res
resid
seqid
consensus
all
use_reduced=True
.rmsd.mean
.rmsd.median
.rmsd.mad
.to_reference(reference_traj, reference_frame, atom_selection="all")
.frame_to_frame(lag=1, atom_selection="all")
.window_frame_to_start()
.window_frame_to_frame()
.rmsf.mean
.rmsf.median
.rmsf.mad
.per_atom
.per_residue
.with_mean_aggregation
.with_median_aggregation
.with_rms_aggregation
.with_rms_median_aggregation
create(name)
select_by_tags(name, tags, match_all=True, mode="add", stride=1)
select_by_cluster(name, clustering_name, cluster_ids, mode="add", stride=1)
select_by_indices(name, trajectory_indices, mode="add")
AnalysisManager
AnalysisManager.__init__()
AnalysisManager.features
AnalysisManager.structure
RMSDCalculator
RMSDCalculator.__init__()
RMSDCalculator.rmsd_to_reference()
RMSDCalculator.frame_to_frame()
RMSDCalculator.window()
RMSFCalculator
RMSFCalculator.__init__()
RMSFCalculator.calculate_per_atom()
RMSFCalculator.calculate_per_residue()
ReferenceStructureHelper
ReferenceStructureHelper.get_mean_coordinates()
ReferenceStructureHelper.get_median_coordinates()
aggregate_residues_jit()
StructureCalculationHelper
StructureCalculationHelper.iterate_chunks()
StructureCalculationHelper.stack_frames()
TrajectoryServiceHelper
TrajectoryServiceHelper.__init__()
TrajectoryServiceHelper.resolve_trajectories_and_atoms()
TrajectoryServiceHelper.build_result_map()
TrajectoryServiceHelper.map_reference_to_local_index()
RMSDFacade
RMSDFacade.__init__()
RMSDFacade.mean
RMSDFacade.median
RMSDFacade.mad
RMSDFacade.to_reference()
RMSDMadService
RMSDMadService.__init__()
RMSDMadService.to_reference()
RMSDMadService.frame_to_frame()
RMSDMadService.window_frame_to_start()
RMSDMadService.window_frame_to_frame()
RMSDMeanService
RMSDMeanService.__init__()
RMSDMeanService.to_reference()
RMSDMeanService.frame_to_frame()
RMSDMeanService.window_frame_to_start()
RMSDMeanService.window_frame_to_frame()
RMSDMedianService
RMSDMedianService.__init__()
RMSDMedianService.to_reference()
RMSDMedianService.frame_to_frame()
RMSDMedianService.window_frame_to_start()
RMSDMedianService.window_frame_to_frame()
RMSFFacade
RMSFFacade.__init__()
RMSFFacade.mean
RMSFFacade.median
RMSFFacade.mad
RMSFFacade.per_atom
RMSFFacade.per_residue
RMSFFacade.to_mean_reference()
RMSFMadVariantFacade
RMSFMadVariantFacade.__init__()
RMSFMadVariantFacade.per_atom
RMSFMadVariantFacade.per_residue
RMSFMeanVariantFacade
RMSFMeanVariantFacade.__init__()
RMSFMeanVariantFacade.per_atom
RMSFMeanVariantFacade.per_residue
RMSFMedianVariantFacade
RMSFMedianVariantFacade.__init__()
RMSFMedianVariantFacade.per_atom
RMSFMedianVariantFacade.per_residue
RMSFPerAtomService
RMSFPerAtomService.__init__()
RMSFPerAtomService.to_mean_reference()
RMSFPerAtomService.to_median_reference()
RMSFPerResidueAggregationSelectionFacade
RMSFPerResidueAggregationSelectionFacade.__init__()
RMSFPerResidueAggregationSelectionFacade.with_mean_aggregation
RMSFPerResidueAggregationSelectionFacade.with_median_aggregation
RMSFPerResidueAggregationSelectionFacade.with_rms_aggregation
RMSFPerResidueAggregationSelectionFacade.with_rms_median_aggregation
RMSFPerResidueAggregationSelectionFacade.to_mean_reference()
BaseRMSFPerResidueAggFacade
BaseRMSFPerResidueAggFacade.service
BaseRMSFPerResidueAggFacade.to_mean_reference()
BaseRMSFPerResidueAggFacade.to_median_reference()
RMSFPerResidueMeanAggFacade
RMSFPerResidueMeanAggFacade.__init__()
RMSFPerResidueMeanAggFacade.service
RMSFPerResidueMedianAggFacade
RMSFPerResidueMedianAggFacade.__init__()
RMSFPerResidueMedianAggFacade.service
RMSFPerResidueRmsAggFacade
RMSFPerResidueRmsAggFacade.__init__()
RMSFPerResidueRmsAggFacade.service
RMSFPerResidueRmsMedianAggFacade
RMSFPerResidueRmsMedianAggFacade.__init__()
RMSFPerResidueRmsMedianAggFacade.service
RMSFPerResidueService
RMSFPerResidueService.__init__()
RMSFPerResidueService.to_mean_reference()
RMSFPerResidueService.to_median_reference()
StructureAnalysisService
StructureAnalysisService.__init__()
StructureAnalysisService.pipeline_data
StructureAnalysisService.rmsd
StructureAnalysisService.rmsf
DBSCAN
DBSCAN.__init__()
DBSCAN.get_type_name()
DBSCAN.init_calculator()
DBSCAN.compute()
DBSCANCalculator
DBSCANCalculator.__init__()
DBSCANCalculator.compute()
DPA
DPA.__init__()
DPA.get_type_name()
DPA.init_calculator()
DPA.compute()
DPACalculator
DPACalculator.__init__()
DPACalculator.compute()
HDBSCAN
HDBSCAN.__init__()
HDBSCAN.get_type_name()
HDBSCAN.init_calculator()
HDBSCAN.compute()
HDBSCANCalculator
HDBSCANCalculator.__init__()
HDBSCANCalculator.compute()
CalculatorBase
CalculatorBase.__init__()
CalculatorBase.compute()
ClusterTypeBase
ClusterTypeBase.__init__()
ClusterTypeBase.get_type_name()
ClusterTypeBase.init_calculator()
ClusterTypeBase.compute()
ClusterTypeMeta
ClusterData
ClusterData.__init__()
ClusterData.get_labels()
ClusterData.get_metadata()
ClusterData.get_cluster_type()
ClusterData.get_cache_path()
ClusterData.has_data()
ClusterData.get_n_clusters()
ClusterData.get_n_frames()
ClusterData.get_frame_mapping()
ClusterData.set_frame_mapping()
ClusterData.get_centers()
ClusterData.save()
ClusterData.load()
ClusterData.print_info()
CenterCalculationHelper
CenterCalculationHelper.VALID_METHODS
CenterCalculationHelper.calculate_centers()
ClusterManager
ClusterManager.__init__()
ClusterManager.reset_clusters()
ClusterManager.add_clustering()
ClusterManager.save()
ClusterManager.load()
ClusterManager.print_info()
ClusterManager.add
ClusterAddService
ClusterAddService.__init__()
ClusterAddService.dbscan
ClusterAddService.hdbscan
ClusterAddService.dpa
DBSCANAddService
DBSCANAddService.__init__()
DBSCANAddService.with_centroid_centers()
DBSCANAddService.with_mean_centers()
DBSCANAddService.with_median_centers()
DBSCANAddService.with_density_peak_centers()
DBSCANAddService.with_median_centroid_centers()
DBSCANAddService.with_rmsd_centroid_centers()
DPAAddService
DPAAddService.__init__()
DPAAddService.with_centroid_centers()
DPAAddService.with_mean_centers()
DPAAddService.with_median_centers()
DPAAddService.with_density_peak_centers()
DPAAddService.with_median_centroid_centers()
DPAAddService.with_rmsd_centroid_centers()
HDBSCANAddService
HDBSCANAddService.__init__()
HDBSCANAddService.with_centroid_centers()
HDBSCANAddService.with_mean_centers()
HDBSCANAddService.with_median_centers()
HDBSCANAddService.with_density_peak_centers()
HDBSCANAddService.with_median_centroid_centers()
HDBSCANAddService.with_rmsd_centroid_centers()
ComparisonData
ComparisonData.__init__()
ComparisonData.add_sub_comparison()
ComparisonData.get_sub_comparison()
ComparisonData.list_sub_comparisons()
ComparisonData.get_comparison_info()
ComparisonData.save()
ComparisonData.load()
ComparisonData.print_info()
ComparisonValidationHelper
ComparisonValidationHelper.validate_comparison_name()
ComparisonValidationHelper.validate_comparison_exists()
ComparisonValidationHelper.validate_mode()
ComparisonValidationHelper.validate_feature_selector()
ComparisonValidationHelper.validate_data_selectors()
ComparisonValidationHelper.validate_has_selectors()
SubComparisonCreationHelper
SubComparisonCreationHelper.create_binary_sub_comparisons()
SubComparisonCreationHelper.create_pairwise_sub_comparisons()
SubComparisonCreationHelper.create_one_vs_rest_sub_comparisons()
SubComparisonCreationHelper.create_multiclass_sub_comparisons()
ComparisonManager
ComparisonManager.__init__()
ComparisonManager.create_comparison()
ComparisonManager.list_comparisons()
ComparisonManager.get_comparison_info()
ComparisonManager.remove_comparison()
ComparisonManager.save()
ComparisonManager.load()
ComparisonManager.print_info()
DataSelectorData
DataSelectorData.__init__()
DataSelectorData.n_selected_frames
DataSelectorData.set_trajectory_frames()
DataSelectorData.get_trajectory_frames()
DataSelectorData.append_selection_criteria()
DataSelectorData.get_selection_criteria()
DataSelectorData.add_trajectory_frames()
DataSelectorData.remove_duplicates()
DataSelectorData.clear_selection()
DataSelectorData.get_selection_info()
DataSelectorData.is_empty()
DataSelectorData.save()
