IMP.pmi.output Namespace Reference

Classes for writing output files and processing them. More...

Detailed Description

Classes for writing output files and processing them.

Classes
class	Cluster
	A container for models organized into clusters. More...
class	DataEntry
	A class to store data associated to a model. More...
class	Output
	Class for easy writing of PDBs, RMFs, and stat files. More...
class	OutputStatistics
	Collect statistics from ProcessOutput.get_fields(). More...
class	ProcessOutput
	A class for reading stat files (either rmf or ascii v1 and v2) More...
class	ProtocolOutput
	Base class for capturing a modeling protocol. More...
class	RMFHierarchyHandler
	class to allow more advanced handling of RMF files. More...
class	StatHierarchyHandler
	class to link stat files to several rmf files More...

Functions
def	plot_field_histogram
	Plot a list of histograms from a value list. More...
def	plot_fields
	Plot the given fields and save a figure as output. More...
def	plot_fields_box_plots
	Plot time series as boxplots. More...

Function Documentation

def IMP.pmi.output.plot_field_histogram	(		name,
			values_lists,
			valuename = None,
			bins = 40,
			colors = None,
			format = 'png',
			reference_xline = None,
			yplotrange = None,
			xplotrange = None,
			normalized = True,
			leg_names = None
	)

Plot a list of histograms from a value list.

Parameters

name	the name of the plot
values_lists	the list of list of values eg: [[...],[...],[...]]
valuename	the y-label
bins	the number of bins
colors	If None, will use rainbow. Else will use specific list
format	output format
reference_xline	plot a reference line parallel to the y-axis
yplotrange	the range for the y-axis
normalized	whether the histogram is normalized or not
leg_names	names for the legend

Note

This function is only available in Python.

Definition at line 1754 of file output.py.

def IMP.pmi.output.plot_fields	(		fields,
			output,
			framemin = None,
			framemax = None
	)

Plot the given fields and save a figure as output.

The fields generally are extracted from a stat file using ProcessOutput.get_fields().

Note

This function is only available in Python.

Definition at line 1718 of file output.py.

def IMP.pmi.output.plot_fields_box_plots	(		name,
			values,
			positions,
			frequencies = None,
			valuename = 'None',
			positionname = 'None',
			xlabels = None,
			scale_plot_length = 1.0
	)

Plot time series as boxplots.

fields is a list of time series, positions are the x-values valuename is the y-label, positionname is the x-label

Note

This function is only available in Python.

Definition at line 1819 of file output.py.