def _color_by_mfpt(self, min1, T=1.):
print "coloring by the mean first passage time to get to minimum", min1._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")
# get an arbitrary second minimum2
for ts in transition_states:
if ts.minimum2 != min1:
min2 = ts.minimum2
break
A = [min1]
B = [min2]
rcalc = RatesLinalg(transition_states, A, B, T=T)
rcalc.compute_rates()
mfptimes = rcalc.get_mfptimes()
tmax = max(mfptimes.itervalues())
def get_mfpt(m):
try:
return mfptimes[m]
except KeyError:
return tmax
self.dg.color_by_value(get_mfpt)
self.redraw_disconnectivity_graph()
def _color_by_mfpt(self, min1, T=1.):
print("coloring by the mean first passage time to get to minimum",
min1._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")
# get an arbitrary second minimum2
for ts in transition_states:
if ts.minimum2 != min1:
min2 = ts.minimum2
break
A = [min1]
B = [min2]
rcalc = RatesLinalg(transition_states, A, B, T=T)
rcalc.compute_rates()
mfptimes = rcalc.get_mfptimes()
tmax = max(mfptimes.values())
def get_mfpt(m):
try:
return mfptimes[m]
except KeyError:
return tmax
self.dg.color_by_value(get_mfpt)
self.redraw_disconnectivity_graph()
def do_check_committors(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates_and_committors()
committors = rcalc.get_committors()
rla = RatesLinalg(self.db.transition_states(), A, B)
cla = rla.compute_committors()
for m, qla in cla.items():
self.assertAlmostEqual(committors[m], qla, 7)
def do_check_rates(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates()
rAB = rcalc.get_rate_AB()
rBA = rcalc.get_rate_BA()
rla = RatesLinalg(self.db.transition_states(), A, B)
rAB_la = rla.compute_rates()
self.assertAlmostEqual(rAB, rAB_la, 7)
def do_check_committors(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates_and_committors()
committors = rcalc.get_committors()
rla = RatesLinalg(self.db.transition_states(), A, B)
cla = rla.compute_committors()
for m, qla in cla.iteritems():
self.assertAlmostEqual(committors[m], qla, 7)
def do_check_rates(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates()
rAB = rcalc.get_rate_AB()
rBA = rcalc.get_rate_BA()
rla = RatesLinalg(self.db.transition_states(), A, B)
rAB_la = rla.compute_rates()
self.assertAlmostEqual(rAB, rAB_la, 7)
def test1(self):
m1 = self.db.getMinimum(1)
m2 = self.db.getMinimum(2)
m3 = self.db.getMinimum(3)
m4 = self.db.getMinimum(4)
rcalc = RateCalculation(self.db.transition_states(), [m1], [m2],
T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 7106337458., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 1955395816., delta=1e4)
rcalc = RateCalculation(self.db.transition_states(), [m1, m3],
[m2, m4],
T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 8638736600., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 3499625167., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1], [m2], T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 7106337458., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1, m3], [m2, m4],
T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 8638736600., delta=1e4)
def test1(self):
m1 = self.db.getMinimum(1)
m2 = self.db.getMinimum(2)
m3 = self.db.getMinimum(3)
m4 = self.db.getMinimum(4)
rcalc = RateCalculation(self.db.transition_states(), [m1], [m2], T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 7106337458., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 1955395816., delta=1e4)
rcalc = RateCalculation(self.db.transition_states(), [m1,m3], [m2, m4], T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 8638736600., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 3499625167., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1], [m2], T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 7106337458., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1, m3], [m2, m4], T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 8638736600., delta=1e4)