DataSelectorData.load()
DataSelectorData.print_info()
DataSelectorGroup
DataSelectorGroup.__init__()
CriteriaBuilderHelper
CriteriaBuilderHelper.build_tag_criteria()
CriteriaBuilderHelper.build_cluster_criteria()
CriteriaBuilderHelper.build_indices_criteria()
CriteriaBuilderHelper.build_combination_criteria()
FrameSelectionHelper
FrameSelectionHelper.select_frames_by_tags()
FrameSelectionHelper.select_frames_by_cluster()
FrameSelectionHelper.resolve_cluster_ids()
FrameSelectionHelper.select_frames_by_indices()
FrameSelectionHelper.validate_selector_exists()
FrameSelectionHelper.validate_trajectories_loaded()
FrameSelectionHelper.validate_clustering_exists()
GroupCreationHelper
GroupCreationHelper.create_cluster_selectors()
GroupCreationHelper.create_tag_selectors()
DataSelectorManager
DataSelectorManager.__init__()
DataSelectorManager.create()
DataSelectorManager.select_by_tags()
DataSelectorManager.select_by_cluster()
DataSelectorManager.select_by_indices()
DataSelectorManager.get_selection_info()
DataSelectorManager.list_selectors()
DataSelectorManager.clear_selector()
DataSelectorManager.remove_selector()
DataSelectorManager.save()
DataSelectorManager.load()
DataSelectorManager.print_info()
DataSelectorManager.create_from_clusters()
DataSelectorManager.create_from_tags()
DataSelectorManager.get_group()
DataSelectorManager.list_groups()
DataSelectorManager.delete_group()
ContactKernelPCA
ContactKernelPCA.__init__()
ContactKernelPCA.get_type_name()
ContactKernelPCA.init_calculator()
ContactKernelPCA.compute()
ContactKernelPCACalculator
ContactKernelPCACalculator.__init__()
ContactKernelPCACalculator.compute()
DiffusionMaps
DiffusionMaps.__init__()
DiffusionMaps.get_type_name()
DiffusionMaps.get_required_feature_type()
DiffusionMaps.init_calculator()
DiffusionMaps.compute()
DiffusionMapsCalculator
DiffusionMapsCalculator.__init__()
DiffusionMapsCalculator.compute()
KernelPCA
KernelPCA.__init__()
KernelPCA.get_type_name()
KernelPCA.init_calculator()
KernelPCA.compute()
KernelPCACalculator
KernelPCACalculator.__init__()
KernelPCACalculator.compute()
PCA
PCA.__init__()
PCA.get_type_name()
PCA.init_calculator()
PCA.compute()
PCACalculator
PCACalculator.__init__()
PCACalculator.compute()
DecompositionTypeBase
DecompositionTypeBase.__init__()
DecompositionTypeBase.get_type_name()
DecompositionTypeBase.init_calculator()
DecompositionTypeBase.compute()
DecompositionTypeBase.get_required_feature_type()
DecompositionTypeMeta
AutomaticParameterHelper
AutomaticParameterHelper.find_elbow()
AutomaticParameterHelper.calculate_gamma_scale()
AutomaticParameterHelper.calculate_gamma_auto()
AutomaticParameterHelper.compute_variance_chunked()
DecompositionData
DecompositionData.__init__()
DecompositionData.get_frame_mapping()
DecompositionData.set_frame_mapping()
DecompositionData.save()
DecompositionData.load()
DecompositionData.print_info()
DecompositionManager
DecompositionManager.__init__()
DecompositionManager.add_decomposition()
DecompositionManager.reset_decompositions()
DecompositionManager.save()
DecompositionManager.load()
DecompositionManager.print_info()
DecompositionManager.add
DecompositionAddService
DecompositionAddService.__init__()
DecompositionAddService.pca()
DecompositionAddService.kernel_pca()
DecompositionAddService.contact_kernel_pca()
DecompositionAddService.diffusion_maps()
ContactsSelectionService
ContactsSelectionService.__init__()
ContactsSelectionService.with_frequency_reduction()
ContactsSelectionService.with_stability_reduction()
ContactsSelectionService.with_transitions_reduction()
ContactsReduceService
ContactsReduceService.__init__()
ContactsReduceService.frequency()
ContactsReduceService.stability()
ContactsReduceService.transitions()
ContactsAnalysisService
ContactsAnalysisService.__init__()
ContactsAnalysisService.frequency()
ContactsAnalysisService.contacts_per_frame_abs()
ContactsAnalysisService.contacts_per_frame_percentage()
ContactsAnalysisService.per_residue_mean()
ContactsAnalysisService.per_residue_std()
ContactsAnalysisService.per_residue_sum()
ContactsAnalysisService.transitions_lagtime()
ContactsAnalysisService.transitions_window()
ContactsAnalysisService.stability()
ContactsAnalysisService.differences()
Contacts
Contacts.__init__()
Contacts.init_calculator()
Contacts.compute()
Contacts.get_dependencies()
Contacts.get_type_name()
Contacts.get_input()
ContactCalculator
ContactCalculator.__init__()
ContactCalculator.compute()
ContactCalculator.compute_pooled_metric_values()
ContactCalculator.compute_dynamic_values()
ContactCalculatorAnalysis
ContactCalculatorAnalysis.REQUIRES_FULL_DATA
ContactCalculatorAnalysis.__init__()
ContactCalculatorAnalysis.compute_frequency()
ContactCalculatorAnalysis.contacts_per_frame_abs()
ContactCalculatorAnalysis.contacts_per_frame_percentage()
ContactCalculatorAnalysis.compute_per_residue_mean()
ContactCalculatorAnalysis.compute_per_residue_std()
ContactCalculatorAnalysis.compute_per_residue_sum()
ContactCalculatorAnalysis.compute_transitions_lagtime()
ContactCalculatorAnalysis.compute_transitions_window()
ContactCalculatorAnalysis.compute_stability()
ContactCalculatorAnalysis.compute_differences()
ContactCalculatorAnalysis.compute_pooled_metric_values()
CoordinatesSelectionService
CoordinatesSelectionService.__init__()
CoordinatesSelectionService.with_rmsf_reduction()
CoordinatesSelectionService.with_std_reduction()
CoordinatesSelectionService.with_cv_reduction()
CoordinatesSelectionService.with_variance_reduction()
CoordinatesSelectionService.with_range_reduction()
CoordinatesSelectionService.with_mad_reduction()
CoordinatesSelectionService.with_mean_reduction()
CoordinatesSelectionService.with_min_reduction()
CoordinatesSelectionService.with_max_reduction()
CoordinatesSelectionService.with_transitions_reduction()
CoordinatesReduceService
CoordinatesReduceService.__init__()
CoordinatesReduceService.std()
CoordinatesReduceService.rmsf()
CoordinatesReduceService.cv()
CoordinatesReduceService.variance()
CoordinatesReduceService.range()
CoordinatesReduceService.mad()
CoordinatesReduceService.mean()
CoordinatesReduceService.min()
CoordinatesReduceService.max()
CoordinatesReduceService.transitions()
CoordinatesAnalysisService
CoordinatesAnalysisService.__init__()
CoordinatesAnalysisService.mean()
CoordinatesAnalysisService.std()
CoordinatesAnalysisService.min()
CoordinatesAnalysisService.max()
CoordinatesAnalysisService.median()
CoordinatesAnalysisService.variance()
CoordinatesAnalysisService.range()
CoordinatesAnalysisService.mad()
CoordinatesAnalysisService.cv()
CoordinatesAnalysisService.coordinates_per_frame_mean()
CoordinatesAnalysisService.coordinates_per_frame_std()
CoordinatesAnalysisService.coordinates_per_frame_min()
CoordinatesAnalysisService.coordinates_per_frame_max()
CoordinatesAnalysisService.coordinates_per_frame_range()
CoordinatesAnalysisService.rmsf()
CoordinatesAnalysisService.transitions_lagtime()
CoordinatesAnalysisService.transitions_window()
CoordinatesAnalysisService.stability()
CoordinatesAnalysisService.differences()
Coordinates
Coordinates.__init__()
Coordinates.init_calculator()
Coordinates.compute()
Coordinates.get_dependencies()
Coordinates.get_type_name()
Coordinates.get_input()
CoordinatesCalculator
CoordinatesCalculator.__init__()
CoordinatesCalculator.compute()
CoordinatesCalculator.compute_dynamic_values()
CoordinatesCalculator.compute_pooled_metric_values()
CoordinatesCalculatorAnalysis
CoordinatesCalculatorAnalysis.__init__()
CoordinatesCalculatorAnalysis.compute_mean()
CoordinatesCalculatorAnalysis.compute_std()
CoordinatesCalculatorAnalysis.compute_min()
CoordinatesCalculatorAnalysis.compute_max()
CoordinatesCalculatorAnalysis.compute_median()
CoordinatesCalculatorAnalysis.compute_variance()
CoordinatesCalculatorAnalysis.compute_range()
CoordinatesCalculatorAnalysis.compute_mad()
CoordinatesCalculatorAnalysis.coordinates_per_frame_mean()
CoordinatesCalculatorAnalysis.coordinates_per_frame_std()
CoordinatesCalculatorAnalysis.coordinates_per_frame_min()
CoordinatesCalculatorAnalysis.coordinates_per_frame_max()
