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.
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()
Details
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.
Value
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:
Make sure your alignment contains the IUPAC standard amino acids only without any gap characters.
This function includes source code of the bio3d package.
Author(s)
Franziska Hoffgaard, Philipp Weil
References
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.
See Also
get.entropy, get.mie, sim, simc
Examples
## 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)