mdxplain
  • mdxplain Overview
    • Data Input
    • mdxplain Tools
      • 1. Feature Calculation
      • 2.1 Dimensionality Reduction and Clustering
      • 2.2 Feature Selection
      • 3. Data Selection and Matrix Construction
      • 4. Comparison
      • 5. Explainability Through Feature Importance
    • Data Output
  • How to Install mdxplain
    • Prerequisites
    • Quick Setup
      • Conda Environment (Recommended)
      • Python Virtual Environment (Alternative)
      • Install in Existing Environment
      • Optional: PyMOL Installation
    • Installation Options
      • Environment Setup Commands
      • Installation in Existing Environment
      • What’s Included
    • Additional Commands
      • Jupyter
      • Development
      • Help
    • Install on Windows
      • PyMOL Installation on Windows
      • Manual Installation (without Make)
  • Learn mdxplain
    • Key Design Principles
    • Basic Usage Examples
      • Quick Start Example
      • Performance Settings (Quick Guide)
        • Key settings
        • Examples
      • Memory-Efficient Processing
        • Memory Mapping Guidelines
      • Trajectory Management
        • Consensus Nomenclature for Structured Proteins
      • Feature Computation
      • Feature Selection
        • How the Parser Works
          • Selection Keywords
            • res - Residue Names
            • resid - Residue IDs
            • seqid - Sequence IDs
            • consensus - Consensus Nomenclature
            • all
          • Logical Operators
        • Practical Examples with Biological Context
          • GPCR Activation Contact (Ionic Lock)
          • G-Protein Binding Interface
          • Binding Pocket Aromatic Cage
          • Hydrophobic Core Interactions
          • TM Helix Interface Including Loop
      • Feature Reduction
        • Statistical Feature Filtering
        • What is Feature Reduction?
        • When to Use Feature Reduction
        • Two Reduction Approaches
          • Approach 1: Inline Reduction (during selection)
          • Approach 2: Pre-Reduction + use_reduced=True
        • Reduction Methods by Feature Type
          • Contacts
          • Distances
          • Coordinates
          • Torsions
          • SASA
          • DSSP
      • Dimensionality Reduction
      • Clustering
      • Structural Analysis
        • RMSD Metrics - Which Variant to Use
          • .rmsd.mean - Standard RMSD (Root Mean Square Deviation)
          • .rmsd.median - Robust RMSD (Root Median Square Deviation)
          • .rmsd.mad - MAD RMSD (Median Absolute Deviation)
        • RMSD Modes - What to Measure
          • .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 Metrics - Which Variant
          • .rmsf.mean - Standard RMSF (Root Mean Square Fluctuation)
          • .rmsf.median - Robust RMSF (Root Median Square Fluctuation)
          • .rmsf.mad - MAD RMSF (Median Absolute Deviation)
        • RMSF Modes - Resolution Level
          • .per_atom
          • .per_residue
        • Per-Residue Aggregation Methods
          • .with_mean_aggregation (Default, Simple Average)
          • .with_median_aggregation (Robust to Outliers)
          • .with_rms_aggregation (Emphasize Larger Values)
          • .with_rms_median_aggregation (Emphasize + Robust)
        • Aggregation Selection Guide
        • Practical Examples
          • Equilibration Monitoring
          • Flexible Multi-Domain Protein
          • Conformational Transition Detection
          • Standard Flexibility Profile
          • Binding Site Side-Chain Flexibility
          • Multi-Domain Protein Flexibility
          • Side-Chain Rotamer Switching (Advanced Aggregation)
      • Feature Statistics
        • Available Statistics
        • Use Cases
      • Data Selection (Frame/Row Selection)
        • Core Concept
        • Why Use Data Selection
        • Methods
          • create(name) - Create Named Frame Selection
          • select_by_tags(name, tags, match_all=True, mode="add", stride=1) - Tag-Based Selection
            • Parameters
            • Why use it
          • select_by_cluster(name, clustering_name, cluster_ids, mode="add", stride=1) - Cluster-Based Selection
            • Parameters
            • Why use it
          • select_by_indices(name, trajectory_indices, mode="add") - Direct Frame Index Selection
            • Parameters
              • Trajectory Selectors (Keys)
              • Frame Specifications (Values)
            • Why use it
        • Examples
          • Simple Frame Selection
          • Time Window (Exclude Equilibration)
          • Range With Stride (Sparse Sampling)
          • Complex Combined Ranges
          • Tag-Based Frame Selection
          • Name Pattern Matching
          • Multi-Trajectory With Different Frame Selections and Stride
        • Practical Examples
          • State-Specific Analysis
          • Multi-State Conformational Analysis
          • Production Run With Data Reduction
          • Multi-Step Complex Selection With Set Operations
          • Systematic Condition Comparison (WT vs Mutant in Same State)
          • Outlier Removal (Quality Control)
        • Integration with Comparative Analysis
          • Common Use Cases
      • Comparative Analysis and Feature Importance
      • Plotting and Visualization
      • Saving and Loading
    • Tutorials
      • mdxplain Quickstart Tutorial: Introduction to Conformational Analysis with mdxplain
      • mdxplain Tutorial: Introduction to Conformational Analysis with mdxplain
        • Introduction
          • Methodology Overview
          • Test System
        • Import
          • Design note
        • Methods
          • Step 1: Data Loading and Preprocessing
          • Step 2: Feature Computation
          • Step 3: Feature Selection
          • Step 4: Dimensionality Reduction
          • Step 5: Conformational State Identification
          • Step 6: Temporal Dynamics - Cluster Membership Timeline
          • Step 7: Free Energy Landscape Visualization with Cluster Analysis
            • Plot Features
            • Interpretation
            • Parameters
          • Step 8: Comparative Analysis Setup
          • Step 9: Identifying Key Contacts with a Decision Tree
          • Step 10: Identifying the Top Contacts
            • Violin Plot Visualisation
            • Density Plot Visualisation
            • Time Series Visualisation
          • Step 11: Structural Visualization of Feature Importance
            • 11.1 Creating PDB Files with Feature Importance Encoding
            • 11.2 PyMOL Visualization
            • 11.3 Interactive Jupyter Visualization with NGLView
          • Step 12: Saving and loading the pipeline
          • Step 13: Info Printing
        • Discussion
          • Limitations and outlook
        • Conclusion
        • References
        • AI Disclaimer
      • Tutorial 3 - Reusing Sharable Archives
        • Continue From The Archive
      • Tutorial 04: Latrophilin-1 Mutation Analysis
        • Introduction
        • Simulation Background
        • Source of the Simulation
        • Download the Tutorial Files
        • Start of the mdxplain Pipeline - Import
        • Initialize the Pipeline
        • Load the Simulation Data
        • Assign Readable Names
        • Add Condition Tags
        • Add Residue Labels and GPCR Numbering
        • Compute Structural Features
        • Focus the Analysis on Contacts
        • Define the WT-vs-Mutant Comparison
        • Rank Discriminative Contacts with a Decision Tree
        • Visualize the Decision Rules
        • Inspect the Top Contacts with Violin Plots
        • Compare Contact Distributions as Densities
        • Follow the Top Contacts over Time
        • Map Importance Scores onto the Structure
        • Create a PyMOL Visualization Script
        • Save a Shareable Analysis Archive
    • Performance and System Stability
      • What we observed
      • Why this happens
        • Memory-mapped files and the page cache
        • The pressure of approximations (e.g., Nyström)
        • Disk I/O saturation
        • Thrashing
        • Too much parallelism (oversubscription)
        • Access pattern confusion
        • Why even the power button may not work