CoordinatesCalculatorAnalysis.coordinates_per_frame_range()
CoordinatesCalculatorAnalysis.compute_cv()
CoordinatesCalculatorAnalysis.compute_rmsf()
CoordinatesCalculatorAnalysis.compute_transitions_lagtime()
CoordinatesCalculatorAnalysis.compute_transitions_window()
CoordinatesCalculatorAnalysis.compute_stability()
CoordinatesCalculatorAnalysis.compute_differences()
CoordinatesCalculatorAnalysis.compute_pooled_metric_values()
DistancesSelectionService
DistancesSelectionService.__init__()
DistancesSelectionService.with_cv_reduction()
DistancesSelectionService.with_std_reduction()
DistancesSelectionService.with_variance_reduction()
DistancesSelectionService.with_range_reduction()
DistancesSelectionService.with_transitions_reduction()
DistancesSelectionService.with_min_reduction()
DistancesSelectionService.with_mad_reduction()
DistancesSelectionService.with_mean_reduction()
DistancesSelectionService.with_max_reduction()
DistancesReduceService
DistancesReduceService.__init__()
DistancesReduceService.cv()
DistancesReduceService.std()
DistancesReduceService.variance()
DistancesReduceService.range()
DistancesReduceService.transitions()
DistancesReduceService.min()
DistancesReduceService.mad()
DistancesReduceService.mean()
DistancesReduceService.max()
DistancesAnalysisService
DistancesAnalysisService.__init__()
DistancesAnalysisService.mean()
DistancesAnalysisService.std()
DistancesAnalysisService.min()
DistancesAnalysisService.max()
DistancesAnalysisService.median()
DistancesAnalysisService.variance()
DistancesAnalysisService.range()
DistancesAnalysisService.q25()
DistancesAnalysisService.q75()
DistancesAnalysisService.iqr()
DistancesAnalysisService.mad()
DistancesAnalysisService.cv()
DistancesAnalysisService.distances_per_frame_mean()
DistancesAnalysisService.distances_per_frame_std()
DistancesAnalysisService.distances_per_frame_min()
DistancesAnalysisService.distances_per_frame_max()
DistancesAnalysisService.distances_per_frame_median()
DistancesAnalysisService.distances_per_frame_range()
DistancesAnalysisService.distances_per_frame_sum()
DistancesAnalysisService.per_residue_mean()
DistancesAnalysisService.per_residue_std()
DistancesAnalysisService.per_residue_min()
DistancesAnalysisService.per_residue_max()
DistancesAnalysisService.per_residue_median()
DistancesAnalysisService.per_residue_sum()
DistancesAnalysisService.per_residue_variance()
DistancesAnalysisService.per_residue_range()
DistancesAnalysisService.transitions_lagtime()
DistancesAnalysisService.transitions_window()
DistancesAnalysisService.stability()
DistancesAnalysisService.differences()
Distances
Distances.__init__()
Distances.init_calculator()
Distances.compute()
Distances.get_dependencies()
Distances.get_type_name()
Distances.get_input()
DistanceCalculator
DistanceCalculator.__init__()
DistanceCalculator.compute()
DistanceCalculator.compute_pooled_metric_values()
DistanceCalculator.compute_dynamic_values()
DistanceCalculatorAnalysis
DistanceCalculatorAnalysis.REQUIRES_FULL_DATA
DistanceCalculatorAnalysis.__init__()
DistanceCalculatorAnalysis.compute_mean()
DistanceCalculatorAnalysis.compute_std()
DistanceCalculatorAnalysis.compute_min()
DistanceCalculatorAnalysis.compute_max()
DistanceCalculatorAnalysis.compute_median()
DistanceCalculatorAnalysis.compute_variance()
DistanceCalculatorAnalysis.compute_range()
DistanceCalculatorAnalysis.compute_q25()
DistanceCalculatorAnalysis.compute_q75()
DistanceCalculatorAnalysis.compute_iqr()
DistanceCalculatorAnalysis.compute_mad()
DistanceCalculatorAnalysis.compute_cv()
DistanceCalculatorAnalysis.distances_per_frame_mean()
DistanceCalculatorAnalysis.distances_per_frame_std()
DistanceCalculatorAnalysis.distances_per_frame_min()
DistanceCalculatorAnalysis.distances_per_frame_max()
DistanceCalculatorAnalysis.distances_per_frame_median()
DistanceCalculatorAnalysis.distances_per_frame_range()
DistanceCalculatorAnalysis.distances_per_frame_sum()
DistanceCalculatorAnalysis.compute_per_residue_mean()
DistanceCalculatorAnalysis.compute_per_residue_std()
DistanceCalculatorAnalysis.compute_per_residue_min()
DistanceCalculatorAnalysis.compute_per_residue_max()
DistanceCalculatorAnalysis.compute_per_residue_median()
DistanceCalculatorAnalysis.compute_per_residue_sum()
DistanceCalculatorAnalysis.compute_per_residue_variance()
DistanceCalculatorAnalysis.compute_per_residue_range()
DistanceCalculatorAnalysis.compute_transitions_lagtime()
DistanceCalculatorAnalysis.compute_transitions_window()
DistanceCalculatorAnalysis.compute_stability()
DistanceCalculatorAnalysis.compute_differences()
DistanceCalculatorAnalysis.compute_pooled_metric_values()
DSSPEncodingHelper
DSSPEncodingHelper.encode_char_chunked()
DSSPEncodingHelper.encode_integer()
DSSPEncodingHelper.encode_integer_chunked()
DSSPEncodingHelper.encode_onehot_chunked()
DSSPEncodingHelper.encode_onehot_direct()
DSSPSelectionService
DSSPSelectionService.__init__()
DSSPSelectionService.with_transitions_reduction()
DSSPSelectionService.with_transition_frequency_reduction()
DSSPSelectionService.with_stability_reduction()
DSSPSelectionService.with_class_frequencies_reduction()
DSSPReduceService
DSSPReduceService.__init__()
DSSPReduceService.transitions()
DSSPReduceService.transition_frequency()
DSSPReduceService.stability()
DSSPReduceService.class_frequencies()
DSSPAnalysisService
DSSPAnalysisService.__init__()
DSSPAnalysisService.compute_transitions_lagtime()
DSSPAnalysisService.compute_transitions_window()
DSSPAnalysisService.compute_class_frequencies()
DSSPAnalysisService.compute_transition_frequency()
DSSPAnalysisService.compute_stability()
DSSPAnalysisService.compute_differences()
DSSPAnalysisService.compute_dominant_class()
DSSP
DSSP.__init__()
DSSP.init_calculator()
DSSP.compute()
DSSP.get_dependencies()
DSSP.get_type_name()
DSSP.get_input()
DSSPCalculator
DSSPCalculator.FULL_CLASSES
DSSPCalculator.SIMPLIFIED_CLASSES
DSSPCalculator.__init__()
DSSPCalculator.compute()
DSSPCalculator.compute_dynamic_values()
DSSPCalculator.compute_pooled_metric_values()
DSSPCalculatorAnalysis
DSSPCalculatorAnalysis.__init__()
DSSPCalculatorAnalysis.compute_transitions_lagtime()
DSSPCalculatorAnalysis.compute_transitions_window()
DSSPCalculatorAnalysis.compute_class_frequencies()
DSSPCalculatorAnalysis.compute_transition_frequency()
DSSPCalculatorAnalysis.compute_pooled_transition_frequency()
DSSPCalculatorAnalysis.compute_stability()
DSSPCalculatorAnalysis.compute_pooled_stability()
DSSPCalculatorAnalysis.compute_pooled_transitions()
DSSPCalculatorAnalysis.compute_pooled_class_frequencies()
DSSPCalculatorAnalysis.compute_pooled_metric_values()
DSSPCalculatorAnalysis.compute_differences()
DSSPCalculatorAnalysis.compute_dominant_class()
SasaSelectionService
SasaSelectionService.__init__()
SasaSelectionService.with_cv_reduction()
SasaSelectionService.with_range_reduction()
SasaSelectionService.with_std_reduction()
SasaSelectionService.with_variance_reduction()
SasaSelectionService.with_mad_reduction()
SasaSelectionService.with_mean_reduction()
SasaSelectionService.with_min_reduction()
SasaSelectionService.with_max_reduction()
SasaSelectionService.with_burial_fraction_reduction()
SasaSelectionService.with_exposure_fraction_reduction()
SasaSelectionService.with_transitions_reduction()
SASAReduceService
SASAReduceService.__init__()
SASAReduceService.cv()
SASAReduceService.range()
SASAReduceService.std()
SASAReduceService.variance()
SASAReduceService.mad()
SASAReduceService.mean()
SASAReduceService.min()
SASAReduceService.max()
SASAReduceService.burial_fraction()
SASAReduceService.exposure_fraction()
SASAReduceService.transitions()
SASAAnalysisService
SASAAnalysisService.__init__()
SASAAnalysisService.mean()
SASAAnalysisService.std()
SASAAnalysisService.variance()
SASAAnalysisService.min()
SASAAnalysisService.max()
SASAAnalysisService.mad()
SASAAnalysisService.range()
SASAAnalysisService.cv()
SASAAnalysisService.burial_fraction()
SASAAnalysisService.exposure_fraction()
SASAAnalysisService.mean_per_frame()
SASAAnalysisService.std_per_frame()
