Description Usage Arguments Details Value Author(s) See Also Examples
The function calculates B factors from the inverse Hessian matrix.
1 | get.bfacs(covmat)
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covmat |
inverse Hesse matrix |
The B factors for each C_{α} atom are computed from the diagonal of the covariance matrix by summing up the corresponding entries.
Return value is a vector with the B factors for each C_{α}.
Franziska Hoffgaard
1 2 3 4 5 6 7 8 9 10 11 12 13 | #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)
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