• mdxplain Overview
• How to Install mdxplain
• Learn mdxplain
  • Quick Start Example
  • Performance Settings (Quick Guide)
  • Memory-Efficient Processing
  • Trajectory Management
  • Feature Computation
  • Feature Selection
  • Feature Reduction
  • Dimensionality Reduction
  • Clustering
  • Structural Analysis
  • Feature Statistics
  • Data Selection (Frame/Row Selection)
  • Comparative Analysis and Feature Importance
  • Plotting and Visualization
  • Saving and Loading
  • mdxplain Quickstart Tutorial: Introduction to Conformational Analysis with mdxplain
  • mdxplain Tutorial: Introduction to Conformational Analysis with mdxplain
  • Tutorial 3 - Reusing Sharable Archives
  • Tutorial 04: Latrophilin-1 Mutation Analysis
  • What we observed
  • Why this happens
  • How mdxplain reduces the risk
  • Summary
  • References
• How to Contribute
• How to Cite mdxplain
• License and Copyright
• Declaration of AI Tool Usage
• API Documentation
  • Project Structure
  • Analysis
    • Analysis Manager
    • Analysis Services
    • Analysis Structure
      • Analysis Structure Calculators
        • RMSD Calculator
        • RMSF Calculator
      • Analysis Structure Helper
        • Reference Structure Helper
        • Residue Aggregation Helper
        • Structure Calculation Helper
        • Trajectory Service Helper
      • Analysis Structure Services
        • RMSD Facade
        • RMSD Mad Service
        • RMSD Mean Service
        • RMSD Median Service
        • RMSF Facade
        • RMSF Mad Variant Facade
        • RMSF Mean Variant Facade
        • RMSF Median Variant Facade
        • RMSF Per Atom Service
        • RMSF Per Residue Aggregation Selection Facade
        • RMSF Per Residue Base Aggregation Facade
        • RMSF Per Residue Mean Aggregation Facade
        • RMSF Per Residue Median AggregationFacade
        • RMSF Per Residue RMS Aggregation Facade
        • RMSF Per Residue Median Aggregation Facade
        • RMSF Per Residue Service
        • Structure Analysis Service
  • Clustering
    • Cluster Types
      • DBSCAN
        • DBSCAN Module
        • DBSCAN Calculator
      • DPA
        • DPA Module
        • DBA Calculator
      • HDBSCAN
        • HDBSCAN Module
        • HDBSCAN Calculator
      • Interfaces
        • Calculator Base
        • Cluster Type Base
        • Cluster Type Meta
    • Clustering Entities
    • Clustering Helper
    • Clustering Manager
    • Cluster Type Services
      • Cluster Add Service
      • DBSCAN Add Service
      • DPA Add Service
      • HDBSCAN Add Service
  • Comparison
    • Comparison Entities
    • Comparison Helper
      • Validation Helper
      • Sub Comparison Creation Helper
    • Comparison Manager
  • Data Selector
    • Data Selection Entities
      • Data Selector Data
      • Data Selector Group
    • Data Selector Helper
      • Criteria Builder Helper
      • Frame Selection Helper
      • Group Creation Helper
    • Data Selector Manager
  • Decomposition
    • Decomposition Types
      • Contact Kernel PCA
        • Contact Kernel PCA Data
        • Contact Kernel PCA Calculator
      • Diffusion Maps
        • Diffusion Maps Data
        • Diffusion Maps Calculator
      • Kernel PCA
        • Kernel PCA Data
        • Kernel PCA Calculator
      • PCA
        • PCA Data
        • PCA Calculator
      • Interfaces
        • Calculator Base
        • Decomposition Types Base
        • Decomposition Types Meta
      • Decomposition Type Helper
    • Decomposition Entities
    • Decomposition Manager
    • Decomposition Services
  • Feature
    • Feature Types
      • Contacts
        • Contacts Services
          • Contacts Selection Service
          • Contacts Reduce Service
          • Contacts Analysis Service
        • Contacts Data
        • Contact Calculator
        • Contact Calculator Analysis
      • Coordinates
        • Coordinates Services
          • Coordinates Selection Service
          • Coordinates Reduce Service
          • Coordinates Analysis Service
        • Coordinates Data
        • Coordinates Calculator
        • Coordinates Calculator Analysis
      • Distances
        • Distances Services
          • Distances Selection Service
          • Distances Reduce Service
          • Distances Analysis Service
        • Distances Data
        • Distance Calculator
        • Distance Calculator Analysis
      • DSSP
        • DSSP Encoding Helper
        • DSSP Services
          • DSSP Selection Service
          • DSSP Reduce Service
          • DSSP Analysis Service
        • DSSP Data
        • DSSP Calculator
        • DSSP Calculator Analysis
      • SASA
        • SASA Services
          • SASA Selection Service
          • SASA Reduce Service
          • SASA Analysis Service
        • SASA Data
        • SASA Calculator
        • SASA Calculator Analysis
      • Torsions
        • Torsions Services
          • Torsions Selection Service
          • Torsions Reduce Service
          • Torsions Analysis Service
        • 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
    • Feature Entities
    • Feature Helper
      • Bound Method
      • Bound Stats
      • Feature Binding Helper
      • Feature Computation Helper
      • Feature Cross Trajectory Reduction Helper