SASAAnalysisService.variance_per_frame()
SASAAnalysisService.min_per_frame()
SASAAnalysisService.max_per_frame()
SASAAnalysisService.mad_per_frame()
SASAAnalysisService.range_per_frame()
SASAAnalysisService.transitions_lagtime()
SASAAnalysisService.transitions_window()
SASAAnalysisService.stability()
SASAAnalysisService.differences()
SASAAnalysisService.differences_mean()
SASA
SASA.__init__()
SASA.init_calculator()
SASA.compute()
SASA.get_dependencies()
SASA.get_type_name()
SASA.get_input()
SASACalculator
SASACalculator.__init__()
SASACalculator.compute()
SASACalculator.compute_dynamic_values()
SASACalculator.compute_pooled_metric_values()
SASACalculatorAnalysis
SASACalculatorAnalysis.__init__()
SASACalculatorAnalysis.compute_mean()
SASACalculatorAnalysis.compute_std()
SASACalculatorAnalysis.compute_variance()
SASACalculatorAnalysis.compute_min()
SASACalculatorAnalysis.compute_max()
SASACalculatorAnalysis.compute_mad()
SASACalculatorAnalysis.compute_range()
SASACalculatorAnalysis.compute_mean_per_frame()
SASACalculatorAnalysis.compute_std_per_frame()
SASACalculatorAnalysis.compute_variance_per_frame()
SASACalculatorAnalysis.compute_min_per_frame()
SASACalculatorAnalysis.compute_max_per_frame()
SASACalculatorAnalysis.compute_mad_per_frame()
SASACalculatorAnalysis.compute_range_per_frame()
SASACalculatorAnalysis.compute_differences()
SASACalculatorAnalysis.compute_differences_mean()
SASACalculatorAnalysis.compute_transitions_lagtime()
SASACalculatorAnalysis.compute_transitions_window()
SASACalculatorAnalysis.compute_stability()
SASACalculatorAnalysis.compute_burial_fraction()
SASACalculatorAnalysis.compute_cv()
SASACalculatorAnalysis.compute_exposure_fraction()
SASACalculatorAnalysis.compute_pooled_metric_values()
TorsionsSelectionService
TorsionsSelectionService.__init__()
TorsionsSelectionService.with_transitions_reduction()
TorsionsSelectionService.with_std_reduction()
TorsionsSelectionService.with_mad_reduction()
TorsionsSelectionService.with_mean_reduction()
TorsionsSelectionService.with_range_reduction()
TorsionsSelectionService.with_min_reduction()
TorsionsSelectionService.with_max_reduction()
TorsionsSelectionService.with_cv_reduction()
TorsionsSelectionService.with_variance_reduction()
TorsionsReduceService
TorsionsReduceService.__init__()
TorsionsReduceService.transitions()
TorsionsReduceService.std()
TorsionsReduceService.mad()
TorsionsReduceService.mean()
TorsionsReduceService.range()
TorsionsReduceService.min()
TorsionsReduceService.max()
TorsionsReduceService.cv()
TorsionsReduceService.variance()
TorsionsAnalysisService
TorsionsAnalysisService.__init__()
TorsionsAnalysisService.mean()
TorsionsAnalysisService.std()
TorsionsAnalysisService.variance()
TorsionsAnalysisService.min()
TorsionsAnalysisService.max()
TorsionsAnalysisService.mad()
TorsionsAnalysisService.range()
TorsionsAnalysisService.cv()
TorsionsAnalysisService.mean_per_frame()
TorsionsAnalysisService.std_per_frame()
TorsionsAnalysisService.variance_per_frame()
TorsionsAnalysisService.min_per_frame()
TorsionsAnalysisService.max_per_frame()
TorsionsAnalysisService.mad_per_frame()
TorsionsAnalysisService.range_per_frame()
TorsionsAnalysisService.transitions_lagtime()
TorsionsAnalysisService.transitions_window()
TorsionsAnalysisService.stability()
TorsionsAnalysisService.differences()
TorsionsAnalysisService.differences_mean()
Torsions
Torsions.__init__()
Torsions.init_calculator()
Torsions.compute()
Torsions.get_dependencies()
Torsions.get_type_name()
Torsions.get_input()
TorsionsCalculator
TorsionsCalculator.__init__()
TorsionsCalculator.compute()
TorsionsCalculator.compute_dynamic_values()
TorsionsCalculator.compute_pooled_metric_values()
TorsionsCalculatorAnalysis
TorsionsCalculatorAnalysis.__init__()
TorsionsCalculatorAnalysis.compute_mean()
TorsionsCalculatorAnalysis.compute_std()
TorsionsCalculatorAnalysis.compute_variance()
TorsionsCalculatorAnalysis.compute_min()
TorsionsCalculatorAnalysis.compute_max()
TorsionsCalculatorAnalysis.compute_mad()
TorsionsCalculatorAnalysis.compute_range()
TorsionsCalculatorAnalysis.compute_mean_per_frame()
TorsionsCalculatorAnalysis.compute_std_per_frame()
TorsionsCalculatorAnalysis.compute_variance_per_frame()
TorsionsCalculatorAnalysis.compute_min_per_frame()
TorsionsCalculatorAnalysis.compute_max_per_frame()
TorsionsCalculatorAnalysis.compute_mad_per_frame()
TorsionsCalculatorAnalysis.compute_range_per_frame()
TorsionsCalculatorAnalysis.compute_differences()
TorsionsCalculatorAnalysis.compute_differences_mean()
TorsionsCalculatorAnalysis.compute_transitions_lagtime()
TorsionsCalculatorAnalysis.compute_transitions_window()
TorsionsCalculatorAnalysis.compute_stability()
TorsionsCalculatorAnalysis.compute_cv()
TorsionsCalculatorAnalysis.compute_pooled_metric_values()
CalculatorComputeHelper
CalculatorComputeHelper.compute_dynamic_values()
CalculatorComputeHelper.calculate_output_dimensions()
CalculatorComputeHelper.create_output_array()
CalculatorStatHelper
CalculatorStatHelper.compute_differences()
CalculatorStatHelper.compute_func_per_feature()
CalculatorStatHelper.compute_func_per_frame()
CalculatorStatHelper.compute_func_per_column()
CalculatorStatHelper.compute_transitions_within_lagtime()
CalculatorStatHelper.compute_transitions_within_window()
CalculatorStatHelper.compute_pooled_transitions()
CalculatorStatHelper.compute_pooled_stability()
CalculatorStatHelper.compute_stability()
FeatureShapeHelper
FeatureShapeHelper.is_memmap()
FeatureShapeHelper.squareform_to_condensed()
FeatureShapeHelper.condensed_to_squareform()
AnalysisServiceBase
AnalysisServiceBase.__init__()
CalculatorBase.compute_pooled_metric_values()
CalculatorBase.compute_pooled_selection_mask()
CalculatorBase.compute_dynamic_values()
FeatureTypeBase
FeatureTypeBase.__init__()
FeatureTypeBase.get_dependencies()
FeatureTypeBase.get_type_name()
FeatureTypeBase.init_calculator()
FeatureTypeBase.compute()
FeatureTypeBase.get_input()
FeatureTypeMeta
ReduceServiceBase
ReduceServiceBase.__init__()
SelectionServiceBase
SelectionServiceBase.__init__()
FeatureData
FeatureData.__init__()
FeatureData.get_data()
FeatureData.get_feature_metadata()
FeatureData.get_feature_names()
FeatureData.save()
FeatureData.load()
FeatureData.print_info()
BoundMethod
BoundMethod.__init__()
BoundStats
FeatureBindingHelper
FeatureBindingHelper.bind_stats_methods()
FeatureBindingHelper.release_bound_methods()
FeatureBindingHelper.repair_bound_methods()
FeatureComputationHelper
FeatureComputationHelper.check_feature_existence()
FeatureComputationHelper.execute_computation()
FeatureComputationHelper.store_computation_results()
FeatureCrossTrajectoryReductionHelper
FeatureCrossTrajectoryReductionHelper.find_common_features()
FeatureCrossTrajectoryReductionHelper.apply_common_reduction()
FeatureCrossTrajectoryReductionHelper.get_reduction_summary()
FeatureCrossTrajectoryReductionHelper.print_cross_trajectory_summary()
FeatureReductionHelper
FeatureReductionHelper.process_reduction_results()
FeatureReductionHelper.reset_reduction()
FeatureReductionHelper.check_reduction_state()
FeatureResetHelper
FeatureResetHelper.reset_all_features()
FeatureResetHelper.reset_specific_features()
FeatureResetHelper.normalize_feature_types()
FeatureResetHelper.check_has_features()
FeatureValidationHelper
FeatureValidationHelper.validate_threshold_parameters()
FeatureValidationHelper.validate_feature_exists()
FeatureValidationHelper.validate_dependencies()
FeatureValidationHelper.validate_computation_requirements()
FeatureValidationHelper.validate_reduction_state()
FeatureManager
FeatureManager.__init__()
FeatureManager.reset_features()
FeatureManager.add_feature()
FeatureManager.reset_reduction()
FeatureManager.reduce_data()
FeatureManager.print_info()
FeatureManager.save()
FeatureManager.load()
FeatureManager.add
FeatureManager.reduce
FeatureManager.analysis
AnalysisDataHelper
AnalysisDataHelper.get_selected_data()
FeatureAddService
FeatureAddService.__init__()
FeatureAddService.distances()
FeatureAddService.contacts()
FeatureAddService.torsions()
FeatureAddService.dssp()
