build.contacts: Determine the Contact Map and Distance Matrices

In BioPhysConnectoR: BioPhysConnectoR

Description

Computation of a binary matrix specifying the contacts between each two amino acids i and j in respect to their spatial distance defined by their coordinates. Distance matrices for Δ x, Δ y and Δ z are computed as well as the matrix containing the squared distances for all amino acid pairs.

Usage

build.contacts(n, cuts, xyz)

Arguments

n	length of the amino acid sequence
cuts	squared cutoff
xyz	matrix with the x-, y- and z-coordinates of all C_{α} atoms of the protein

Details

If the squared distance between two C_{α} atoms of amino acids i and j is smaller than or equal to cuts, we assume a contact. In the contact map the value at indices [i,j] and [j,i] is set to 1. Otherwise, the two C_{α} atoms are not in contact, and the value is set to 0. Per definition an atom is not in contact with itself. The contact map is a symmetric matrix. The matrices in $deltas ($dx, $dy and $dz and $ds) are symmetric matrices as well. The number of contacts between distinct amino acids is stored in $cnr.

Value

Return value is a list with the following components:

$cm	contact map
$deltas	list with distance matrices for x-, y- and z-direction as well as for the squared distance between all pairs of C_{α} atoms
$cnr	number of contacts

Author(s)

Franziska Hoffgaard

See Also

get.contact.list

Examples

n<-10
xyz<-matrix(rep(1:10, 3), ncol = 3)
bc<-build.contacts(n, 3, xyz)

BioPhysConnectoR documentation built on May 30, 2017, 6:46 a.m.