      • How mdxplain reduces the risk
        • Chunk-level flushing of memmaps
        • Explicit access-pattern hints
        • Controlled parallelism
        • CPU and I/O fairness
        • Platform safety and HPC environments
      • Summary
      • References
  • How to Contribute
    • Guidelines
    • Contribution License
  • How to Cite mdxplain
    • BibTeX Reference
  • License and Copyright
    • Contributors
    • License
  • Declaration of AI Tool Usage
    • Primary Development Environment
    • Supplementary Tools and Specific Applications
    • AI-Assisted Development Tasks
    • Early-Phase Research and Prototyping
    • Author’s Independent Contributions
  • API Documentation
    • Project Structure
    • Analysis
      • Analysis Manager
        • AnalysisManager
          • AnalysisManager.__init__()
          • AnalysisManager.features
          • AnalysisManager.structure
      • Analysis Services
      • Analysis Structure
        • Analysis Structure Calculators
          • RMSD Calculator
            • RMSDCalculator
              • RMSDCalculator.__init__()
              • RMSDCalculator.rmsd_to_reference()
              • RMSDCalculator.frame_to_frame()
              • RMSDCalculator.window()
          • RMSF Calculator
            • RMSFCalculator
              • RMSFCalculator.__init__()
              • RMSFCalculator.calculate_per_atom()
              • RMSFCalculator.calculate_per_residue()
        • Analysis Structure Helper
          • Reference Structure Helper
            • ReferenceStructureHelper
              • ReferenceStructureHelper.get_mean_coordinates()
              • ReferenceStructureHelper.get_median_coordinates()
          • Residue Aggregation Helper
            • aggregate_residues_jit()
          • Structure Calculation Helper
            • StructureCalculationHelper
              • StructureCalculationHelper.iterate_chunks()
              • StructureCalculationHelper.stack_frames()
          • Trajectory Service Helper
            • TrajectoryServiceHelper
              • TrajectoryServiceHelper.__init__()
              • TrajectoryServiceHelper.resolve_trajectories_and_atoms()
              • TrajectoryServiceHelper.build_result_map()
              • TrajectoryServiceHelper.map_reference_to_local_index()
        • Analysis Structure Services
          • RMSD Facade
            • RMSDFacade
              • RMSDFacade.__init__()
              • RMSDFacade.mean
              • RMSDFacade.median
              • RMSDFacade.mad
              • RMSDFacade.to_reference()
          • RMSD Mad Service
            • RMSDMadService
              • RMSDMadService.__init__()
              • RMSDMadService.to_reference()
              • RMSDMadService.frame_to_frame()
              • RMSDMadService.window_frame_to_start()
              • RMSDMadService.window_frame_to_frame()
          • RMSD Mean Service
            • RMSDMeanService
              • RMSDMeanService.__init__()
              • RMSDMeanService.to_reference()
              • RMSDMeanService.frame_to_frame()
              • RMSDMeanService.window_frame_to_start()
              • RMSDMeanService.window_frame_to_frame()
          • RMSD Median Service
            • RMSDMedianService
              • RMSDMedianService.__init__()
              • RMSDMedianService.to_reference()
              • RMSDMedianService.frame_to_frame()
              • RMSDMedianService.window_frame_to_start()
              • RMSDMedianService.window_frame_to_frame()
          • RMSF Facade
            • RMSFFacade
              • RMSFFacade.__init__()
              • RMSFFacade.mean
              • RMSFFacade.median
              • RMSFFacade.mad
              • RMSFFacade.per_atom
              • RMSFFacade.per_residue
              • RMSFFacade.to_mean_reference()
          • RMSF Mad Variant Facade
            • RMSFMadVariantFacade
              • RMSFMadVariantFacade.__init__()
              • RMSFMadVariantFacade.per_atom
              • RMSFMadVariantFacade.per_residue
          • RMSF Mean Variant Facade
            • RMSFMeanVariantFacade
              • RMSFMeanVariantFacade.__init__()
              • RMSFMeanVariantFacade.per_atom
              • RMSFMeanVariantFacade.per_residue
          • RMSF Median Variant Facade
            • RMSFMedianVariantFacade
              • RMSFMedianVariantFacade.__init__()
              • RMSFMedianVariantFacade.per_atom
              • RMSFMedianVariantFacade.per_residue
          • RMSF Per Atom Service
            • RMSFPerAtomService
              • RMSFPerAtomService.__init__()
              • RMSFPerAtomService.to_mean_reference()
              • RMSFPerAtomService.to_median_reference()
          • RMSF Per Residue Aggregation Selection Facade
            • RMSFPerResidueAggregationSelectionFacade
              • RMSFPerResidueAggregationSelectionFacade.__init__()
              • RMSFPerResidueAggregationSelectionFacade.with_mean_aggregation
              • RMSFPerResidueAggregationSelectionFacade.with_median_aggregation
              • RMSFPerResidueAggregationSelectionFacade.with_rms_aggregation
              • RMSFPerResidueAggregationSelectionFacade.with_rms_median_aggregation
              • RMSFPerResidueAggregationSelectionFacade.to_mean_reference()
          • RMSF Per Residue Base Aggregation Facade
            • BaseRMSFPerResidueAggFacade
              • BaseRMSFPerResidueAggFacade.service
              • BaseRMSFPerResidueAggFacade.to_mean_reference()
              • BaseRMSFPerResidueAggFacade.to_median_reference()
          • RMSF Per Residue Mean Aggregation Facade
            • RMSFPerResidueMeanAggFacade
              • RMSFPerResidueMeanAggFacade.__init__()
              • RMSFPerResidueMeanAggFacade.service
          • RMSF Per Residue Median AggregationFacade
            • RMSFPerResidueMedianAggFacade
              • RMSFPerResidueMedianAggFacade.__init__()
              • RMSFPerResidueMedianAggFacade.service
          • RMSF Per Residue RMS Aggregation Facade
            • RMSFPerResidueRmsAggFacade
              • RMSFPerResidueRmsAggFacade.__init__()
              • RMSFPerResidueRmsAggFacade.service
          • RMSF Per Residue Median Aggregation Facade
            • RMSFPerResidueRmsMedianAggFacade
              • RMSFPerResidueRmsMedianAggFacade.__init__()
              • RMSFPerResidueRmsMedianAggFacade.service
          • RMSF Per Residue Service
            • RMSFPerResidueService
              • RMSFPerResidueService.__init__()
              • RMSFPerResidueService.to_mean_reference()
              • RMSFPerResidueService.to_median_reference()
          • Structure Analysis Service
            • StructureAnalysisService
              • StructureAnalysisService.__init__()
              • StructureAnalysisService.pipeline_data
              • StructureAnalysisService.rmsd
              • StructureAnalysisService.rmsf
    • Clustering
      • Cluster Types
        • DBSCAN
          • DBSCAN Module
            • DBSCAN
              • DBSCAN.__init__()
              • DBSCAN.get_type_name()
              • DBSCAN.init_calculator()
              • DBSCAN.compute()
          • DBSCAN Calculator
            • DBSCANCalculator
              • DBSCANCalculator.__init__()
              • DBSCANCalculator.compute()
        • DPA
          • DPA Module
            • DPA
              • DPA.__init__()
              • DPA.get_type_name()
              • DPA.init_calculator()
              • DPA.compute()
          • DBA Calculator
            • DPACalculator
              • DPACalculator.__init__()
              • DPACalculator.compute()
        • HDBSCAN
          • HDBSCAN Module
            • HDBSCAN
              • HDBSCAN.__init__()
              • HDBSCAN.get_type_name()
              • HDBSCAN.init_calculator()
              • HDBSCAN.compute()
          • HDBSCAN Calculator
            • HDBSCANCalculator
              • HDBSCANCalculator.__init__()
              • HDBSCANCalculator.compute()
        • Interfaces
          • Calculator Base
            • CalculatorBase
              • CalculatorBase.__init__()
              • CalculatorBase.compute()
          • Cluster Type Base
            • ClusterTypeBase
