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IMP Reference Guide  2.11.1
The Integrative Modeling Platform
IMP.multifit.cluster.AlignmentClustering Class Reference

Clusters assembly models. More...

Detailed Description

Clusters assembly models.

  • The solutions are chosen by sorting the database according to the parameter orderby
  • The models are aligned and clustered by RMSD
Note
This class is only available in Python.

Definition at line 64 of file cluster.py.

Public Member Functions

def do_clustering
 Cluster configurations for a model based on RMSD. More...
 
def get_cc
 bb_native = self.dmap.get_bounding_box() bb_solution = IMP.core.get_bounding_box(IMP.core.XYZs(ps))

bounding box enclosing both the particles of the native assembly

and the particles of the model

bb_union = IMP.algebra.get_union(bb_native, bb_solution)

add border of 4 voxels

border = 4*voxel_size bottom = bb_union.get_corner(0) bottom += IMP.algebra.Vector3D(-border, -border, -border) top = bb_union.get_corner(1) top += IMP.algebra.Vector3D(border, border, border) bb_union = IMP.algebra.BoundingBox3D(bottom, top) 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...
 

Member Function Documentation

def IMP.multifit.cluster.AlignmentClustering.do_clustering (   self,
  max_comb_ind,
  max_rmsd 
)

Cluster configurations for a model based on RMSD.

An IMP.ConfigurationSet is built using the reference frames for all of the components of the assembly for each solution

Parameters
max_comb_indMaximum number of components to consider
max_rmsdMaximum RMSD tolerated when clustering

Definition at line 111 of file cluster.py.

def IMP.multifit.cluster.AlignmentClustering.get_cc (   self,
  ps 
)

bb_native = self.dmap.get_bounding_box() bb_solution = IMP.core.get_bounding_box(IMP.core.XYZs(ps))

bounding box enclosing both the particles of the native assembly

and the particles of the model

bb_union = IMP.algebra.get_union(bb_native, bb_solution)

add border of 4 voxels

border = 4*voxel_size bottom = bb_union.get_corner(0) bottom += IMP.algebra.Vector3D(-border, -border, -border) top = bb_union.get_corner(1) top += IMP.algebra.Vector3D(border, border, border) bb_union = IMP.algebra.BoundingBox3D(bottom, top)

Definition at line 184 of file cluster.py.

def IMP.multifit.cluster.AlignmentClustering.get_placement_score_from_coordinates (   self,
  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 160 of file cluster.py.


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