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  • HTMD
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      • Introduction to HTMD
        • Python primer
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      • Building with HTMD
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      • Changelog
        • 1.12.0 (stable) - 2018/03/22
        • 1.10.0 (stable) - 2017/10/25
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        • 1.6.0 (stable) - 2017/03/01
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        • 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
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      • Subpackages
        • htmd.adaptive package
        • htmd.builder package
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        • htmd.molecule package
        • htmd.projections package
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  • Moleculekit
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    • The Molecule class
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      • Contents
        • Protein segmentation: Automatically detects and assigns segments in proteins
        • Protein preparation: Protonates proteins and optimizes hbond networks
        • Sequence-based structure alignment: Aligns two protein structures by their sequence alignment
        • Voxel Descriptors: Calculates 3D voxels channels containing features of a Molecule or SmallMol
        • Maximal substructure alignment: Aligns two small molecules by their maximal substructure
    • Projections
      • Contents
        • MetricCoordinate: xyz coordinate projection
        • MetricDihedral: dihedral angles projection
        • MetricDistance: atom distances/contacts projection
        • MetricFluctuation: atom position fluctuations
        • MetricPlumed2: support for Plumed2 projections
        • MetricRmsd: root mean square deviation of structures to a reference
        • MetricSasa: solvent accessible surface area projection
        • MetricSecondaryStructure: protein secondary structure projection
        • MetricShell: density of atoms in shells around other atoms
        • MetricSphericalCoordinate: spherical coordinates of two COMs
        • MetricTMscore: TMscore projection
    • Tutorials
      • Contents
        • Voxelization
  • ACEMD
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    • Release notes
      • 3.5.0 (2021-09-27)
      • 3.4.1 (2021-04-21)
      • 3.4.0 (2021-03-30)
      • 3.3.0 (2020-06-23)
      • 3.2.4 (2020-04-23)
      • 3.2.3 (2019-11-12)
      • 3.2.2 (2019-10-08)
      • 3.2.1 (2019-09-20)
      • 3.2.0 (2019-08-27)
      • 3.1.2 (2019-06-04)
      • 3.1.1 (2019-05-08)
      • 3.1.0 (2019-04-18)
      • 3.0.4 (2019-02-27)
      • 3.0.3 (2019-02-25)
      • 3.0.2 (2018-03-28)
      • 3.0.1 (2017-12-18)
      • 3.0.0 (2017-12-12)
    • Installation
      • Requiments
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  • PlayMolecule-API
    • Installation
      • Miniconda installation
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      • Install playmolecule python api package
    • Tutorials
      • Contents
        • PlayMolecule API Tutorial
        • Interacting with the PlayMolecule server
        • App pipeline example on Adaptive Sampling
    • The Session class
    • The Job class
    • The DataCenter class
    • Dev Only: PlayMolecule Dev Tools
 
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  • htmd.projections package

htmd.projections package¶

Submodules¶

  • 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

Module contents¶

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