              • ClusterTypeBase.__init__()
              • ClusterTypeBase.get_type_name()
              • ClusterTypeBase.init_calculator()
              • ClusterTypeBase.compute()
          • Cluster Type Meta
            • ClusterTypeMeta
      • Clustering Entities
        • Cluster Data
          • 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()
      • Clustering Helper
        • Center Calculation Helper
          • CenterCalculationHelper
            • CenterCalculationHelper.VALID_METHODS
            • CenterCalculationHelper.calculate_centers()
      • Clustering Manager
        • Cluster Manager
          • ClusterManager
            • ClusterManager.__init__()
            • ClusterManager.reset_clusters()
            • ClusterManager.add_clustering()
            • ClusterManager.save()
            • ClusterManager.load()
            • ClusterManager.print_info()
            • ClusterManager.add
      • Cluster Type Services
        • Cluster Add Service
          • ClusterAddService
            • ClusterAddService.__init__()
            • ClusterAddService.dbscan
            • ClusterAddService.hdbscan
            • ClusterAddService.dpa
        • DBSCAN Add Service
          • 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()
        • DPA Add Service
          • 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()
        • HDBSCAN Add Service
          • 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()
    • Comparison
      • Comparison Entities
        • 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()
      • Comparison Helper
        • Validation Helper
          • ComparisonValidationHelper
            • ComparisonValidationHelper.validate_comparison_name()
            • ComparisonValidationHelper.validate_comparison_exists()
            • ComparisonValidationHelper.validate_mode()
            • ComparisonValidationHelper.validate_feature_selector()
            • ComparisonValidationHelper.validate_data_selectors()
            • ComparisonValidationHelper.validate_has_selectors()
        • Sub Comparison Creation Helper
          • SubComparisonCreationHelper
            • SubComparisonCreationHelper.create_binary_sub_comparisons()
            • SubComparisonCreationHelper.create_pairwise_sub_comparisons()
            • SubComparisonCreationHelper.create_one_vs_rest_sub_comparisons()
            • SubComparisonCreationHelper.create_multiclass_sub_comparisons()
      • Comparison Manager
        • ComparisonManager
          • ComparisonManager.__init__()
          • ComparisonManager.create_comparison()
          • ComparisonManager.list_comparisons()
          • ComparisonManager.get_comparison_info()
          • ComparisonManager.remove_comparison()
          • ComparisonManager.save()
          • ComparisonManager.load()
          • ComparisonManager.print_info()
    • Data Selector
      • Data Selection Entities
        • Data Selector Data
          • 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()
        • Data Selector Group
          • DataSelectorGroup
            • DataSelectorGroup.__init__()
      • Data Selector Helper
        • Criteria Builder Helper
          • CriteriaBuilderHelper
            • CriteriaBuilderHelper.build_tag_criteria()
            • CriteriaBuilderHelper.build_cluster_criteria()
            • CriteriaBuilderHelper.build_indices_criteria()
            • CriteriaBuilderHelper.build_combination_criteria()
        • Frame Selection Helper
          • 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()
        • Group Creation Helper
          • GroupCreationHelper
            • GroupCreationHelper.create_cluster_selectors()
            • GroupCreationHelper.create_tag_selectors()
      • Data Selector Manager
        • 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()
    • Decomposition
      • Decomposition Types
        • Contact Kernel PCA
          • Contact Kernel PCA Data
            • ContactKernelPCA
              • ContactKernelPCA.__init__()
              • ContactKernelPCA.get_type_name()
              • ContactKernelPCA.init_calculator()
              • ContactKernelPCA.compute()
          • Contact Kernel PCA Calculator
            • ContactKernelPCACalculator
              • ContactKernelPCACalculator.__init__()
              • ContactKernelPCACalculator.compute()
        • Diffusion Maps
          • Diffusion Maps Data
            • DiffusionMaps
              • DiffusionMaps.__init__()
              • DiffusionMaps.get_type_name()
              • DiffusionMaps.get_required_feature_type()
              • DiffusionMaps.init_calculator()
              • DiffusionMaps.compute()
          • Diffusion Maps Calculator
            • DiffusionMapsCalculator
              • DiffusionMapsCalculator.__init__()
              • DiffusionMapsCalculator.compute()
        • Kernel PCA
          • Kernel PCA Data
            • KernelPCA
              • KernelPCA.__init__()
              • KernelPCA.get_type_name()
              • KernelPCA.init_calculator()
              • KernelPCA.compute()
          • Kernel PCA Calculator
            • KernelPCACalculator
              • KernelPCACalculator.__init__()
              • KernelPCACalculator.compute()
        • PCA
          • PCA Data
            • PCA
              • PCA.__init__()
              • PCA.get_type_name()
              • PCA.init_calculator()
              • PCA.compute()
          • PCA Calculator
            • PCACalculator
              • PCACalculator.__init__()
              • PCACalculator.compute()
        • Interfaces
          • Calculator Base
            • CalculatorBase
              • CalculatorBase.__init__()
              • CalculatorBase.compute()
          • Decomposition Types Base
            • DecompositionTypeBase
              • DecompositionTypeBase.__init__()
              • DecompositionTypeBase.get_type_name()
              • DecompositionTypeBase.init_calculator()
              • DecompositionTypeBase.compute()
              • DecompositionTypeBase.get_required_feature_type()
          • Decomposition Types Meta
            • DecompositionTypeMeta
        • Decomposition Type Helper
          • Automatic Parameter Helper
            • AutomaticParameterHelper
              • AutomaticParameterHelper.find_elbow()
              • AutomaticParameterHelper.calculate_gamma_scale()
              • AutomaticParameterHelper.calculate_gamma_auto()
              • AutomaticParameterHelper.compute_variance_chunked()
      • Decomposition Entities
        • DecompositionData
          • DecompositionData.__init__()
          • DecompositionData.get_frame_mapping()
          • DecompositionData.set_frame_mapping()
          • DecompositionData.save()
          • DecompositionData.load()
          • DecompositionData.print_info()
      • Decomposition Manager
        • DecompositionManager
          • DecompositionManager.__init__()
          • DecompositionManager.add_decomposition()
          • DecompositionManager.reset_decompositions()
          • DecompositionManager.save()
          • DecompositionManager.load()
          • DecompositionManager.print_info()
          • DecompositionManager.add
      • Decomposition Services
        • Decomposition Add Service
          • DecompositionAddService
            • DecompositionAddService.__init__()
            • DecompositionAddService.pca()
            • DecompositionAddService.kernel_pca()
            • DecompositionAddService.contact_kernel_pca()
            • DecompositionAddService.diffusion_maps()
    • Feature
      • Feature Types
        • Contacts
          • Contacts Services
            • Contacts Selection Service
              • ContactsSelectionService
                • ContactsSelectionService.__init__()
                • ContactsSelectionService.with_frequency_reduction()
                • ContactsSelectionService.with_stability_reduction()
                • ContactsSelectionService.with_transitions_reduction()
            • Contacts Reduce Service
              • ContactsReduceService
                • ContactsReduceService.__init__()
                • ContactsReduceService.frequency()
                • ContactsReduceService.stability()
