Documentation

You can find here documentation for most of the modules that HTMD provides. One can either explore the tree of contents or, if looking for a particular module/class/function, use the search box on the sidebar.

Contents:

• Building
  • Solvating
  • CHARMM builder
  • AMBER builder
• MD Simulations
  • Adaptive sampling
• Simulation List
  • Frame
  • Sim
  • simfilter()
  • simlist()
  • simmerge()
• 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
  • Model
  • getStateStatistic()
  • macroAccumulate()
• Kinetics
  • Kinetics
  • Rates