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:

• Molecule
  • Molecule
  • Representations
  • TopologyInconsistencyError
  • UniqueAtomID
  • UniqueResidueID
  • calculateUniqueBonds()
  • getBondedGroups()
  • mol_equal()
• Building
  • System preparation
  • Solvating
  • CHARMM builder
  • AMBER builder
• MD Simulations
  • MD Engines
  • Queues
  • Adaptive sampling
  • State-of-the-art protocols for molecular simulations
• Simulation List
  • Frame
  • Sim
  • simfilter()
  • simlist()
  • simmerge()
• 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
  • Model
  • getStateStatistic()
  • macroAccumulate()
• Kinetics
  • Kinetics
  • Rates