                • ContactsReduceService.transitions()
            • Contacts Analysis Service
              • 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 Data
            • Contacts
              • Contacts.__init__()
              • Contacts.init_calculator()
              • Contacts.compute()
              • Contacts.get_dependencies()
              • Contacts.get_type_name()
              • Contacts.get_input()
          • Contact Calculator
            • ContactCalculator
              • ContactCalculator.__init__()
              • ContactCalculator.compute()
              • ContactCalculator.compute_pooled_metric_values()
              • ContactCalculator.compute_dynamic_values()
          • Contact Calculator Analysis
            • 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()
        • Coordinates
          • Coordinates Services
            • Coordinates Selection Service
              • 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()
            • Coordinates Reduce Service
              • CoordinatesReduceService
                • CoordinatesReduceService.__init__()
                • CoordinatesReduceService.std()
                • CoordinatesReduceService.rmsf()
                • CoordinatesReduceService.cv()
                • CoordinatesReduceService.variance()
                • CoordinatesReduceService.range()
                • CoordinatesReduceService.mad()
                • CoordinatesReduceService.mean()
                • CoordinatesReduceService.min()
                • CoordinatesReduceService.max()
                • CoordinatesReduceService.transitions()
            • Coordinates Analysis Service
              • 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 Data
            • Coordinates
              • Coordinates.__init__()
              • Coordinates.init_calculator()
              • Coordinates.compute()
              • Coordinates.get_dependencies()
              • Coordinates.get_type_name()
              • Coordinates.get_input()
          • Coordinates Calculator
            • CoordinatesCalculator
              • CoordinatesCalculator.__init__()
              • CoordinatesCalculator.compute()
              • CoordinatesCalculator.compute_dynamic_values()
              • CoordinatesCalculator.compute_pooled_metric_values()
          • Coordinates Calculator Analysis
            • 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()
        • Distances
          • Distances Services
            • Distances Selection Service
              • 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()
            • Distances Reduce Service
              • DistancesReduceService
                • DistancesReduceService.__init__()
                • DistancesReduceService.cv()
                • DistancesReduceService.std()
                • DistancesReduceService.variance()
                • DistancesReduceService.range()
                • DistancesReduceService.transitions()
                • DistancesReduceService.min()
                • DistancesReduceService.mad()
                • DistancesReduceService.mean()
                • DistancesReduceService.max()
            • Distances Analysis Service
              • 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 Data
            • Distances
              • Distances.__init__()
              • Distances.init_calculator()
              • Distances.compute()
              • Distances.get_dependencies()
              • Distances.get_type_name()
              • Distances.get_input()
          • Distance Calculator
            • DistanceCalculator
              • DistanceCalculator.__init__()
              • DistanceCalculator.compute()
              • DistanceCalculator.compute_pooled_metric_values()
              • DistanceCalculator.compute_dynamic_values()
          • Distance Calculator Analysis
            • 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()
        • DSSP
          • DSSP Encoding Helper
            • DSSPEncodingHelper
              • DSSPEncodingHelper.encode_char_chunked()
              • DSSPEncodingHelper.encode_integer()
              • DSSPEncodingHelper.encode_integer_chunked()
              • DSSPEncodingHelper.encode_onehot_chunked()
              • DSSPEncodingHelper.encode_onehot_direct()
          • DSSP Services
            • DSSP Selection Service
              • DSSPSelectionService
                • DSSPSelectionService.__init__()
                • DSSPSelectionService.with_transitions_reduction()
                • DSSPSelectionService.with_transition_frequency_reduction()
                • DSSPSelectionService.with_stability_reduction()
                • DSSPSelectionService.with_class_frequencies_reduction()
            • DSSP Reduce Service
              • DSSPReduceService
                • DSSPReduceService.__init__()
                • DSSPReduceService.transitions()
                • DSSPReduceService.transition_frequency()
                • DSSPReduceService.stability()
                • DSSPReduceService.class_frequencies()
            • DSSP Analysis Service
              • 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 Data
            • DSSP
              • DSSP.__init__()
              • DSSP.init_calculator()
              • DSSP.compute()
              • DSSP.get_dependencies()
              • DSSP.get_type_name()
              • DSSP.get_input()
          • DSSP Calculator
            • DSSPCalculator
              • DSSPCalculator.FULL_CLASSES
              • DSSPCalculator.SIMPLIFIED_CLASSES
              • DSSPCalculator.__init__()
              • DSSPCalculator.compute()
              • DSSPCalculator.compute_dynamic_values()
              • DSSPCalculator.compute_pooled_metric_values()
          • DSSP Calculator Analysis
            • 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()
        • SASA
          • SASA Services
            • SASA Selection Service
              • 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()
            • SASA Reduce Service
              • 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()
            • SASA Analysis Service
              • 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 Data
            • SASA
              • SASA.__init__()
              • SASA.init_calculator()
              • SASA.compute()
              • SASA.get_dependencies()
              • SASA.get_type_name()
              • SASA.get_input()
          • SASA Calculator
            • SASACalculator
              • SASACalculator.__init__()
              • SASACalculator.compute()
              • SASACalculator.compute_dynamic_values()
              • SASACalculator.compute_pooled_metric_values()
          • SASA Calculator Analysis
            • 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()
        • Torsions
          • Torsions Services
            • Torsions Selection Service
              • 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()
            • Torsions Reduce Service
              • TorsionsReduceService
                • TorsionsReduceService.__init__()
                • TorsionsReduceService.transitions()
                • TorsionsReduceService.std()
                • TorsionsReduceService.mad()
                • TorsionsReduceService.mean()
                • TorsionsReduceService.range()
                • TorsionsReduceService.min()
                • TorsionsReduceService.max()
                • TorsionsReduceService.cv()
                • TorsionsReduceService.variance()
            • Torsions Analysis Service
              • 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 Data
            • Torsions
              • Torsions.__init__()
              • Torsions.init_calculator()
              • Torsions.compute()
              • Torsions.get_dependencies()
              • Torsions.get_type_name()
              • Torsions.get_input()
          • Torsions Calculator
            • TorsionsCalculator
              • TorsionsCalculator.__init__()
              • TorsionsCalculator.compute()
              • TorsionsCalculator.compute_dynamic_values()
              • TorsionsCalculator.compute_pooled_metric_values()
