# Construct reference if available
try:
reference = MDAnalysis.Universe(options.topology_filename,
options.topology_filename)
except:
reference = None
# Construct ensemble
ensemble = Ensemble(topology=options.topology_filename,
trajectory=options.trajectory_filename,
atom_selection_string=options.atom_selection_string,
frame_interval=options.frame_interval)
# Align ensemble to reference
if not options.no_align:
ensemble.align(reference)
# Select covariance estimator
estimator = EstimatorML()
if options.covariance_estimator == "shrinkage":
estimator = EstimatorShrinkage()
# Disable reference unless use_distance_to_reference is set
if not options.use_distance_to_reference:
reference = None
# Calculate covariance matrix
cov_matrix = covariance_matrix(
ensemble,
estimator=estimator,
mass_weighted=options.mass_weighted_analysis,
# Construct reference if available
try:
reference = MDAnalysis.Universe(options.topology_filename,
options.topology_filename)
except:
reference = None
# Construct ensemble
ensemble = Ensemble(topology=options.topology_filename,
trajectory=options.trajectory_filename,
atom_selection_string=options.atom_selection_string,
frame_interval=options.frame_interval)
# Align ensemble to reference
if not options.no_align:
ensemble.align(reference)
# Select covariance estimator
estimator = EstimatorML()
if options.covariance_estimator == "shrinkage":
estimator = EstimatorShrinkage()
# Disable reference unless use_distance_to_reference is set
if not options.use_distance_to_reference:
reference = None
# Calculate covariance matrix
cov_matrix = covariance_matrix(ensemble,
estimator = estimator,
mass_weighted=options.mass_weighted_analysis,
reference=reference)
