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IMP Reference Guide  develop.d3e3923077,2019/12/11
The Integrative Modeling Platform
IMP.EMageFit.imp_general.comparisons Namespace Reference

Utility functions for comparisons. More...

Detailed Description

Utility functions for comparisons.

Functions

def get_assembly_placement_score
 Computes the placement score of an assembly respect to the native_assembly. More...
 
def get_ccc
 Threshold - threshold used for the map of the native assembly. More...
 
def get_components_placement_scores
 Compute the placement score of each of the children of an assembly. More...
 
def get_drms_for_backbone
 Measure the DRMS ob the backbone between two assemblies. More...
 
def get_placement_score_from_coordinates
 Computes the position error (placement distance) and the orientation error (placement angle) of the coordinates in model_coords respect to the coordinates in native_coords. More...
 
def get_placement_scores_from_coordinates
 Computes the placement score for each of the components. More...
 

Function Documentation

def IMP.EMageFit.imp_general.comparisons.get_assembly_placement_score (   assembly,
  native_assembly,
  align = False 
)

Computes the placement score of an assembly respect to the native_assembly.

Parameters
assemblyAn IMP.atom.Molecule object
native_assemblyAn IMP.atom.Molecule object
alignIf True, assembly is aligned to native_assembly before calculating the placement score
Note
This function is only available in Python.

Definition at line 28 of file comparisons.py.

def IMP.EMageFit.imp_general.comparisons.get_ccc (   native_assembly,
  assembly,
  resolution,
  voxel_size,
  threshold,
  write_maps = False 
)

Threshold - threshold used for the map of the native assembly.

Pixels with values above this threshold in the native map are used for the calculation of the cross_correlation_coefficient

Note
This function is only available in Python.

Definition at line 131 of file comparisons.py.

def IMP.EMageFit.imp_general.comparisons.get_components_placement_scores (   assembly,
  native_assembly,
  align = False 
)

Compute the placement score of each of the children of an assembly.

The function does not do any time of alignment of the coordinates

Parameters
assemblyAn IMP.atom.Molecule object
native_assemblyAn IMP.atom.Molecule object with the native conformation Obviously the atoms in assembly and native assembly must be the same
alignIf True, assembly is aligned to native_assembly before calculating the placement score
Returns
The function returns 2 lists. The first list contains the placement distances of the children. The second list contains the placement angles
Note
This function is only available in Python.

Definition at line 43 of file comparisons.py.

def IMP.EMageFit.imp_general.comparisons.get_drms_for_backbone (   assembly,
  native_assembly 
)

Measure the DRMS ob the backbone between two assemblies.

Parameters
assemblyThe DRMS is computed for this assembly
native_assemblyThe assembly that acts as a reference

Notes: 1) The components of the assembly can be proteins or nucleic acids 2) If a protein, the c-alphas are used for calculating the drms 3) If a nucleic acid, the backbone of C4' atoms is used 4) The chains are treated as rigid bodies to speed the calculation.

WARNING: if the function fails with a segmentation fault, one of the possible problems is that IMP reads some HETATM as calphas. Check that the chain does not have heteroatoms.

Note
This function is only available in Python.

Definition at line 183 of file comparisons.py.

def IMP.EMageFit.imp_general.comparisons.get_placement_score_from_coordinates (   model_coords,
  native_coords 
)

Computes the position error (placement distance) and the orientation error (placement angle) of the coordinates in model_coords respect to the coordinates in native_coords.

placement distance - translation between the centroids of the coordinates placement angle - Angle in the axis-angle formulation of the rotation aligning the two rigid bodies.

Note
This function is only available in Python.

Definition at line 99 of file comparisons.py.

def IMP.EMageFit.imp_general.comparisons.get_placement_scores_from_coordinates (   model_components_coords,
  native_components_coords 
)

Computes the placement score for each of the components.

Parameters
model_components_coordsA list with the coordinates for each component
native_components_coordsA list with the coordinates for each component in the native assembly
Note
This function is only available in Python.

Definition at line 79 of file comparisons.py.