BioPhysConnectoR (version 1.6-5)

sim: Compute the Covariance Matrices and B Factors for a List of PDBs

Description

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

Usage

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

Arguments

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()

Value

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

Details

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.

References

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

See Also

sims, simc

Examples

#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)