1.])
def get_committor(m):
try:
return committors[m]
except KeyError:
return 1.
self.dg.get_value = get_committor
self.dg._layout_x_axis(self.dg.tree_graph)
self.dg.color_by_value(get_committor)
self.redraw_disconnectivity_graph()
