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_ind	Maximum number of components to consider
max_rmsd	Maximum 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:

• cluster.py