          • Torsions Calculator Analysis
            • 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()
        • Feature Type Helper
          • Calculator Compute Helper
            • CalculatorComputeHelper
              • CalculatorComputeHelper.compute_dynamic_values()
              • CalculatorComputeHelper.calculate_output_dimensions()
              • CalculatorComputeHelper.create_output_array()
          • Calculator Stat Helper
            • 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()
          • Feature Shape Helper
            • FeatureShapeHelper
              • FeatureShapeHelper.is_memmap()
              • FeatureShapeHelper.squareform_to_condensed()
              • FeatureShapeHelper.condensed_to_squareform()
        • Interfaces
          • Analysis Service Base
            • AnalysisServiceBase
              • AnalysisServiceBase.__init__()
          • Calculator Base
            • CalculatorBase
              • CalculatorBase.__init__()
              • CalculatorBase.compute_pooled_metric_values()
              • CalculatorBase.compute_pooled_selection_mask()
              • CalculatorBase.compute()
              • CalculatorBase.compute_dynamic_values()
          • Feature Type Base
            • FeatureTypeBase
              • FeatureTypeBase.__init__()
              • FeatureTypeBase.get_dependencies()
              • FeatureTypeBase.get_type_name()
              • FeatureTypeBase.init_calculator()
              • FeatureTypeBase.compute()
              • FeatureTypeBase.get_input()
          • Feature Type Meta
            • FeatureTypeMeta
          • Reduce Service Base
            • ReduceServiceBase
              • ReduceServiceBase.__init__()
          • Selection Service Base
            • SelectionServiceBase
              • SelectionServiceBase.__init__()
      • Feature Entities
        • FeatureData
          • FeatureData.__init__()
          • FeatureData.get_data()
          • FeatureData.get_feature_metadata()
          • FeatureData.get_feature_names()
          • FeatureData.save()
          • FeatureData.load()
          • FeatureData.print_info()
      • Feature Helper
        • Bound Method
          • BoundMethod
            • BoundMethod.__init__()
        • Bound Stats
          • BoundStats
        • Feature Binding Helper
          • FeatureBindingHelper
            • FeatureBindingHelper.bind_stats_methods()
            • FeatureBindingHelper.release_bound_methods()
            • FeatureBindingHelper.repair_bound_methods()
        • Feature Computation Helper
          • FeatureComputationHelper
            • FeatureComputationHelper.check_feature_existence()
            • FeatureComputationHelper.execute_computation()
            • FeatureComputationHelper.store_computation_results()
        • Feature Cross Trajectory Reduction Helper
          • FeatureCrossTrajectoryReductionHelper
            • FeatureCrossTrajectoryReductionHelper.find_common_features()
            • FeatureCrossTrajectoryReductionHelper.apply_common_reduction()
            • FeatureCrossTrajectoryReductionHelper.get_reduction_summary()
            • FeatureCrossTrajectoryReductionHelper.print_cross_trajectory_summary()
        • Feature Reduction Helper
          • FeatureReductionHelper
            • FeatureReductionHelper.process_reduction_results()
            • FeatureReductionHelper.reset_reduction()
            • FeatureReductionHelper.check_reduction_state()
        • Feature Reset Helper
          • FeatureResetHelper
            • FeatureResetHelper.reset_all_features()
            • FeatureResetHelper.reset_specific_features()
            • FeatureResetHelper.normalize_feature_types()
            • FeatureResetHelper.check_has_features()
        • Feature Validation Helper
          • FeatureValidationHelper
            • FeatureValidationHelper.validate_threshold_parameters()
            • FeatureValidationHelper.validate_feature_exists()
            • FeatureValidationHelper.validate_dependencies()
            • FeatureValidationHelper.validate_computation_requirements()
            • FeatureValidationHelper.validate_reduction_state()
      • Feature Manager
        • 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
      • Feature Services
        • Services Helper
          • Analysis Data Helper
            • AnalysisDataHelper
              • AnalysisDataHelper.get_selected_data()
        • Feature Add Service
          • FeatureAddService
            • FeatureAddService.__init__()
            • FeatureAddService.distances()
            • FeatureAddService.contacts()
            • FeatureAddService.torsions()
            • FeatureAddService.dssp()
            • FeatureAddService.sasa()
            • FeatureAddService.coordinates()
        • Feature Analysis Service
          • FeatureAnalysisService
            • FeatureAnalysisService.__init__()
            • FeatureAnalysisService.distances
            • FeatureAnalysisService.contacts
            • FeatureAnalysisService.torsions
            • FeatureAnalysisService.dssp
            • FeatureAnalysisService.sasa
            • FeatureAnalysisService.coordinates
        • Feature Reduce Service
          • FeatureReduceService
            • FeatureReduceService.__init__()
            • FeatureReduceService.distances
            • FeatureReduceService.contacts
            • FeatureReduceService.torsions
            • FeatureReduceService.dssp
            • FeatureReduceService.sasa
            • FeatureReduceService.coordinates
        • Feature Selector Add Service
          • FeatureSelectorAddService
            • FeatureSelectorAddService.__init__()
            • FeatureSelectorAddService.distances
            • FeatureSelectorAddService.contacts
            • FeatureSelectorAddService.coordinates
            • FeatureSelectorAddService.torsions
            • FeatureSelectorAddService.dssp
            • FeatureSelectorAddService.sasa
    • Feature Importance
      • Feature Importance Analyzer Types
        • Decision Tree
          • Decision Tree Data
            • DecisionTree
              • DecisionTree.__init__()
              • DecisionTree.get_type_name()
              • DecisionTree.init_calculator()
              • DecisionTree.compute()
              • DecisionTree.get_params()
          • Decision Tree Calculator
            • DecisionTreeCalculator
              • DecisionTreeCalculator.__init__()
              • DecisionTreeCalculator.compute()
        • Interfaces
          • Analyzer Type Base
            • AnalyzerTypeBase
              • AnalyzerTypeBase.__init__()
              • AnalyzerTypeBase.compute()
              • AnalyzerTypeBase.get_type_name()
              • AnalyzerTypeBase.init_calculator()
              • AnalyzerTypeBase.get_params()
          • Analyzer Type Meta
            • AnalyzerTypeMeta
          • Calculator Base
            • CalculatorBase
              • CalculatorBase.__init__()
              • CalculatorBase.compute()
      • Feature Importance Entities
        • 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()
      • Feature Importance Helper
        • Notes
        • Analysis Runner Helper
          • AnalysisRunnerHelper
            • AnalysisRunnerHelper.store_analysis_result()
            • AnalysisRunnerHelper.run_comparison_analysis()
        • Validation Helper
          • FeatureImportanceValidationHelper
            • FeatureImportanceValidationHelper.validate_analysis_name()
            • FeatureImportanceValidationHelper.validate_analysis_exists()
            • FeatureImportanceValidationHelper.validate_comparison_exists()
        • Metadata Builder Helper
          • MetadataBuilderHelper
            • MetadataBuilderHelper.add_group_information()
            • MetadataBuilderHelper.add_model_metadata()
            • MetadataBuilderHelper.generate_sub_comparison_name()
            • MetadataBuilderHelper.extract_class_names()
        • Representative Finder Helper
          • RepresentativeFinderHelper
            • RepresentativeFinderHelper.find_best_tree_based()
        • Top Features Helper
          • TopFeaturesHelper
            • TopFeaturesHelper.get_top_features_for_comparison()
