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Site Navigation

  • Installation
  • HTMD
  • Moleculekit
  • ACEMD
  • PlayMolecule Installation
  • PM-API
  • JobQueues
  • Help
  • Internal Docs
  • Acellera

Section Navigation

  • Installation
  • Tutorials
    • Introduction to HTMD
      • Python primer
      • Getting started with HTMD
      • HTMD Molecules
      • Visualization in HTMD
    • Building with HTMD
      • Protein preparation
      • Advanced building
      • System building protein-ligand
      • System building protein in Membrane
    • Simulations in HTMD
      • Molecular Dynamics in HTMD
      • Wrapping Simulations
      • Adaptive Sampling Explained
      • Adaptive Sampling Tutorial
      • Adaptive Bandit Tutorial
    • Analysis in HTMD
      • Getting Started with Projections
      • Ligand binding analysis
      • Protein folding analysis
      • CXCL12 conformational analysis
    • Advanced uses
      • System building Protein-Protein
      • Using docking to initialize positions
      • Equilibration protocol for the mu opioid GPCR
    • Tools
      • Maximal Substructural Alignment
      • Sequence Based Alignment
      • FFEvaluate
      • Membrane Builder
    • Changelog
  • Documentation
    • Molecule
    • Building
      • System preparation
      • Solvating
      • CHARMM builder
      • AMBER builder
    • MD Simulations
      • MD Engines
        • htmd.mdengine.acemd package
      • Queues
        • jobqueues.celeryfiles package
        • jobqueues.celeryqueue module
        • jobqueues.config module
        • jobqueues.home module
        • jobqueues.localqueue module
        • jobqueues.lsfqueue module
        • jobqueues.pbsqueue module
        • jobqueues.playqueue module
        • jobqueues.sgequeue module
        • jobqueues.simqueue module
        • jobqueues.slurmqueue module
        • jobqueues.util module
      • Adaptive sampling
        • Adaptive sampling
      • State-of-the-art protocols for molecular simulations
        • htmd.protocols.equilibration_v3 module
        • htmd.protocols.production_v6 module
    • Simulation List
    • Projections
      • MetricData - Storage for projected data
      • Metric - Helper class for combining Metrics for projection
      • MetricCoordinate - coordinates of an atom selection
      • MetricDistance - (Self-)distance-based metrics between atoms selections
      • MetricDihedral - Dihedral-based metrics
      • MetricRmsd - RMSD-based metric
      • MetricShell - occupancy of an atom selection (e.g. water) around another selection
      • MetricSecondaryStructure - secondary structure-based metric
      • MetricPlumed2 - access all Plumed2 metrics (CVs)
      • MetricSasa - Solvent accessible surface area
      • MetricTMscore - TMscore-based metric
      • MetricFluctuation - RMSF-based metric
    • Dimensionality Reduction
      • TICA - Time independent component analysis
      • KMeansTri - kmeans triangle inequality
      • GWPCA Principal Component Analysis
    • Clustering
      • KCenters clustering method
      • RegCluster regular sized clustering
    • Markov state models
    • Kinetics
  • API
    • htmd.adaptive package
      • htmd.adaptive.adaptive module
      • htmd.adaptive.adaptivebandit module
      • htmd.adaptive.adaptivegoal module
      • htmd.adaptive.adaptivegoaleg module
      • htmd.adaptive.adaptiverun module
      • htmd.adaptive.util module
    • htmd.builder package
      • htmd.builder.amber module
      • htmd.builder.builder module
      • htmd.builder.charmm module
      • htmd.builder.ionize module
      • htmd.builder.loopmodeler module
      • htmd.builder.noncanonical module
      • htmd.builder.solvate module
    • htmd.clustering package
      • htmd.clustering.kcenters module
      • htmd.clustering.regular module
    • htmd.mdengine package
      • htmd.mdengine.acemd package
        • htmd.mdengine.acemd.acemd module
    • htmd.membranebuilder package
      • htmd.membranebuilder.build_membrane module
      • htmd.membranebuilder.globalminimization module
      • htmd.membranebuilder.ljfluid module
      • htmd.membranebuilder.pdbreporter module
      • htmd.membranebuilder.ringpenetration module
      • htmd.membranebuilder.simulate_openmm module
    • htmd.molecule package
      • htmd.molecule.molecule module
      • htmd.molecule.util module
    • htmd.projections package
      • htmd.projections.gwpca module
      • htmd.projections.kmeanstri module
      • htmd.projections.metric module
      • htmd.projections.metriccoordinate module
      • htmd.projections.metricdihedral module
      • htmd.projections.metricdistance module
      • htmd.projections.metricfluctuation module
      • htmd.projections.metricplumed2 module
      • htmd.projections.metricrmsd module
      • htmd.projections.metricsasa module
      • htmd.projections.metricsecondarystructure module
      • htmd.projections.metricshell module
      • htmd.projections.metricsphericalcoordinate module
      • htmd.projections.metrictmscore module
      • htmd.projections.tica module
    • htmd.protocols package
      • htmd.protocols.equilibration_v3 module
      • htmd.protocols.production_v6 module
    • htmd.queues package
      • htmd.queues.localqueue module
      • htmd.queues.lsfqueue module
      • htmd.queues.pbsqueue module
      • htmd.queues.playqueue module
      • htmd.queues.simqueue module
      • htmd.queues.slurmqueue module
    • htmd.config module
    • htmd.decorators module
    • htmd.dock module
    • htmd.home module
    • htmd.kinetics module
    • htmd.latest module
    • htmd.license module
    • htmd.metricdata module
    • htmd.metricdatagenerator module
    • htmd.model module
    • htmd.mutualinformation module
    • htmd.parallelprogress module
    • htmd.pathplanning module
    • htmd.session module
    • htmd.simlist module
    • htmd.ui module
    • htmd.units module
    • htmd.util module
    • htmd.version module
    • htmd.versionwarnings module

Dimensionality Reduction#

On top of projection methods it is also highly recommended to use dimensionality reduction methods to further reduce the space. HTMD provides, for instance, time independent component analysis (TICA) and Kmeans with triangle inequality. These can be used on MetricData objects. TICA is recommended for Markov Model construction.

Contents:

  • TICA - Time independent component analysis
  • KMeansTri - kmeans triangle inequality
  • GWPCA Principal Component Analysis

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moleculekit.projections.metricfluctuation module

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htmd.projections.tica module

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