Rknots (version 1.3.0)

PCAProjection: Two-dimensional projection by Principal Component Analysis

Description

Two-dimensional projection by Principal Component Analysis

Usage

PCAProjection(points3D)

Arguments

points3D

an $N$ x 3 matrix of the $x$, $y$, $z$ coordinates of a polygonal link

Value

• points3D.rot
  an N x 3 matrix containing the x, y, z coordinates of the rotated structure. The first two columns represent the 2D projection of the structure.

References

Comoglio F. and Rinaldi M. A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins (2011) PLoS ONE 6(4): e18693, doi:10.1371/journal.pone.0018693 ArXiv:1104.3405

Examples

protein <- loadProtein('3MDZ')
par(mfrow = c(1,2))
plotDiagram(protein$A, ends = c(), lwd = 2.5, main = 'Original')

protein.rot <- PCAProjection(protein$A)
plotDiagram(protein.rot, ends = c(), lwd = 2.5, main = 'Reduced')