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IMP Reference Guide  develop.cb469e0f11,2024/05/28
The Integrative Modeling Platform
IMP.pmi1.analysis.GetModelDensity Class Reference

Compute mean density maps from structures. More...

Inherits object.

Detailed Description

Compute mean density maps from structures.

Keeps a dictionary of density maps, keys are in the custom ranges. When you call add_subunits_density, it adds particle coordinates to the existing density maps.

This class is only available in Python.

Definition at line 1095 of file pmi1/

Public Member Functions

def __init__
 Constructor. More...
def add_subunits_density
 Add a frame to the densities. More...
def get_density
 Get the current density for some component name. More...

Constructor & Destructor Documentation

def IMP.pmi1.analysis.GetModelDensity.__init__ (   self,
  representation = None,
  resolution = 20.0,
  voxel = 5.0 


custom_rangesRequired. It's a dictionary, keys are the density component names, values are selection tuples e.g. {'kin28':[['kin28',1,-1]], 'density_name_1' :[('ccl1')], 'density_name_2' :[(1,142,'tfb3d1'), (143,700,'tfb3d2')],
representationPMI representation, for doing selections. Not needed if you only pass hierarchies
resolutionThe MRC resolution of the output map (in Angstrom unit)
voxelThe voxel size for the output map (lower is slower)

Definition at line 1107 of file pmi1/

Member Function Documentation

def IMP.pmi1.analysis.GetModelDensity.add_subunits_density (   self,
  hierarchy = None 

Add a frame to the densities.

hierarchyOptionally read the hierarchy from somewhere. If not passed, will just read the representation.

Definition at line 1124 of file pmi1/

def IMP.pmi1.analysis.GetModelDensity.get_density (   self,

Get the current density for some component name.

Definition at line 1204 of file pmi1/

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