FeatureAddService.sasa()
FeatureAddService.coordinates()
FeatureAnalysisService
FeatureAnalysisService.__init__()
FeatureAnalysisService.distances
FeatureAnalysisService.contacts
FeatureAnalysisService.torsions
FeatureAnalysisService.dssp
FeatureAnalysisService.sasa
FeatureAnalysisService.coordinates
FeatureReduceService
FeatureReduceService.__init__()
FeatureReduceService.distances
FeatureReduceService.contacts
FeatureReduceService.torsions
FeatureReduceService.dssp
FeatureReduceService.sasa
FeatureReduceService.coordinates
FeatureSelectorAddService
FeatureSelectorAddService.__init__()
FeatureSelectorAddService.distances
FeatureSelectorAddService.contacts
FeatureSelectorAddService.coordinates
FeatureSelectorAddService.torsions
FeatureSelectorAddService.dssp
FeatureSelectorAddService.sasa
DecisionTree
DecisionTree.__init__()
DecisionTree.get_type_name()
DecisionTree.init_calculator()
DecisionTree.compute()
DecisionTree.get_params()
DecisionTreeCalculator
DecisionTreeCalculator.__init__()
DecisionTreeCalculator.compute()
AnalyzerTypeBase
AnalyzerTypeBase.__init__()
AnalyzerTypeBase.compute()
AnalyzerTypeBase.get_type_name()
AnalyzerTypeBase.init_calculator()
AnalyzerTypeBase.get_params()
AnalyzerTypeMeta
FeatureImportanceData
FeatureImportanceData.__init__()
FeatureImportanceData.add_comparison_result()
FeatureImportanceData.get_comparison()
FeatureImportanceData.get_all_comparisons()
FeatureImportanceData.list_comparisons()
FeatureImportanceData.get_top_features()
FeatureImportanceData.get_average_importance()
FeatureImportanceData.get_analysis_info()
FeatureImportanceData.save()
FeatureImportanceData.load()
FeatureImportanceData.print_info()
FeatureImportanceData.get_representative_frame()
AnalysisRunnerHelper
AnalysisRunnerHelper.store_analysis_result()
AnalysisRunnerHelper.run_comparison_analysis()
FeatureImportanceValidationHelper
FeatureImportanceValidationHelper.validate_analysis_name()
FeatureImportanceValidationHelper.validate_analysis_exists()
FeatureImportanceValidationHelper.validate_comparison_exists()
MetadataBuilderHelper
MetadataBuilderHelper.add_group_information()
MetadataBuilderHelper.add_model_metadata()
MetadataBuilderHelper.generate_sub_comparison_name()
MetadataBuilderHelper.extract_class_names()
RepresentativeFinderHelper
RepresentativeFinderHelper.find_best_tree_based()
TopFeaturesHelper
TopFeaturesHelper.get_top_features_for_comparison()
TopFeaturesHelper.get_top_features_averaged()
TopFeaturesHelper.format_features_with_names()
TopFeaturesHelper.get_top_features_with_names()
FeatureImportanceManager
FeatureImportanceManager.__init__()
FeatureImportanceManager.add_analysis()
FeatureImportanceManager.get_analysis_info()
FeatureImportanceManager.get_top_features()
FeatureImportanceManager.get_all_top_features()
FeatureImportanceManager.print_top_n_features()
FeatureImportanceManager.list_analyses()
FeatureImportanceManager.remove_analysis()
FeatureImportanceManager.save()
FeatureImportanceManager.load()
FeatureImportanceManager.print_info()
FeatureImportanceManager.add
FeatureImportanceManager.get_representative_frames()
FeatureImportanceAddService
FeatureImportanceAddService.__init__()
FeatureImportanceAddService.decision_tree()
FeatureSelectorData
FeatureSelectorData.__init__()
FeatureSelectorData.add_selection()
FeatureSelectorData.get_selections()
FeatureSelectorData.has_feature()
FeatureSelectorData.get_feature_keys()
FeatureSelectorData.clear_selections()
FeatureSelectorData.get_summary()
FeatureSelectorData.store_results()
FeatureSelectorData.get_results()
FeatureSelectorData.get_all_results()
FeatureSelectorData.has_results()
FeatureSelectorData.clear_results()
FeatureSelectorData.set_reference_trajectory()
FeatureSelectorData.get_reference_trajectory()
FeatureSelectorData.set_n_columns()
FeatureSelectorData.get_n_columns()
FeatureSelectorData.save()
FeatureSelectorData.load()
FeatureSelectorData.print_info()
CommonDenominatorHelper
CommonDenominatorHelper.apply_common_denominator()
CommonDenominatorHelper.filter_using_identities()
CommonDenominatorHelper.extract_feature_identities()
CommonDenominatorHelper.find_common_feature_identities()
CommonDenominatorHelper.filter_to_common_features()
CommonDenominatorHelper.identity_present_in_list()
FeatureSelectorConsensusParseHelper
FeatureSelectorConsensusParseHelper.parse_consensus_category()
FeatureSelectorConsensusParseHelper.parse_consensus_pattern()
FeatureSelectorNumericParseHelper
FeatureSelectorNumericParseHelper.parse_numeric_category()
FeatureSelectorParseCoreHelper
FeatureSelectorParseCoreHelper.parse_selection()
FeatureSelectorResidParseHelper
FeatureSelectorResidParseHelper.parse_resid_category()
FeatureSelectorResnameParseHelper
FeatureSelectorResnameParseHelper.parse_res_category()
FeatureSelectorSeqidParseHelper
FeatureSelectorSeqidParseHelper.parse_seqid_category()
ReductionIndexMapper
ReductionIndexMapper.map_reduced_to_original()
ReductionIndexMapper.get_kept_indices()
PostSelectionReductionHelper
PostSelectionReductionHelper.apply_reduction()
FeatureSelectorManager
FeatureSelectorManager.__init__()
FeatureSelectorManager.create()
FeatureSelectorManager.add
FeatureSelectorManager.add_selection()
FeatureSelectorManager.select()
FeatureSelectorManager.list_selectors()
FeatureSelectorManager.get_selector_summary()
FeatureSelectorManager.remove_selector()
FeatureSelectorManager.save()
FeatureSelectorManager.load()
FeatureSelectorManager.print_info()
PipelineData
PipelineData.__init__()
PipelineData.clear_all_data()
PipelineData.update_max_memory_from_trajectories()
PipelineData.update_max_memory_from_features()
PipelineData.get_data_summary()
PipelineData.add_custom_metadata()
PipelineData.get_custom_metadata()
PipelineData.has_trajectories()
PipelineData.has_features()
PipelineData.has_clusterings()
PipelineData.has_decompositions()
PipelineData.get_feature()
PipelineData.get_decomposition()
PipelineData.list_decompositions()
PipelineData.get_cluster()
PipelineData.list_clusters()
PipelineData.save()
PipelineData.load()
PipelineData.get_selected_metadata()
PipelineData.validate_selection_exists()
PipelineData.get_selected_data()
PipelineData.get_centroid_frame()
PipelineData.get_comparison_data()
PipelineData.get_config()
PipelineData.clear_matrix_cache()
CacheRemapHelper
CacheRemapHelper.remap_pipeline_memmaps()
CentroidHelper
CentroidHelper.find_centroid()
ComparisonDataHelper
ComparisonDataHelper.get_sub_comparison_data()
SelectionMatrixHelper
SelectionMatrixHelper.build_selection_matrix()
SelectionMemmapHelper
SelectionMemmapHelper.create_memmap_selection()
SelectionMemmapHelper.memmap_hstack()
SelectionMemmapHelper.create_memmap_frame_selection()
SelectionMetadataHelper
SelectionMetadataHelper.collect_metadata_for_selection()
SelectionMetadataHelper.finalize_metadata_result()
PerformanceConfig
PerformanceConfig.__init__()
PerformanceConfig.update()
PipelineManager
PipelineManager.__init__()
PipelineManager.report_resource_limits()
PipelineManager.trajectory
PipelineManager.set_show_progress()
PipelineManager.feature
PipelineManager.clustering
PipelineManager.decomposition
PipelineManager.feature_selector
PipelineManager.data_selector
PipelineManager.comparison
PipelineManager.feature_importance
PipelineManager.analysis
PipelineManager.plots
PipelineManager.structure_visualization
PipelineManager.data
PipelineManager.summary()
PipelineManager.add_custom_metadata()
PipelineManager.get_custom_metadata()
PipelineManager.clear_all()
PipelineManager.close()
PipelineManager.save_to_single_file()
PipelineManager.load_from_single_file()
PipelineManager.create_sharable_archive()
PipelineManager.load_from_archive()
PipelineManager.print_info()
PipelineManager.update_config()
PipelineManager.get_config()
AutoInjectProxy
AutoInjectProxy.__init__()
DecisionTreePlotter
DecisionTreePlotter.__init__()
DecisionTreePlotter.plot()
DecisionTreeVisualizationConfig
DecisionTreeVisualizationConfig.max_visualizable_depth
DecisionTreeVisualizationConfig.default_depth_fallback
DecisionTreeVisualizationConfig.base_y_spacing
DecisionTreeVisualizationConfig.y_spacing_formula_base
DecisionTreeVisualizationConfig.y_spacing_depth_factor
DecisionTreeVisualizationConfig.y_spacing_depth_offset
DecisionTreeVisualizationConfig.default_subplot_height
DecisionTreeVisualizationConfig.height_margin
DecisionTreeVisualizationConfig.height_divisor
DecisionTreeVisualizationConfig.min_subplot_height
DecisionTreeVisualizationConfig.min_subplot_width
DecisionTreeVisualizationConfig.default_subplot_width
DecisionTreeVisualizationConfig.width_divisor
DecisionTreeVisualizationConfig.width_extra_margin
DecisionTreeVisualizationConfig.default_tree_width_fallback
DecisionTreeVisualizationConfig.depth_width_limits
DecisionTreeVisualizationConfig.depth_height_limits
DecisionTreeVisualizationConfig.default_width_limit
DecisionTreeVisualizationConfig.default_height_limit
DecisionTreeVisualizationConfig.max_dimension_for_dpi_reduction
DecisionTreeVisualizationConfig.reduced_dpi
DecisionTreeVisualizationConfig.grid_wspace
DecisionTreeVisualizationConfig.grid_hspace_dynamic
DecisionTreeVisualizationConfig.grid_top
DecisionTreeVisualizationConfig.grid_bottom
DecisionTreeVisualizationConfig.grid_left
DecisionTreeVisualizationConfig.grid_right
DecisionTreeVisualizationConfig.subplot_border_width
DecisionTreeVisualizationConfig.subplot_title_pad
DecisionTreeVisualizationConfig.main_title_y
DecisionTreeVisualizationConfig.subplot_title_fontsize
DecisionTreeVisualizationConfig.default_subplot_title_fontsize
DecisionTreeVisualizationConfig.main_title_fontsize
DecisionTreeVisualizationConfig.default_main_title_fontsize
DecisionTreeVisualizationConfig.separate_tree_title_fontsize
DecisionTreeVisualizationConfig.separate_tree_title_pad
DecisionTreeVisualizationConfig.visualizer_fontsize_depth_6
DecisionTreeVisualizationConfig.visualizer_fontsize_depth_5
DecisionTreeVisualizationConfig.visualizer_fontsize_min
DecisionTreeVisualizationConfig.visualizer_fontsize_base
DecisionTreeVisualizationConfig.visualizer_fontsize_factor
DecisionTreeVisualizationConfig.edge_fontsize_offset
DecisionTreeVisualizationConfig.edge_fontsize_min
DecisionTreeVisualizationConfig.node_pad_deep
DecisionTreeVisualizationConfig.node_pad_shallow
DecisionTreeVisualizationConfig.node_pad_depth_threshold
DecisionTreeVisualizationConfig.default_spacing_depth_6
DecisionTreeVisualizationConfig.default_spacing_depth_5
DecisionTreeVisualizationConfig.default_spacing_fallback
DecisionTreeVisualizationConfig.optimal_spacing_min
DecisionTreeVisualizationConfig.optimal_spacing_max
DecisionTreeVisualizationConfig.optimal_spacing_single_node
DecisionTreeVisualizationConfig.padding_x_base
DecisionTreeVisualizationConfig.padding_x_depth_factor
DecisionTreeVisualizationConfig.padding_x_min_percent
DecisionTreeVisualizationConfig.padding_x_min_absolute
DecisionTreeVisualizationConfig.padding_y_percent
DecisionTreeVisualizationConfig.padding_y_min_absolute
DecisionTreeVisualizationConfig.padding_y_default_range
DecisionTreeVisualizationConfig.padding_default_x_range
DecisionTreeVisualizationConfig.discrete_label_wrap_length
DecisionTreeVisualizationConfig.auto_mode_separate_threshold
DecisionTreeVisualizationConfig.__init__()
DecisionTreeVisualizer
DecisionTreeVisualizer.__init__()
DecisionTreeVisualizer.build_graph()
DecisionTreeVisualizer.plot_tree()
DecisionTreeVisualizer.visualize()
EdgeLabelFormatter
EdgeLabelFormatter.get_edge_symbols()
EdgeLabelFormatter.format_path_label_with_symbol()
EdgeLabelFormatter.get_path_labels()
EdgeLabelFormatter.get_edge_labels()
EdgeLabelFormatter.format_short_edge_labels()
EdgeLabelFormatter.format_default_edge_labels()
EdgeLabelFormatter.format_continuous_edge_labels()
FeatureLabelBuilder
FeatureLabelBuilder.build_feature_label()
FeatureLabelBuilder.build_base_label()
FeatureLabelBuilder.get_rule_suffix_from_metadata()
FeatureLabelBuilder.add_rule_suffix()
FeatureLabelBuilder.get_reverse_edge_semantics()
NodeTextFormatter
NodeTextFormatter.shorten_class_name()
NodeTextFormatter.get_discrete_labels()
NodeTextFormatter.format_node_text()
NodeTextFormatter.format_root_node_text()
NodeTextFormatter.format_path_section()
NodeTextFormatter.format_class_statistics_section()
NodeTextFormatter.format_split_criterion_section()
NodeTextFormatter.format_decision_node_text()
NodeTextFormatter.format_leaf_node_text()
NodeTextFormatter.should_hide_prefix()
NodeTextFormatter.get_split_criterion_rule()
PlotConfigurationHelper
PlotConfigurationHelper.validate_and_get_data()
PlotConfigurationHelper.calculate_effective_depth()
PlotConfigurationHelper.calculate_subplot_sizes()
PlotConfigurationHelper.calculate_grid_layout()
PlotConfigurationHelper.determine_separate_trees_mode()
PlotConfigurationHelper.validate_tree_depth()
PlotConfigurationHelper.auto_determine_mode()
PlotConfigurationHelper.apply_dimension_limits()
PlotConfigurationHelper.set_depth_based_dimensions()
PlotConfigurationHelper.adjust_dpi_if_needed()
PlotConfigurationHelper.validate_output_methods()
PlotConfigurationHelper.calculate_required_tree_widths()
PlotConfigurationHelper.calculate_single_tree_width()
PlotConfigurationHelper.extract_width_from_visualizer()
PlotConfigurationHelper.extract_class_names()
SeparateTreeModeHelper
SeparateTreeModeHelper.plot_separate_trees()
TreePositionCalculator
TreePositionCalculator.calculate_optimal_spacing()
TreePositionCalculator.get_text_size()
TreePositionCalculator.compute_positions()
DensityPlotter
DensityPlotter.plot()
DensityCalculationHelper
DensityCalculationHelper.calculate_density()
DensityDiscreteBarHelper
DensityDiscreteBarHelper.plot_grouped_probability_bars()
DensityDataPreparer
FeatureImportanceBasePlotter
FeatureImportanceBasePlotter.__init__()
LandscapePlotter
LandscapePlotter.__init__()
LandscapePlotter.plot()
EnergyCalculatorHelper
EnergyCalculatorHelper.calculate_kde_grid()
EnergyCalculatorHelper.calculate_kde_energy_landscape()
EnergyCalculatorHelper.calculate_histogram_grid()
EnergyCalculatorHelper.calculate_histogram_energy_landscape()
EnergyCalculatorHelper.get_energy_range()
EnergyCalculatorHelper.mask_high_energy_regions()
LandscapeRenderingHelper
LandscapeRenderingHelper.plot_energy_background()
LandscapeRenderingHelper.plot_density_background()
LandscapeRenderingHelper.create_scatter()
LandscapeRenderingHelper.plot_cluster_voronoi()
LandscapeRenderingHelper.plot_cluster_density_contours()
LandscapeRenderingHelper.plot_tag_density_contours()
LandscapeRenderingHelper.plot_centers()
LandscapeStylingHelper
LandscapeStylingHelper.finalize_figure()
LandscapeStylingHelper.add_central_legend()
LandscapeStylingHelper.add_tag_legend()
LandscapeStylingHelper.set_axis_labels()
LandscapeStylingHelper.set_axis_limits()
LandscapeTagColoringHelper
LandscapeTagColoringHelper.build_frame_tag_map()
LayoutCalculatorHelper
LayoutCalculatorHelper.calculate_grid_layout()
LayoutCalculatorHelper.calculate_figure_size()
LayoutCalculatorHelper.create_dimension_pairs()
LayoutCalculatorHelper.get_subplot_position()
MembershipPlotter
MembershipPlotter.__init__()
MembershipPlotter.plot()
BlockOptimizerHelper
BlockOptimizerHelper.labels_to_blocks()
TimeSeriesPlotConfig
TimeSeriesPlotConfig.pipeline_data
TimeSeriesPlotConfig.mode_type
TimeSeriesPlotConfig.mode_name
TimeSeriesPlotConfig.feature_importance_name
TimeSeriesPlotConfig.n_top
TimeSeriesPlotConfig.feature_selector
TimeSeriesPlotConfig.traj_selection
TimeSeriesPlotConfig.use_time
TimeSeriesPlotConfig.tags_for_coloring
TimeSeriesPlotConfig.allow_multi_tag_plotting
TimeSeriesPlotConfig.clustering_name
TimeSeriesPlotConfig.membership_per_feature
TimeSeriesPlotConfig.membership_traj_selection
TimeSeriesPlotConfig.contact_transformation
TimeSeriesPlotConfig.max_cols
TimeSeriesPlotConfig.long_labels
TimeSeriesPlotConfig.subplot_height
TimeSeriesPlotConfig.membership_bar_height
TimeSeriesPlotConfig.show_legend
TimeSeriesPlotConfig.contact_threshold
TimeSeriesPlotConfig.title
TimeSeriesPlotConfig.save_fig
TimeSeriesPlotConfig.filename
TimeSeriesPlotConfig.file_format
TimeSeriesPlotConfig.dpi
