build.hess: Construct the Hessian Matrix
In BioPhysConnectoR: BioPhysConnectoR

Description Usage Arguments Details Value Author(s) References See Also

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

1	build.hess(cm, im, deltas)

`cm`	contact map
`im`	interaction map
`deltas`	list of difference matrices computed with `build.contacts`

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.

Return value is the Hessian Matrix.

Franziska Hoffgaard

Hamacher (2006) Journal of Chemical Theory and Computation 2, 873–878.

build.interact, build.contacts

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