Fix _decorrelated_iterations,
Simplify dependency tree
@@ -2034,7 +2034,7 @@ class MultiStateSamplerAnalyzer(PhaseAnalyzer):
_unbiased_decorrelated_u_ln = CachedProperty(
name='unbiased_decorrelated_u_ln',
dependencies=['unbias_restraint', 'restraint_energy_cutoff', 'restraint_distance_cutoff',
- 'decorrelated_state_indices_ln', 'decorrelated_u_ln', 'decorrelated_N_l', 'use_full_trajectory'],
+ 'decorrelated_state_indices_ln', 'decorrelated_u_ln', 'decorrelated_N_l'],
)
@_unbiased_decorrelated_u_ln.default
@@ -2044,7 +2044,7 @@ class MultiStateSamplerAnalyzer(PhaseAnalyzer):
_unbiased_decorrelated_N_l = CachedProperty(
name='unbiased_decorrelated_N_l',
dependencies=['unbias_restraint', 'restraint_energy_cutoff', 'restraint_distance_cutoff',
- 'decorrelated_state_indices_ln', 'decorrelated_u_ln', 'decorrelated_N_l', 'use_full_trajectory'],
+ 'decorrelated_state_indices_ln', 'decorrelated_u_ln', 'decorrelated_N_l'],
)
@_unbiased_decorrelated_N_l.default
@@ -2054,7 +2054,7 @@ class MultiStateSamplerAnalyzer(PhaseAnalyzer):
mbar = CachedProperty(
name='mbar',
dependencies=['unbiased_decorrelated_u_ln', 'unbiased_decorrelated_N_l',
- '_extra_analysis_kwargs', 'use_full_trajectory'],
+ '_extra_analysis_kwargs'],
)
@mbar.default
@@ -2079,6 +2079,8 @@ class MultiStateSamplerAnalyzer(PhaseAnalyzer):
@property
def _decorrelated_iterations(self):
"""list of int: the indices of the decorrelated iterations truncated to max_n_iterations."""
+ if self.use_full_trajectory:
+ return np.arange(self.max_n_iterations + 1, dtype=int)
equilibrium_iterations = np.array(range(self.n_equilibration_iterations, self.max_n_iterations + 1))
decorrelated_iterations_indices = timeseries.subsampleCorrelatedData(equilibrium_iterations,
self.statistical_inefficiency)
