get.bfacs: Determine B factors

Description

The function calculates B factors from the inverse Hessian matrix.

Usage

get.bfacs(covmat)

Arguments

covmat

inverse Hesse matrix

Value

Return value is a vector with the B factors for each $C_{\alpha}$.

Details

The B factors for each $C_{\alpha}$ atom are computed from the diagonal of the covariance matrix by summing up the corresponding entries.

Examples

Run this code

#extract the example pdb
pdb<-extractPDB(system.file("1KZK.pdb", package = "BioPhysConnectoR"))

#build the contact matrix for a given squared cutoff of 169
bc<-build.contacts(pdb$lca, 169, pdb$coords)

#for this example we use the fictitious value 12 as interaction strength
interaction.mat<-build.interact(cseq = rep(0, 198), mj1 = matrix(12, 20, 20),
d = pdb$chains)

#compute the inverse hessian matrix
cov.mat<-get.cov(cm = bc$cm, im = interaction.mat, deltas = bc$deltas)
bfac<-get.bfacs(cov.mat)