            • TopFeaturesHelper.get_top_features_averaged()
            • TopFeaturesHelper.format_features_with_names()
            • TopFeaturesHelper.get_top_features_with_names()
      • Feature Importance Manager
        • 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()
      • Feature Importance Add Service
        • FeatureImportanceAddService
          • FeatureImportanceAddService.__init__()
          • FeatureImportanceAddService.decision_tree()
    • Feature Selection
      • Feature Selection Entities
        • 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()
      • Feature Selection Helper
        • Common Denominator Helper
          • 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()
        • Feature Selector Consensus Parse Helper
          • FeatureSelectorConsensusParseHelper
            • FeatureSelectorConsensusParseHelper.parse_consensus_category()
            • FeatureSelectorConsensusParseHelper.parse_consensus_pattern()
        • Feature Selector Numeric Parse Helper
          • FeatureSelectorNumericParseHelper
            • FeatureSelectorNumericParseHelper.parse_numeric_category()
        • Feature Selector Parse Core Helper
          • FeatureSelectorParseCoreHelper
            • FeatureSelectorParseCoreHelper.parse_selection()
        • Feature Selector ResID Parse Helper
          • FeatureSelectorResidParseHelper
            • FeatureSelectorResidParseHelper.parse_resid_category()
        • Feature Selector ResName Parse Helper
          • FeatureSelectorResnameParseHelper
            • FeatureSelectorResnameParseHelper.parse_res_category()
        • Feature Selector SeqID Parse Helper
          • FeatureSelectorSeqidParseHelper
            • FeatureSelectorSeqidParseHelper.parse_seqid_category()
        • Reduction Index Mapper
          • ReductionIndexMapper
            • ReductionIndexMapper.map_reduced_to_original()
            • ReductionIndexMapper.get_kept_indices()
        • Post Selection Reduction Helper
          • PostSelectionReductionHelper
            • PostSelectionReductionHelper.apply_reduction()
      • Feature Selection Manager
        • 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()
    • Pipeline
      • Pipeline Entities
        • Pipeline Data
          • 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()
      • Pipeline Helper
        • Cache Remap Helper
          • CacheRemapHelper
            • CacheRemapHelper.remap_pipeline_memmaps()
        • Centroid Helper
          • CentroidHelper
            • CentroidHelper.find_centroid()
        • Comparison Data Helper
          • ComparisonDataHelper
            • ComparisonDataHelper.get_sub_comparison_data()
        • Selection Matrix Helper
          • SelectionMatrixHelper
            • SelectionMatrixHelper.build_selection_matrix()
        • Selection MemMap Helper
          • SelectionMemmapHelper
            • SelectionMemmapHelper.create_memmap_selection()
            • SelectionMemmapHelper.memmap_hstack()
            • SelectionMemmapHelper.create_memmap_frame_selection()
        • Selection Metadata Helper
          • SelectionMetadataHelper
            • SelectionMetadataHelper.collect_metadata_for_selection()
            • SelectionMetadataHelper.finalize_metadata_result()
      • Pipeline Manager
        • Performance Config
          • PerformanceConfig
            • PerformanceConfig.__init__()
            • PerformanceConfig.update()
        • Pipeline Manager
          • 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()
        • Auto Inject Proxy
          • AutoInjectProxy
            • AutoInjectProxy.__init__()
    • Plots
      • Plot Types
        • Decision Trees
          • Decision Tree Plotter
            • DecisionTreePlotter
              • DecisionTreePlotter.__init__()
              • DecisionTreePlotter.plot()
          • Decision Tree Helper
            • Decision Tree Visualization Config
              • 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__()
            • Decision Tree Visualizer
              • DecisionTreeVisualizer
                • DecisionTreeVisualizer.__init__()
                • DecisionTreeVisualizer.build_graph()
                • DecisionTreeVisualizer.plot_tree()
                • DecisionTreeVisualizer.visualize()
            • Edge Label Formatter
              • 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()
            • Feature Label Builder
              • FeatureLabelBuilder
                • FeatureLabelBuilder.build_feature_label()
                • FeatureLabelBuilder.build_base_label()
                • FeatureLabelBuilder.get_rule_suffix_from_metadata()
                • FeatureLabelBuilder.add_rule_suffix()
                • FeatureLabelBuilder.get_reverse_edge_semantics()
            • Node Text Formatter
              • 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()
            • Plot Configuration Helper
              • 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()
            • Separate Tree Mode Helper
              • SeparateTreeModeHelper
                • SeparateTreeModeHelper.plot_separate_trees()
            • Tree Position Calculator
              • TreePositionCalculator
                • TreePositionCalculator.calculate_optimal_spacing()
                • TreePositionCalculator.get_text_size()
                • TreePositionCalculator.compute_positions()
        • Density
          • Density Plotter
            • DensityPlotter
              • DensityPlotter.plot()
          • Density Helper
            • Density Calculation Helper
              • DensityCalculationHelper
                • DensityCalculationHelper.calculate_density()
            • Density Discrete Bar Helper
              • DensityDiscreteBarHelper
                • DensityDiscreteBarHelper.plot_grouped_probability_bars()
            • Density Data Preparer
              • DensityDataPreparer
        • Feature Importance Base
          • FeatureImportanceBasePlotter
            • FeatureImportanceBasePlotter.__init__()
        • Landscape
          • Landscape Plotter
            • LandscapePlotter
              • LandscapePlotter.__init__()
              • LandscapePlotter.plot()
          • Landscape Helper
            • Energy Calculator Helper
              • 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()
            • Landscape Rendering Helper
              • 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()
            • Landscape Styling Helper
              • LandscapeStylingHelper
                • LandscapeStylingHelper.finalize_figure()
                • LandscapeStylingHelper.add_central_legend()
                • LandscapeStylingHelper.add_tag_legend()
                • LandscapeStylingHelper.set_axis_labels()
                • LandscapeStylingHelper.set_axis_limits()
            • Landscape Tag Coloring Helper
              • LandscapeTagColoringHelper
                • LandscapeTagColoringHelper.build_frame_tag_map()
            • Layout Calculator Helper
              • LayoutCalculatorHelper
                • LayoutCalculatorHelper.calculate_grid_layout()
                • LayoutCalculatorHelper.calculate_figure_size()
                • LayoutCalculatorHelper.create_dimension_pairs()
                • LayoutCalculatorHelper.get_subplot_position()
        • Membership
          • Membership Plotter
            • MembershipPlotter
              • MembershipPlotter.__init__()
              • MembershipPlotter.plot()
          • Membership Helper
            • Block Optimizer Helper
              • BlockOptimizerHelper
                • BlockOptimizerHelper.labels_to_blocks()
        • Time Series
          • Time Series Plot Config
            • 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__()
          • Time Series Plotter
            • TimeSeriesPlotter
              • TimeSeriesPlotter.plot()
          • Time Series Helper
            • Membership Bar Renderer
              • MembershipBarRenderer
                • MembershipBarRenderer.prepare_membership_data()
                • MembershipBarRenderer.render_membership_bars_from_prepared()
            • Smoothing Helper
              • SmoothingHelper
                • SmoothingHelper.apply_smoothing()
