sim: Compute the Covariance Matrices and B Factors for a List of...
In BioPhysConnectoR: BioPhysConnectoR

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

For a given list of PDB-files the respective covariance matrices and resulting B factors are computed.

1 2	sim(pdbs, mj1 = NULL, mj2 = NULL, mj.avg = FALSE, alpha = 82, cuts = 169, path = getwd(), cluster = NULL)

`pdbs`	list of PDB file names
`mj1`	matrix for the intrachain interaction strengths
`mj2`	matrix for the interchain interaction strengths
`mj.avg`	logical, if TRUE only the average value of the interaction matrix is used as value for the interaction of any two amino acids
`alpha`	strength of the peptide bond
`cuts`	squared distance cutoff
`path`	path to the output files
`cluster`	snow cluster object created with `makeCluster()`

Each PDB file is extracted. All features necessary for the computation of the covariance matrix in the elastic network model are computed. Both the covariance matrix and the B factors are computed and written to a file. The computation is parallelized using parLapply() from the package snow. If cluster is left at its default value the computation is carried out in serial.

No values are returned. The B factors and inverse Hessian matrices are written into files.

Franziska Hoffgaard, Philipp Weil

Hamacher and McCammon (2005) Journal of Chemical Theory and Computation 2, 873.
Tierney, Rossini, Li (2009) Int J Parallel Proc 37, 78–90.

sims, simc

## Not run: 
#build a list of pdb-files
pdbs<-list(system.file("1KZK.pdb", package = "BioPhysConnectoR"),
           system.file("1EBY.pdb", package = "BioPhysConnectoR"))
sim(pdbs, cuts = 169)

## Cluster example
 clu<-makeCluster(2)
 sim(pdbs, cuts = 169, cluster = clu)
 stopCluster(clu)

## End(Not run)