      • Feature Reduction Helper
      • Feature Reset Helper
      • Feature Validation Helper
    • Feature Manager
    • Feature Services
      • Services Helper
      • Feature Add Service
      • Feature Analysis Service
      • Feature Reduce Service
      • Feature Selector Add Service
  • Feature Importance
    • Feature Importance Analyzer Types
      • Decision Tree
        • Decision Tree Data
        • Decision Tree Calculator
      • Interfaces
        • Analyzer Type Base
        • Analyzer Type Meta
        • Calculator Base
    • Feature Importance Entities
    • Feature Importance Helper
      • Analysis Runner Helper
      • Validation Helper
      • Metadata Builder Helper
      • Representative Finder Helper
      • Top Features Helper
    • Feature Importance Manager
    • Feature Importance Add Service
  • Feature Selection
    • Feature Selection Entities
    • Feature Selection Helper
      • Common Denominator Helper
      • Feature Selector Consensus Parse Helper
      • Feature Selector Numeric Parse Helper
      • Feature Selector Parse Core Helper
      • Feature Selector ResID Parse Helper
      • Feature Selector ResName Parse Helper
      • Feature Selector SeqID Parse Helper
      • Reduction Index Mapper
      • Post Selection Reduction Helper
    • Feature Selection Manager
  • Pipeline
    • Pipeline Entities
    • Pipeline Helper
      • Cache Remap Helper
      • Centroid Helper
      • Comparison Data Helper
      • Selection Matrix Helper
      • Selection MemMap Helper
      • Selection Metadata Helper
    • Pipeline Manager
      • Performance Config
      • Pipeline Manager
      • Auto Inject Proxy
  • Plots
    • Plot Types
      • Decision Trees
        • Decision Tree Plotter
        • Decision Tree Helper
          • Decision Tree Visualization Config
          • Decision Tree Visualizer
          • Edge Label Formatter
          • Feature Label Builder
          • Node Text Formatter
          • Plot Configuration Helper
          • Separate Tree Mode Helper
          • Tree Position Calculator
      • Density
        • Density Plotter
        • Density Helper
          • Density Calculation Helper
          • Density Discrete Bar Helper
          • Density Data Preparer
      • Feature Importance Base
      • Landscape
        • Landscape Plotter
        • Landscape Helper
          • Energy Calculator Helper
          • Landscape Rendering Helper
          • Landscape Styling Helper
          • Landscape Tag Coloring Helper
          • Layout Calculator Helper
      • Membership
        • Membership Plotter
        • Membership Helper
      • Time Series
        • Time Series Plot Config
        • Time Series Plotter
        • Time Series Helper
          • Membership Bar Renderer
          • Smoothing Helper
          • Time Series Data Preparer
          • Time Series Discrete Plot Helper
          • Time Series Feature Plot Helper
          • Time Series Grid Layout Helper
          • Time Series Membership Plot Helper
          • Time Series Tag Coloring Helper
      • Violin
        • Violin Plotter
        • Violin Helper
    • Plot Helper
      • Base Feature Importance Plot Data Preparer
      • Clustering Data Helper
      • Color Mapping Helper
      • Color Resolution Helper
      • Comparison Data Extractor
      • Contact to Distances Converter
      • Discrete Feature Helper
      • Feature Metadata Helper
      • Grid Layout Helper
      • SVG Export Helper
      • Tag Helper
      • Title Legend Helper
      • Vertical Marker Helper
      • Validation Helper
    • Plot Manager
    • Plot Services
      • Clustering Facade
      • Decomposition Facade
      • Feature Facade
      • Feature Importance Facade
  • Structure Visualization
    • Structure Visualization Entities
    • Structure Visualization Helper
      • Color Coversion Helper
      • Environment Helper
      • Feature Overlap Helper
      • NGLView Helper
      • PDB Beta Factor Helper
      • Pymol Script Generator
      • Residue Importance Calculator
      • Validation Helper
      • Visualization Data Helper
    • Structure Visualization Manager
    • Structure Visualization Services
      • Feature Service
      • Feature Importance Service
  • Trajectory
    • Trajectory Entities
      • Dask MD Trajectory
      • Trajectory Data
    • Trajectory Helper
      • Dask Trajectory Helper
        • Dask Trajectory Archive Helper
        • Dask Trajectory Build Helper
        • Dask Trajectory Join Stack Helper
        • Dask Trajectory Store Helper
        • Parallel Operations Helper
        • Zarr Cache Helper
      • Metadata Helper
        • Nomenclature Helper
        • Tag Helper
      • Process Helper
        • Label Operation Helper
        • Selection Resolve Helper
        • Trajectory Load Helper
        • Trajectory Process Helper
      • Validation Helper
    • Trajectory Manager
  • Utilities
    • Archive Fetch Helper
    • Archive Utils
    • Cleanup Utils
    • Color Utils
    • Data Utils
    • Feature Meta Data Utils
    • Utils Helper
    • Memmap Utils
    • Output Utils
    • Path Utils
    • Progress Utils
    • Resource Utils
    • Text Utils
    • Top Features Utils
• mdxplain Orchestration
• mdxplain Benchmarks
• GitHub Repository