                • SmoothingHelper.validate_smoothing_params()
            • Time Series Data Preparer
              • TimeSeriesDataPreparer
                • TimeSeriesDataPreparer.prepare()
                • TimeSeriesDataPreparer.prepare_from_manual_selection()
                • TimeSeriesDataPreparer.get_x_values()
            • Time Series Discrete Plot Helper
              • 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()
            • Time Series Feature Plot Helper
              • TimeSeriesFeaturePlotHelper
                • TimeSeriesFeaturePlotHelper.plot_all_features()
            • Time Series Grid Layout Helper
              • TimeSeriesGridLayoutHelper
                • TimeSeriesGridLayoutHelper.calculate_grid_dimensions()
                • TimeSeriesGridLayoutHelper.create_gridspec()
            • Time Series Membership Plot Helper
              • TimeSeriesMembershipPlotHelper
                • TimeSeriesMembershipPlotHelper.get_membership_indices()
                • TimeSeriesMembershipPlotHelper.plot_membership_bars()
            • Time Series Tag Coloring Helper
              • 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()
        • Violin
          • Violin Plotter
            • ViolinPlotter
              • ViolinPlotter.plot()
          • Violin Helper
            • Violin Data Preparer
              • ViolinDataPreparer
      • Plot Helper
        • Base Feature Importance Plot Data Preparer
          • BaseFeatureImportancePlotDataPreparer
            • BaseFeatureImportancePlotDataPreparer.prepare_from_feature_importance()
            • BaseFeatureImportancePlotDataPreparer.prepare_from_manual_selection()
        • Clustering Data Helper
          • ClusteringDataHelper
            • ClusteringDataHelper.load_clustering_data()
        • Color Mapping Helper
          • ColorMappingHelper
            • ColorMappingHelper.get_cluster_colors()
            • ColorMappingHelper.get_landscape_colormap()
            • ColorMappingHelper.parse_cluster_id()
            • ColorMappingHelper.create_data_selector_color_mapping()
        • Color Resolution Helper
          • ColorResolutionHelper
            • ColorResolutionHelper.resolve_label_colors()
            • ColorResolutionHelper.build_colors_from_colormap()
        • Comparison Data Extractor
          • ComparisonDataExtractor
            • ComparisonDataExtractor.get_all_data_selectors_from_comparison()
        • Contact to Distances Converter
          • ContactToDistancesConverter
            • ContactToDistancesConverter.convert_contacts_to_distances()
            • ContactToDistancesConverter.cleanup_temporary_selector()
        • Discrete Feature Helper
          • DiscreteFeatureHelper
            • DiscreteFeatureHelper.prepare_discrete_data()
            • DiscreteFeatureHelper.build_axis_config()
            • DiscreteFeatureHelper.calculate_discrete_probabilities()
        • Feature Metadata Helper
          • FeatureMetadataHelper
            • FeatureMetadataHelper.collect_metadata_for_type()
            • FeatureMetadataHelper.get_top_level_metadata()
            • FeatureMetadataHelper.get_feature_info()
            • FeatureMetadataHelper.extract_feature_info_from_entry()
        • Grid Layout Helper
          • GridLayoutHelper
            • GridLayoutHelper.compute_uniform_grid_layout()
        • SVG Export Helper
          • 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()
        • Tag Helper
          • TagHelper
            • TagHelper.get_matching_tags()
            • TagHelper.filter_by_priority()
            • TagHelper.prepare_tag_colors()
            • TagHelper.create_tag_legend_handles()
        • Title Legend Helper
          • 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()
        • Vertical Marker Helper
          • VerticalMarkerHelper
            • VerticalMarkerHelper.validate_markers()
            • VerticalMarkerHelper.validate_labels()
            • VerticalMarkerHelper.validate_label_colors()
            • VerticalMarkerHelper.normalize_positions()
            • VerticalMarkerHelper.resolve_markers()
            • VerticalMarkerHelper.build_legend_handles()
        • Validation Helper
          • 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()
      • Plot Manager
        • PlotsManager
          • PlotsManager.__init__()
          • PlotsManager.decomposition
          • PlotsManager.clustering
          • PlotsManager.feature_importance
          • PlotsManager.feature
          • PlotsManager.landscape()
          • PlotsManager.membership()
      • Plot Services
        • Clustering Facade
          • ClusteringFacade
            • ClusteringFacade.__init__()
            • ClusteringFacade.landscape()
            • ClusteringFacade.membership()
        • Decomposition Facade
          • DecompositionFacade
            • DecompositionFacade.__init__()
            • DecompositionFacade.landscape()
        • Feature Facade
          • FeatureFacade
            • FeatureFacade.__init__()
            • FeatureFacade.violins()
            • FeatureFacade.densities()
            • FeatureFacade.time_series()
        • Feature Importance Facade
          • FeatureImportanceFacade
            • FeatureImportanceFacade.__init__()
            • FeatureImportanceFacade.violins()
            • FeatureImportanceFacade.densities()
            • FeatureImportanceFacade.time_series()
            • FeatureImportanceFacade.decision_trees()
    • Structure Visualization
      • Structure Visualization Entities
        • StructureVisualizationData
          • StructureVisualizationData.__init__()
          • StructureVisualizationData.add_pdb()
          • StructureVisualizationData.get_pdb()
          • StructureVisualizationData.get_all_pdbs()
          • StructureVisualizationData.has_pdb()
          • StructureVisualizationData.add_feature_info()
          • StructureVisualizationData.get_feature_info()
      • Structure Visualization Helper
        • Color Coversion Helper
          • ColorConversionHelper
            • ColorConversionHelper.hex_to_rgb()
            • ColorConversionHelper.hex_to_pymol_rgb()
            • ColorConversionHelper.calculate_average_rgb()
            • ColorConversionHelper.mix_hex_colors()
        • Environment Helper
          • EnvironmentHelper
            • EnvironmentHelper.is_jupyter_environment()
            • EnvironmentHelper.is_pymol_available()
        • Feature Overlap Helper
          • FeatureOverlapHelper
            • FeatureOverlapHelper.build_residue_feature_map()
            • FeatureOverlapHelper.detect_residue_overlaps()
        • NGLView Helper
          • NGLViewHelper
            • NGLViewHelper.create_widget()
        • PDB Beta Factor Helper
          • PdbBetaFactorHelper
            • PdbBetaFactorHelper.create_pdb_with_beta_factors()
            • PdbBetaFactorHelper.get_topology()
        • Pymol Script Generator
          • PyMolScriptGenerator
            • PyMolScriptGenerator.generate_script()
        • Residue Importance Calculator
          • ResidueImportanceCalculator
            • ResidueImportanceCalculator.calculate_residue_importance()
            • ResidueImportanceCalculator.importance_to_beta_factors()
            • ResidueImportanceCalculator.calculate_beta_factors_from_features()
        • Validation Helper
          • ValidationHelper
            • ValidationHelper.validate_jupyter_environment()
            • ValidationHelper.validate_visualization_data()
            • ValidationHelper.validate_terminal_environment()
            • ValidationHelper.validate_pymol_available()
            • ValidationHelper.validate_data_selectors()
        • Visualization Data Helper
          • 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()
      • Structure Visualization Manager
        • StructureVisualizationManager
          • StructureVisualizationManager.__init__()
          • StructureVisualizationManager.feature_importance
          • StructureVisualizationManager.feature
      • Structure Visualization Services
        • Feature Service
          • StructureVizFeatureService
            • StructureVizFeatureService.__init__()
