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IMP Reference Guide  develop.9f755902c2,2022/12/07
The Integrative Modeling Platform
IMP.pmi1.plotting.topology.TopologyPlot Class Reference

A class to read RMF files and make a network contact map. More...

Inherits object.

Detailed Description

A class to read RMF files and make a network contact map.

This class is only available in Python.

Definition at line 12 of file /plotting/

Public Member Functions

def __init__
 Set up a new graphXL object. More...
def add_rmf
 Add selections from an RMF file. More...
def make_plot
 plot the interaction matrix More...

Constructor & Destructor Documentation

def IMP.pmi1.plotting.topology.TopologyPlot.__init__ (   self,
  colors = None,
  fixed = None,
  pos = None,
  proteomic_edges = None,
  quantitative_proteomic_data = None 

Set up a new graphXL object.

modelThe IMP model
selection_dictA dictionary containing component names. Keys are labels values are either moleculename or start,stop,moleculename
cutoffThe distance cutoff
frequency_cutoffThe frequency cutoff
colorsA dictionary of colors (HEX code,values) for subunits (keywords)
fixedA list of subunits that are kept fixed
posA dictionary with positions (tuple, values) of subunits (keywords)
proteomic_edgesA list edges to represent proteomic data
quantitative_proteomic_dataA dictionary of edges to represent quantitative proteomic data such as PE Scores, or genetic interactions

Definition at line 26 of file /plotting/

Member Function Documentation

def IMP.pmi1.plotting.topology.TopologyPlot.add_rmf (   self,

Add selections from an RMF file.

Definition at line 55 of file /plotting/

def IMP.pmi1.plotting.topology.TopologyPlot.make_plot (   self,
  quantitative_proteomic_data = False 

plot the interaction matrix

groupsis the list of groups of domains, eg, [["protA_1-10","prot1A_11-100"],["protB"]....] it will plot a space between different groups
out_fnname of the plot file
quantitative_proteomic_dataplot the quantitative proteomic data

Definition at line 97 of file /plotting/

The documentation for this class was generated from the following file: