fixed namespace clash for utils
@@ -1435,9 +1435,9 @@ class MultiStateSamplerAnalyzer(PhaseAnalyzer):
if not self.use_full_trajectory:
for i, energies in enumerate(energy_data):
# Discard equilibration iterations.
- energies = utils.remove_unequilibrated_data(energies, number_equilibrated, -1)
+ energies = multistate.utils.remove_unequilibrated_data(energies, number_equilibrated, -1)
# Subsample along the decorrelation data.
- energy_data[i] = utils.subsample_data_along_axis(energies, g_t, -1)
+ energy_data[i] = multistate.utils.subsample_data_along_axis(energies, g_t, -1)
sampled_energy_matrix, unsampled_energy_matrix, neighborhood, replicas_state_indices = energy_data
# Initialize the MBAR matrices in ln form.
@@ -1976,7 +1976,7 @@ class MultiStateSamplerAnalyzer(PhaseAnalyzer):
# Discard equilibration samples.
# TODO: if we include u_n[0] (the energy right after minimization) in the equilibration detection,
# TODO: then number_equilibrated is 0. Find a better way than just discarding first frame.
- i_t, g_i, n_effective_i = utils.get_equilibration_data_per_sample(u_n[t0:])
+ i_t, g_i, n_effective_i = multistate.utils.get_equilibration_data_per_sample(u_n[t0:])
n_effective_max = n_effective_i.max()
i_max = n_effective_i.argmax()
n_equilibration = i_t[i_max]
@@ -2296,7 +2296,7 @@ class MultiPhaseAnalyzer(object):
final_new_names = []
for name in new_names:
other_names = [n for n in new_names if n != name]
- final_new_names.append(utils.generate_phase_name(name, other_names + names))
+ final_new_names.append(multistate.utils.generate_phase_name(name, other_names + names))
names.extend(final_new_names)
for new_sign in new_signs:
if (operator == '-' and new_sign == '+') or (operator == '+' and new_sign == '-'):
@@ -2306,7 +2306,7 @@ class MultiPhaseAnalyzer(object):
signs.extend(new_signs)
phases.extend(new_phases)
elif isinstance(other, PhaseAnalyzer):
- names.append(utils.generate_phase_name(other.name, names))
+ names.append(multistate.utils.generate_phase_name(other.name, names))
if (operator == '-' and other._sign == '+') or (operator == '+' and other._sign == '-'):
signs.append('-')
else:
