openpathsampling.analysis.PathDensityHistogram

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

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)

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)
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