TimeSeriesPlotConfig.smoothing
TimeSeriesPlotConfig.smoothing_method
TimeSeriesPlotConfig.smoothing_window
TimeSeriesPlotConfig.smoothing_polyorder
TimeSeriesPlotConfig.show_unsmoothed_background
TimeSeriesPlotConfig.discrete_plot_style
TimeSeriesPlotConfig.discrete_layout
TimeSeriesPlotConfig.discrete_offset_span
TimeSeriesPlotConfig.discrete_auto_offset_threshold
TimeSeriesPlotConfig.thickness
TimeSeriesPlotConfig.colors
TimeSeriesPlotConfig.vertical_markers
TimeSeriesPlotConfig.vertical_marker_labels
TimeSeriesPlotConfig.vertical_marker_label_colors
TimeSeriesPlotConfig.vertical_marker_mode
TimeSeriesPlotConfig.title_fontsize
TimeSeriesPlotConfig.subplot_title_fontsize
TimeSeriesPlotConfig.xlabel_fontsize
TimeSeriesPlotConfig.ylabel_fontsize
TimeSeriesPlotConfig.tick_fontsize
TimeSeriesPlotConfig.legend_fontsize
TimeSeriesPlotConfig.legend_title_fontsize
TimeSeriesPlotConfig.feature_data
TimeSeriesPlotConfig.feature_indices
TimeSeriesPlotConfig.metadata_map
TimeSeriesPlotConfig.contact_cutoff
TimeSeriesPlotConfig.feature_selector_name
TimeSeriesPlotConfig.is_temporary
TimeSeriesPlotConfig.tag_map
TimeSeriesPlotConfig.all_features
TimeSeriesPlotConfig.selected_matrix
TimeSeriesPlotConfig.frame_mapping
TimeSeriesPlotConfig.global_frame_indices_by_traj
TimeSeriesPlotConfig.local_frame_indices_by_traj
TimeSeriesPlotConfig.x_values_by_traj
TimeSeriesPlotConfig.layout
TimeSeriesPlotConfig.n_rows
TimeSeriesPlotConfig.n_cols
TimeSeriesPlotConfig.n_frames
TimeSeriesPlotConfig.n_membership_rows
TimeSeriesPlotConfig.membership_row_height_inches
TimeSeriesPlotConfig.use_tag_coloring
TimeSeriesPlotConfig.tag_colors
TimeSeriesPlotConfig.traj_colors
TimeSeriesPlotConfig.discrete_state_colors
TimeSeriesPlotConfig.has_discrete_features
TimeSeriesPlotConfig.resolved_discrete_layout
TimeSeriesPlotConfig.effective_subplot_height
TimeSeriesPlotConfig.resolved_vertical_markers
TimeSeriesPlotConfig.resolved_vertical_marker_legend_entries
TimeSeriesPlotConfig.fig
TimeSeriesPlotConfig.gs
TimeSeriesPlotConfig.wrapped_title
TimeSeriesPlotConfig.top
TimeSeriesPlotConfig.rightmost_ax_first_row
TimeSeriesPlotConfig.__init__()
TimeSeriesPlotter
TimeSeriesPlotter.plot()
MembershipBarRenderer
MembershipBarRenderer.prepare_membership_data()
MembershipBarRenderer.render_membership_bars_from_prepared()
SmoothingHelper
SmoothingHelper.apply_smoothing()
SmoothingHelper.validate_smoothing_params()
TimeSeriesDataPreparer
TimeSeriesDataPreparer.prepare()
TimeSeriesDataPreparer.prepare_from_manual_selection()
TimeSeriesDataPreparer.get_x_values()
TimeSeriesDiscretePlotHelper
TimeSeriesDiscretePlotHelper.build_axis_config()
TimeSeriesDiscretePlotHelper.plot_discrete_overlay_or_offset()
TimeSeriesDiscretePlotHelper.plot_discrete_occupancy()
TimeSeriesDiscretePlotHelper.configure_discrete_y_axis()
TimeSeriesDiscretePlotHelper.compute_symmetric_offsets()
TimeSeriesDiscretePlotHelper.calculate_time_resolved_probabilities()
TimeSeriesDiscretePlotHelper.render_discrete_trace()
TimeSeriesFeaturePlotHelper
TimeSeriesFeaturePlotHelper.plot_all_features()
TimeSeriesGridLayoutHelper
TimeSeriesGridLayoutHelper.calculate_grid_dimensions()
TimeSeriesGridLayoutHelper.create_gridspec()
TimeSeriesMembershipPlotHelper
TimeSeriesMembershipPlotHelper.get_membership_indices()
TimeSeriesMembershipPlotHelper.plot_membership_bars()
TimeSeriesTagColoringHelper
TimeSeriesTagColoringHelper.should_use_tag_coloring()
TimeSeriesTagColoringHelper.build_tag_map()
TimeSeriesTagColoringHelper.prepare_tag_legend_colors()
TimeSeriesTagColoringHelper.prepare_trajectory_legend_colors()
TimeSeriesTagColoringHelper.plot_feature_with_tag_colors()
TimeSeriesTagColoringHelper.plot_feature_with_trajectory_colors()
ViolinPlotter
ViolinPlotter.plot()
ViolinDataPreparer
BaseFeatureImportancePlotDataPreparer
BaseFeatureImportancePlotDataPreparer.prepare_from_feature_importance()
BaseFeatureImportancePlotDataPreparer.prepare_from_manual_selection()
ClusteringDataHelper
ClusteringDataHelper.load_clustering_data()
ColorMappingHelper
ColorMappingHelper.get_cluster_colors()
ColorMappingHelper.get_landscape_colormap()
ColorMappingHelper.parse_cluster_id()
ColorMappingHelper.create_data_selector_color_mapping()
ColorResolutionHelper
ColorResolutionHelper.resolve_label_colors()
ColorResolutionHelper.build_colors_from_colormap()
ComparisonDataExtractor
ComparisonDataExtractor.get_all_data_selectors_from_comparison()
ContactToDistancesConverter
ContactToDistancesConverter.convert_contacts_to_distances()
ContactToDistancesConverter.cleanup_temporary_selector()
DiscreteFeatureHelper
DiscreteFeatureHelper.prepare_discrete_data()
DiscreteFeatureHelper.build_axis_config()
DiscreteFeatureHelper.calculate_discrete_probabilities()
FeatureMetadataHelper
FeatureMetadataHelper.collect_metadata_for_type()
FeatureMetadataHelper.get_top_level_metadata()
FeatureMetadataHelper.get_feature_info()
FeatureMetadataHelper.extract_feature_info_from_entry()
GridLayoutHelper
GridLayoutHelper.compute_uniform_grid_layout()
SvgExportHelper
SvgExportHelper.configure_svg_text_editability()
SvgExportHelper.restore_default_svg_settings()
SvgExportHelper.get_current_svg_settings()
SvgExportHelper.apply_svg_config_if_needed()
SvgExportHelper.save_figure_with_export_optimizations()
TagHelper
TagHelper.get_matching_tags()
TagHelper.filter_by_priority()
TagHelper.prepare_tag_colors()
TagHelper.create_tag_legend_handles()
TitleLegendHelper
TitleLegendHelper.wrap_title()
TitleLegendHelper.format_bold_superscript_title()
TitleLegendHelper.estimate_title_height()
TitleLegendHelper.compute_title_max_chars_from_width()
TitleLegendHelper.add_title()
TitleLegendHelper.add_legend()
TitleLegendHelper.get_side_legend_anchor()
VerticalMarkerHelper
VerticalMarkerHelper.validate_markers()
VerticalMarkerHelper.validate_labels()
VerticalMarkerHelper.validate_label_colors()
VerticalMarkerHelper.normalize_positions()
VerticalMarkerHelper.resolve_markers()
VerticalMarkerHelper.build_legend_handles()
ValidationHelper
ValidationHelper.validate_decomposition_exists()
ValidationHelper.validate_dimensions_list()
ValidationHelper.validate_show_centers_requirement()
ValidationHelper.validate_clustering_compatibility()
ValidationHelper.validate_clustering_exists()
ValidationHelper.validate_trajectory_selection()
ValidationHelper.validate_dimensions_for_layout()
ValidationHelper.validate_feature_importance_exists()
ValidationHelper.validate_positive_integer()
ValidationHelper.validate_feature_selector_exists()
ValidationHelper.has_discrete_features()
PlotsManager
PlotsManager.__init__()
PlotsManager.decomposition
PlotsManager.clustering
PlotsManager.feature_importance
PlotsManager.feature
PlotsManager.landscape()
PlotsManager.membership()
ClusteringFacade
ClusteringFacade.__init__()
ClusteringFacade.landscape()
ClusteringFacade.membership()
DecompositionFacade
DecompositionFacade.__init__()
DecompositionFacade.landscape()
FeatureFacade
FeatureFacade.__init__()
FeatureFacade.violins()
FeatureFacade.densities()
FeatureFacade.time_series()
FeatureImportanceFacade
FeatureImportanceFacade.__init__()
FeatureImportanceFacade.violins()
FeatureImportanceFacade.densities()
FeatureImportanceFacade.time_series()
FeatureImportanceFacade.decision_trees()
StructureVisualizationData
StructureVisualizationData.__init__()
StructureVisualizationData.add_pdb()
StructureVisualizationData.get_pdb()
StructureVisualizationData.get_all_pdbs()
StructureVisualizationData.has_pdb()
StructureVisualizationData.add_feature_info()
StructureVisualizationData.get_feature_info()
ColorConversionHelper
ColorConversionHelper.hex_to_rgb()
ColorConversionHelper.hex_to_pymol_rgb()
ColorConversionHelper.calculate_average_rgb()
ColorConversionHelper.mix_hex_colors()
EnvironmentHelper
EnvironmentHelper.is_jupyter_environment()
EnvironmentHelper.is_pymol_available()
FeatureOverlapHelper
FeatureOverlapHelper.build_residue_feature_map()
FeatureOverlapHelper.detect_residue_overlaps()
NGLViewHelper
NGLViewHelper.create_widget()
PdbBetaFactorHelper
PdbBetaFactorHelper.create_pdb_with_beta_factors()
