Skip to main content
Ctrl+K

HTMD

  • Installation
  • Tutorials
  • Documentation
  • API
  • Acellera
  • Twitter
  • GitHub
  • LinkedIn
  • Youtube
  • Medium
  • Installation
  • Tutorials
  • Documentation
  • API
  • Acellera
  • Twitter
  • GitHub
  • LinkedIn
  • Youtube
  • Medium

Section Navigation

  • Building
    • Solvating
    • CHARMM builder
    • AMBER builder
  • MD Simulations
    • Adaptive sampling
      • Adaptive sampling
  • Simulation List
  • Projections
    • MetricData - Storage for projected data
    • Metric - Helper class for combining Metrics for projection
  • 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
  • Documentation
  • Clustering

Clustering#

Clustering is done using the scikit-learn clustering library. Other clustering classes can be used as long as they adhere to the same interface (Methods: fit; Attributes: cluster_centers_, labels_).

For example, MiniBatchKMeans can be directly passed to the cluster command of MetricData:

metricdata.cluster(MiniBatchKMeans(n_clusters=1000), mergesmall=3)

Contents:

  • KCenters clustering method
  • RegCluster regular sized clustering

previous

htmd.projections.gwpca module

next

htmd.clustering.kcenters module

Show Source

© Copyright 2026, Acellera.