            • StructureVizFeatureService.create_representative_pdbs()
            • StructureVizFeatureService.visualize_nglview_jupyter()
            • StructureVizFeatureService.create_pymol_script()
            • StructureVizFeatureService.visualize_pymol()
        • Feature Importance Service
          • StructureVizFeatureImportanceService
            • StructureVizFeatureImportanceService.__init__()
            • StructureVizFeatureImportanceService.create_pdb_with_beta_factors()
            • StructureVizFeatureImportanceService.visualize_nglview_jupyter()
            • StructureVizFeatureImportanceService.create_pymol_script()
            • StructureVizFeatureImportanceService.visualize_pymol()
    • Trajectory
      • Trajectory Entities
        • Dask MD Trajectory
          • 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()
        • Trajectory Data
          • 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()
      • Trajectory Helper
        • Dask Trajectory Helper
          • Dask Trajectory Archive Helper
            • DaskMDTrajectoryArchiveHelper
              • DaskMDTrajectoryArchiveHelper.save()
              • DaskMDTrajectoryArchiveHelper.load()
          • Dask Trajectory Build Helper
            • DaskMDTrajectoryBuildHelper
              • DaskMDTrajectoryBuildHelper.__init__()
              • DaskMDTrajectoryBuildHelper.initialize_instance()
              • DaskMDTrajectoryBuildHelper.initialize_from_mdtraj()
              • DaskMDTrajectoryBuildHelper.create_from_zarr_store()
          • Dask Trajectory Join Stack Helper
            • DaskMDTrajectoryJoinStackHelper
              • DaskMDTrajectoryJoinStackHelper.__init__()
              • DaskMDTrajectoryJoinStackHelper.join_trajectories()
              • DaskMDTrajectoryJoinStackHelper.stack_trajectories()
          • Dask Trajectory Store Helper
            • DaskMDTrajectoryStoreHelper
              • DaskMDTrajectoryStoreHelper.__init__()
              • DaskMDTrajectoryStoreHelper.create_slice_store()
          • Parallel Operations Helper
            • ParallelOperationsHelper
              • ParallelOperationsHelper.__init__()
              • ParallelOperationsHelper.cleanup()
              • ParallelOperationsHelper.center_coordinates()
              • ParallelOperationsHelper.superpose()
              • ParallelOperationsHelper.smooth()
              • ParallelOperationsHelper.atom_slice()
              • ParallelOperationsHelper.image_molecules()
              • ParallelOperationsHelper.remove_solvent()
          • Zarr Cache Helper
            • 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()
        • Metadata Helper
          • Nomenclature Helper
            • Notes
            • NomenclatureHelper
              • NomenclatureHelper.__init__()
              • NomenclatureHelper.create_trajectory_label_dicts()
          • Tag Helper
            • TagHelper
              • TagHelper.resolve_trajectory_selectors()
        • Process Helper
          • Label Operation Helper
            • LabelOperationHelper
              • LabelOperationHelper.apply_atom_selection_to_labels()
              • LabelOperationHelper.combine_stack_labels()
              • LabelOperationHelper.map_residues_to_original_indices()
          • Selection Resolve Helper
            • SelectionResolveHelper
              • SelectionResolveHelper.get_indices_to_process()
              • SelectionResolveHelper.get_all_trajectories_with_tag()
          • Trajectory Load Helper
            • TrajectoryLoadHelper
              • TrajectoryLoadHelper.load_trajectories()
          • Trajectory Process Helper
            • 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()
        • Validation Helper
          • 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()
      • Trajectory Manager
        • 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()
    • Utilities
      • Archive Fetch Helper
        • ArchiveFetchHelper
          • ArchiveFetchHelper.is_url()
          • ArchiveFetchHelper.validate_load_inputs()
          • ArchiveFetchHelper.should_verify_archive()
          • ArchiveFetchHelper.resolve_archive_path()
          • ArchiveFetchHelper.resolve_expected_sha256()
          • ArchiveFetchHelper.verify_archive_sha256()
      • Archive Utils
        • 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()
      • Cleanup Utils
        • CleanupUtils
          • CleanupUtils.close_zarr_store()
          • CleanupUtils.remove_file()
          • CleanupUtils.remove_tree()
          • CleanupUtils.remove_path()
      • Color Utils
        • ColorUtils
          • ColorUtils.generate_distinct_colors()
          • ColorUtils.add_special_color()
      • Data Utils
        • DataUtils
          • DataUtils.save_object()
          • DataUtils.load_object()
          • DataUtils.get_type_key()
      • Feature Meta Data Utils
        • FeatureMetadataUtils
          • FeatureMetadataUtils.get_feature_name()
          • FeatureMetadataUtils.get_feature_type()
          • FeatureMetadataUtils.get_feature_residues()
          • FeatureMetadataUtils.create_feature_map()
          • FeatureMetadataUtils.get_top_level_metadata()
      • Utils Helper
        • Load And Save Helper
          • LoadAndSaveHelper
            • LoadAndSaveHelper.save_object()
            • LoadAndSaveHelper.load_object()
            • LoadAndSaveHelper.peek_cache_dir()
      • Memmap Utils
        • 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()
      • Output Utils
        • OutputUtils
          • OutputUtils.suppress_output()
      • Path Utils
        • PathUtils
          • PathUtils.prepare_file_path()
          • PathUtils.prepare_directory_path()
          • PathUtils.get_cache_file_path()
          • PathUtils.create_pipeline_cache_dir()
      • Progress Utils
        • ProgressUtils
          • ProgressUtils.set_enabled()
          • ProgressUtils.iterate()
      • Resource Utils
        • ResourceUtils
          • ResourceUtils.recommend_cpu_affinity()
          • ResourceUtils.apply_auto_limits()
          • ResourceUtils.apply_blas_thread_limits()
          • ResourceUtils.apply_process_limits()
          • ResourceUtils.tune_memmap()
      • Text Utils
        • TextUtils
          • TextUtils.wrap_text()
      • Top Features Utils
        • TopFeaturesUtils
          • TopFeaturesUtils.get_top_features_with_names()
  • mdxplain Orchestration
  • mdxplain Benchmarks
    • System Specifications for Linux
    • System Specifications for Windows
    • Benchmark Data Generation
    • Benchmark Workflow and Configurations
    • Benchmark Scripts delivered by mdxplain
    • Memory Measurement Method
    • Benchmark results
    • Linux Benchmark
    • Windows Benchmark
    • References
  • GitHub Repository
mdxplain
  • <no title>
  • API Documentation
  • Feature
  • Feature Types
  • View page source

Feature Types

Feature type implementations for molecular dynamics analysis.

This module provides concrete implementations of feature types for calculating distances and contacts from MD trajectories. These feature types can be used with the FeatureData container for analysis workflows.

  • Contacts
    • Contacts Services
    • Contacts Data
    • Contact Calculator
    • Contact Calculator Analysis
  • Coordinates
    • Coordinates Services
    • Coordinates Data
    • Coordinates Calculator
    • Coordinates Calculator Analysis
  • Distances
    • Distances Services
    • Distances Data
    • Distance Calculator
    • Distance Calculator Analysis
  • DSSP
    • DSSP Encoding Helper
    • DSSP Services
    • DSSP Data
    • DSSP Calculator
    • DSSP Calculator Analysis
  • SASA
    • SASA Services
    • SASA Data
    • SASA Calculator
    • SASA Calculator Analysis
  • Torsions
    • Torsions Services
    • Torsions Data
    • Torsions Calculator
    • Torsions Calculator Analysis
  • Feature Type Helper
    • Calculator Compute Helper
    • Calculator Stat Helper
    • Feature Shape Helper
  • Interfaces
    • Analysis Service Base
    • Calculator Base
    • Feature Type Base
    • Feature Type Meta
    • Reduce Service Base
    • Selection Service Base
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