openpathsampling.analysis.PathDensityHistogram

class openpathsampling.analysis.PathDensityHistogram(cvs, left_bin_edges, bin_widths, interpolate=True)[source]

Histogram for path density plot.

Parameters
  • cvs (list of paths.CollectiveVariable) – the collective variables to define the reduced space

  • left_bin_edges (array-like) – lesser side of the bin (for each direction)

  • bin_widths (array-like) – bin (voxel) size

  • interpolate (bool or string) – whether to interpolate missing bin visits. String value determines interpolation type (currently only “subdivide” allowed). Default True gives “subdivide” method, False gives no interpolation.

__init__(cvs, left_bin_edges, bin_widths, interpolate=True)[source]

Methods

__init__(cvs, left_bin_edges, bin_widths[, ...])

add_data_to_histogram(trajectories[, weights])

Adds data to the internal histogram counter.

add_trajectory(trajectory[, weight])

Add a single trajectory to internal counter, with given weight

compare_parameters(other)

Test whether the other histogram has the same parameters.

empty_copy()

Returns a new histogram with the same bin shape, but empty

histogram([data, weights])

Build the histogram.

map_to_bins(data)

param data

input data

map_to_float_bins(trajectory)

Map trajectory to the bin value, without rounding bin number.

normalized([raw_probability, bin_edge])

Callable normalized version of the sparse histogram.

single_trajectory_counter(trajectory)

Calculate the counter (local histogram) for an unweighted trajectory

sum_histograms(hists)

xvals(bin_edge_type)

Position values for the bin

Attributes

progress