PdbBetaFactorHelper.get_topology()
PyMolScriptGenerator
PyMolScriptGenerator.generate_script()
ResidueImportanceCalculator
ResidueImportanceCalculator.calculate_residue_importance()
ResidueImportanceCalculator.importance_to_beta_factors()
ResidueImportanceCalculator.calculate_beta_factors_from_features()
ValidationHelper.validate_jupyter_environment()
ValidationHelper.validate_visualization_data()
ValidationHelper.validate_terminal_environment()
ValidationHelper.validate_pymol_available()
ValidationHelper.validate_data_selectors()
VisualizationDataHelper
VisualizationDataHelper.prepare_pdb_info_from_comp_data()
VisualizationDataHelper.prepare_pdb_info_from_viz_data()
VisualizationDataHelper.assign_feature_colors()
VisualizationDataHelper.extract_local_features_and_colors()
VisualizationDataHelper.extract_features_from_selector()
StructureVisualizationManager
StructureVisualizationManager.__init__()
StructureVisualizationManager.feature_importance
StructureVisualizationManager.feature
StructureVizFeatureService
StructureVizFeatureService.__init__()
StructureVizFeatureService.create_representative_pdbs()
StructureVizFeatureService.visualize_nglview_jupyter()
StructureVizFeatureService.create_pymol_script()
StructureVizFeatureService.visualize_pymol()
StructureVizFeatureImportanceService
StructureVizFeatureImportanceService.__init__()
StructureVizFeatureImportanceService.create_pdb_with_beta_factors()
StructureVizFeatureImportanceService.visualize_nglview_jupyter()
StructureVizFeatureImportanceService.create_pymol_script()
StructureVizFeatureImportanceService.visualize_pymol()
DaskMDTrajectory
DaskMDTrajectory.__init__()
DaskMDTrajectory.from_mdtraj()
DaskMDTrajectory.n_frames
DaskMDTrajectory.n_atoms
DaskMDTrajectory.n_residues
DaskMDTrajectory.topology
DaskMDTrajectory.top
DaskMDTrajectory.time
DaskMDTrajectory.timestep
DaskMDTrajectory.xyz
DaskMDTrajectory.unitcell_vectors
DaskMDTrajectory.unitcell_lengths
DaskMDTrajectory.unitcell_angles
DaskMDTrajectory.atom_slice()
DaskMDTrajectory.center_coordinates()
DaskMDTrajectory.superpose()
DaskMDTrajectory.smooth()
DaskMDTrajectory.image_molecules()
DaskMDTrajectory.remove_solvent()
DaskMDTrajectory.join()
DaskMDTrajectory.stack()
DaskMDTrajectory.slice()
DaskMDTrajectory.cleanup()
DaskMDTrajectory.memory_usage()
DaskMDTrajectory.save()
DaskMDTrajectory.load()
TrajectoryData
TrajectoryData.__init__()
TrajectoryData.get_trajectory_tags()
TrajectoryData.set_trajectory_tags()
TrajectoryData.n_frames_total
TrajectoryData.get_trajectory_names()
TrajectoryData.print_info()
TrajectoryData.save()
TrajectoryData.load()
TrajectoryData.reset()
TrajectoryData.get_trajectory_indices()
DaskMDTrajectoryArchiveHelper
DaskMDTrajectoryArchiveHelper.save()
DaskMDTrajectoryArchiveHelper.load()
DaskMDTrajectoryBuildHelper
DaskMDTrajectoryBuildHelper.__init__()
DaskMDTrajectoryBuildHelper.initialize_instance()
DaskMDTrajectoryBuildHelper.initialize_from_mdtraj()
DaskMDTrajectoryBuildHelper.create_from_zarr_store()
DaskMDTrajectoryJoinStackHelper
DaskMDTrajectoryJoinStackHelper.__init__()
DaskMDTrajectoryJoinStackHelper.join_trajectories()
DaskMDTrajectoryJoinStackHelper.stack_trajectories()
DaskMDTrajectoryStoreHelper
DaskMDTrajectoryStoreHelper.__init__()
DaskMDTrajectoryStoreHelper.create_slice_store()
ParallelOperationsHelper
ParallelOperationsHelper.__init__()
ParallelOperationsHelper.cleanup()
ParallelOperationsHelper.center_coordinates()
ParallelOperationsHelper.superpose()
ParallelOperationsHelper.smooth()
ParallelOperationsHelper.atom_slice()
ParallelOperationsHelper.image_molecules()
ParallelOperationsHelper.remove_solvent()
ZarrCacheHelper
ZarrCacheHelper.__init__()
ZarrCacheHelper.get_cache_path()
ZarrCacheHelper.cache_exists()
ZarrCacheHelper.create_cache()
ZarrCacheHelper.load_cache_metadata()
ZarrCacheHelper.get_or_create_cache()
ZarrCacheHelper.store_topology()
ZarrCacheHelper.load_topology()
ZarrCacheHelper.create_cache_from_mdtraj()
NomenclatureHelper
NomenclatureHelper.__init__()
NomenclatureHelper.create_trajectory_label_dicts()
TagHelper.resolve_trajectory_selectors()
LabelOperationHelper
LabelOperationHelper.apply_atom_selection_to_labels()
LabelOperationHelper.combine_stack_labels()
LabelOperationHelper.map_residues_to_original_indices()
SelectionResolveHelper
SelectionResolveHelper.get_indices_to_process()
SelectionResolveHelper.get_all_trajectories_with_tag()
TrajectoryLoadHelper
TrajectoryLoadHelper.load_trajectories()
TrajectoryProcessHelper
TrajectoryProcessHelper.apply_slicing()
TrajectoryProcessHelper.apply_selection_to_new_trajectories()
TrajectoryProcessHelper.execute_removal()
TrajectoryProcessHelper.validate_name_mapping()
TrajectoryProcessHelper.rename_with_list()
TrajectoryProcessHelper.rename_with_dict()
TrajectoryValidationHelper
TrajectoryValidationHelper.check_features_before_trajectory_changes()
TrajectoryValidationHelper.validate_slice_parameters()
TrajectoryValidationHelper.validate_data_selector()
TrajectoryValidationHelper.resolve_and_validate_traj_pair()
TrajectoryValidationHelper.validate_superpose_parameters()
TrajectoryManager
TrajectoryManager.__init__()
TrajectoryManager.load_trajectories()
TrajectoryManager.add_trajectory()
TrajectoryManager.remove_trajectory()
TrajectoryManager.slice_traj()
TrajectoryManager.select_atoms()
TrajectoryManager.add_labels()
TrajectoryManager.add_tags()
TrajectoryManager.set_tags()
TrajectoryManager.rename_trajectories()
TrajectoryManager.reset_trajectory_data()
TrajectoryManager.save()
TrajectoryManager.load()
TrajectoryManager.print_info()
TrajectoryManager.select_trajs()
TrajectoryManager.superpose()
TrajectoryManager.center_coordinates()
TrajectoryManager.smooth()
TrajectoryManager.image_molecules()
TrajectoryManager.remove_solvent()
TrajectoryManager.join()
TrajectoryManager.stack()
ArchiveFetchHelper
ArchiveFetchHelper.is_url()
ArchiveFetchHelper.validate_load_inputs()
ArchiveFetchHelper.should_verify_archive()
ArchiveFetchHelper.resolve_archive_path()
ArchiveFetchHelper.resolve_expected_sha256()
ArchiveFetchHelper.verify_archive_sha256()
ArchiveUtils
ArchiveUtils.is_essential_file()
ArchiveUtils.is_zarr_directory()
ArchiveUtils.is_visualization_file()
ArchiveUtils.is_structure_file()
ArchiveUtils.should_include_file()
ArchiveUtils.collect_cache_files()
ArchiveUtils.is_sha256_string()
ArchiveUtils.parse_sha256_text()
ArchiveUtils.compute_sha256()
ArchiveUtils.get_sha256_file_path()
ArchiveUtils.write_sha256_file()
ArchiveUtils.resolve_sha_output_path()
ArchiveUtils.create_archive()
ArchiveUtils.extract_archive()
CleanupUtils
CleanupUtils.close_zarr_store()
CleanupUtils.remove_file()
CleanupUtils.remove_tree()
CleanupUtils.remove_path()
ColorUtils
ColorUtils.generate_distinct_colors()
ColorUtils.add_special_color()
DataUtils
DataUtils.save_object()
DataUtils.load_object()
DataUtils.get_type_key()
FeatureMetadataUtils
FeatureMetadataUtils.get_feature_name()
FeatureMetadataUtils.get_feature_type()
FeatureMetadataUtils.get_feature_residues()
FeatureMetadataUtils.create_feature_map()
FeatureMetadataUtils.get_top_level_metadata()
LoadAndSaveHelper
LoadAndSaveHelper.save_object()
LoadAndSaveHelper.load_object()
LoadAndSaveHelper.peek_cache_dir()
MemmapUtils
MemmapUtils.prepare_memmap_path()
MemmapUtils.is_memmap_view()
MemmapUtils.evict_from_os_cache()
MemmapUtils.evict_memory_range()
MemmapUtils.close_memmap_view()
MemmapUtils.close_memmaps_for_path()
MemmapUtils.close_memmaps_under_path()
MemmapUtils.create_memmap()
OutputUtils
OutputUtils.suppress_output()
PathUtils
PathUtils.prepare_file_path()
PathUtils.prepare_directory_path()
PathUtils.get_cache_file_path()
PathUtils.create_pipeline_cache_dir()
ProgressUtils
ProgressUtils.set_enabled()
ProgressUtils.iterate()
ResourceUtils
ResourceUtils.recommend_cpu_affinity()
ResourceUtils.apply_auto_limits()
ResourceUtils.apply_blas_thread_limits()
ResourceUtils.apply_process_limits()
ResourceUtils.tune_memmap()
TextUtils
TextUtils.wrap_text()
TopFeaturesUtils
TopFeaturesUtils.get_top_features_with_names()
Trajectory metadata helper utilities.