centroidClosure: Structure closure with the centroid method

In Rknots: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

Description

For being treated as a mathematical knot, the protein backbone needs to be closed. This function implements the centroid method (also called CENTER), where the protein endpoints (C-terminus and N-terminus) are extended outside the sphere containing the protein backbone in the direction of the centroid of the structure.

Usage

centroidClosure(points3D, w = 2)

Arguments

points3D	an N x 3 matrix of the x, y, z coordinates of a polygonal link
w	given the radius r of the sphere that contains the structure, the endpoints will be extended by w r.

Value

an (N+2) x 3 matrix of the x, y, z coordinates of a polygonal link. The first and the last rows contain the coordinates of the extended endpoints.

Note

This is a low-level function.

Author(s)

Federico Comoglio, [e-mail]

References

Lua RC, Grosberg AY (2006) Statistics of Knots, Geometry of Conformations, and Evolution of Proteins. PLoS Comput Biol 2(5): e45. doi:10.1371/journal.pcbi.0020045

Examples

## Not run: 
## Import a PDB file from the web
protein <- makeExampleProtein()
closed <- centroidClosure(protein$A)
	
##Plot the result
plotKnot3D(closed, ends = c(), text = TRUE, showNC = TRUE, 
    radius = 0.01, lwd = 5)

## End(Not run)

Rknots documentation built on May 1, 2019, 10:19 p.m.