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@alias('dtrajs_full')
def discrete_trajectories_full(self):
"""
A list of integer arrays with the original (unmapped) discrete trajectories:
"""
self._check_is_estimated()
return self._dtrajs_full
@alias('dtrajs_active')
def discrete_trajectories_active(self):
"""
A list of integer arrays with the discrete trajectories mapped to the connectivity mode used.
For example, for connectivity='largest', the indexes will be given within the connected set.
Frames that are not in the connected set will be -1.
"""
self._check_is_estimated()
# compute connected dtrajs
self._dtrajs_active = []
for dtraj in self._dtrajs_full:
self._dtrajs_active.append(self._full2active[dtraj])
return self._dtrajs_active
@alias('mu')
def stationary_distribution(self):
r"""Returns the stationary distribution
"""
return self._mu
@_alias('stationary_distribution')
def pi(self):
r"""The stationary distribution on the configuration states."""
return self._pi
@alias('hist_lagged')
def histogram_lagged(self, connected_set=None, subset=None, effective=False):
r""" Histogram of discrete state counts
"""
C = self.count_matrix(connected_set=connected_set, subset=subset, effective=effective)
return C.sum(axis=1)
@alias('forward_committor', 'qplus')
def committor(self):
r"""Returns the forward committor probability
"""
return self._qplus
@alias('dtrajs')
def discrete_trajectories(self):
"""
A list of integer arrays with the original (unmapped) discrete trajectories:
"""
return self._dtrajs
@alias('cluster_centers_') # sk-learn compat.
def clustercenters(self):
""" Array containing the coordinates of the calculated cluster centers. """
return self._clustercenters
@_alias('free_energies')
def f(self):
r"""The free energies (in units of kT) on the configuration states."""
return self._f
@alias('number_of_timescales')
def nits(self):
"""Return the number of timescales."""
return self._nits