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IMP Reference Guide  2.20.2
The Integrative Modeling Platform
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
namethe name of the plot
values_liststhe list of list of values eg: [[...],[...],[...]]
valuenamethe y-label
binsthe number of bins
colorsIf None, will use rainbow. Else will use specific list
formatoutput format
reference_xlineplot a reference line parallel to the y-axis
yplotrangethe range for the y-axis
normalizedwhether the histogram is normalized or not
leg_namesnames for the legend
Note
This function is only available in Python.

Definition at line 1758 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 1722 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 1823 of file output.py.