Projections

Simulation trajectories have very large dimensionality not only in terms of number of frames but also for the intrinsic dimensionality of each frame made by all three-dimensional coordinates. It is therefore necessary to reduce this space by projecting these coordinates into a simpler space. HTMD provides many projection types, e.g. MetricCoordinate to only keep the coordinate of few atoms, or MetricDistance to keep the matrix distance between two sets of atoms.

Contents:

• 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