IMP
2.4.0
The Integrative Modeling Platform
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Utility functions for comparisons. More...
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... | |
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.
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
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 |
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.
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.
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.