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IMP Reference Guide  develop.9f755902c2,2022/12/07
The Integrative Modeling Platform
IMP.pmi.analysis.RMSD Class Reference

Compute the RMSD (without alignment) taking into account the copy ambiguity. More...

Inherits object.

Detailed Description

Compute the RMSD (without alignment) taking into account the copy ambiguity.

To be used with pmi2 hierarchies. Can be used for instance as follows:

rmsd = IMP.pmi.analysis.RMSD( hier, hier, [mol.get_name() for mol in mols], dynamic0=True, dynamic1=False) output_objects.append(rmsd)

before shuffling the coordinates

Note
This class is only available in Python.

Definition at line 462 of file pmi/Analysis.py.

Public Member Functions

def __init__
 
def get_moldict_coorddict
 return data structure for the RMSD calculation More...
 
def get_output
 Returns output for IMP.pmi.output.Output object. More...
 

Constructor & Destructor Documentation

def IMP.pmi.analysis.RMSD.__init__ (   self,
  hier0,
  hier1,
  molnames,
  label = 'None',
  dynamic0 = True,
  dynamic1 = True,
  metric = IMP.algebra.get_rmsd 
)
Parameters
hier0first input hierarchy
hier1second input hierarchy
molnamethe names of the molecules used for the RMSD if True stores the decorators XYZ and coordinates of hier0 can be update. If false coordinates are static (stored in Vector3Ds) and will never be updated same as above metric what metric should be used

Definition at line 475 of file pmi/Analysis.py.

Member Function Documentation

def IMP.pmi.analysis.RMSD.get_moldict_coorddict (   self,
  hier,
  molnames 
)

return data structure for the RMSD calculation

Definition at line 496 of file pmi/Analysis.py.

def IMP.pmi.analysis.RMSD.get_output (   self)

Returns output for IMP.pmi.output.Output object.

Definition at line 580 of file pmi/Analysis.py.


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