build.hess: Construct the Hessian Matrix

Description

The Hessian matrix is computed using the interaction matrix, the contact map, and the coordinate differences.

Usage

build.hess(cm, im, deltas)

Arguments

contact map

interaction map

deltas

list of difference matrices computed with build.contacts

Value

Return value is the Hessian Matrix.

Details

For a sequence of length $n$ a $3n \times 3n$ matrix is computed. Only if amino acids are in contact (cm entry equals $1$) values for the Hessian matrix are computed as proposed in Hamacher (2006). If amino acids are not in contact their respective matrix entries equal $0$. Values for amino acids in contact depend on coordinate differences and interaction strengths.

References