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

assembly.	An atom.Molecule object
native_assembly	An atom.Molecule object
align	If True, assembly is aligned to native_assembly before calculating the placement score

Definition at line 29 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

Definition at line 130 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

assembly	An atom.Molecule object
native_assembly	An atom.Molecule object with the native conformation Obviously the atoms in assembly and native assembly must be the same

Returns

The function returns 2 lists. The first list contains the placement distances of the children. The second list contains the placnement angles

Definition at line 44 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

assembly	The DRMS is computed for this assembly
native_assembly	The 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.

Definition at line 182 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.

Definition at line 98 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_coords	A list with the coordinates for each component
native_components_coords	A list with the coordinates for each component in the native assembly

Definition at line 78 of file comparisons.py.