sims: Apply a List of Different Amino Acid Sequences
In BioPhysConnectoR: BioPhysConnectoR

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

For a set of sequences given in an alignment and a corresponding PDB file the covariance matrix for each sequence is computed based on the given molecular structure. The latter can be directed into a file. The Frobenius norms are computed upon request.

sims(pdb, alignment, mj1 = NULL, mj2 = NULL, mj.avg = FALSE,
     alpha = 82, cuts = 169, path = getwd(), mimethod = "ORMI",
     gapchar = "NOGAPCHAR", inv2file = FALSE, bfacs = TRUE,
     frob = TRUE, loc = NULL, norm = FALSE, cluster = NULL)

`pdb`	PDB file
`alignment`	alignment file in fasta format
`mj1`	matrix for the intrachain interaction strengths
`mj2`	matrix for the interchain interaction strengths
`mj.avg`	logical, if TRUE only the average value of each 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
`mimethod`	method for the computation of the mutual information
`gapchar`	character vector denoting gaps in the alignment
`inv2file`	logical, if TRUE, the inverse Hessian matrix is written to a file
`bfacs`	logical, if TRUE, the B factors are written to a file
`frob`	logical, if TRUE, the Frobenius norm is computed
`loc`	dimensions `i1, j1, i2, j2` for a matrix subset of which the Frobenius norm should be computed
`norm`	logical, if TRUE the Frobenius norm is computed for the normalized matrices
`cluster`	snow cluster object created with `makeCluster()`

For an alignment the sequence entropy and mutual information is computed. Furthermore for each sequence in the alignment and the structure information from the PDB file the covariance matrix and B factors can be computed and the output can be written to files. 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.

Return value is a list with the following components:

`$entropy`	sequence entropy of the alignment
`$mi`	mutual information of the alignment

If the Frobenius norm is computed, the value(s) will be returned as well:

$res

vector consisting of: row number, sequence name, Frobenius norm

Make sure your alignment contains the IUPAC standard amino acids only without any gap characters.
This function includes source code of the bio3d package.

Franziska Hoffgaard, Philipp Weil

Hamacher and McCammon (2005) Journal of Chemical Theory and Computation 2, 873.
Grant, Rodrigues, ElSawy, McCammon, Caves, (2006) Bioinformatics 22, 2695–2696.
Tierney, Rossini, Li (2009) Int J Parallel Proc 37, 78–90.

get.entropy, get.mie, sim, simc

## Not run: 
sims(system.file("1KZK.pdb",package="BioPhysConnectoR"),system.file("align.fasta",
     package="BioPhysConnectoR"))

## Cluster example
clu<-makeCluster(2)
sims(system.file("1KZK.pdb",package="BioPhysConnectoR"),system.file("align.fasta",
     package="BioPhysConnectoR",cluster = clu))
stopCluster(clu)


## End(Not run)