cmap {bio3d}R Documentation

Contact Map

Description

Construct a Contact Map for a Given Protein Structure.

Usage

cmap(xyz, grpby=NULL, dcut = 4, scut = 3, mask.lower = TRUE)

Arguments

xyz numeric vector of xyz coordinates.
grpby a vector counting connective duplicated elements that indicate the elements of xyz that should be considered as a group (e.g. atoms from a particular residue).
dcut a cuttoff distance value below which atoms are considered in contact.
scut a cuttoff neighbour value which has the effect of excluding atoms that are sequentially within this value.
mask.lower logical, if TRUE the lower matrix elements (i.e. those below the diagonal) are returned as NA.

Details

A contact map is a simplified distance matrix. See the distance matrix function dm for further details.

Value

Returns a N by N numeric matrix composed of zeros and ones, where one indicates a contact between selected atoms.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

dm, dccm, dist, dist.xyz

Examples


##- Read PDB and Traj files
pdb <- read.pdb( system.file("examples/hivp.pdb", package="bio3d") )
##trj <- read.dcd( system.file("examples/hivp.dcd", package="bio3d") )

## Atom Selection indices
inds <- atom.select(pdb, "calpha")

## Reference contact map
ref.cont <- cmap( pdb$xyz[inds$xyz], dcut=6, scut=3 )
plot.dmat(ref.cont)

## Not run: 
## For each frame of trajectory
sum.cont <- NULL
for(i in 1:nrow(trj)) {

  ## Contact map for frame 'i'
  cont <- cmap(trj[i,inds$xyz], dcut=6, scut=3)

  ## Product with reference
  prod.cont <- ref.cont * cont
  sum.cont <- c(sum.cont, sum(prod.cont,na.rm=TRUE))
}

plot(sum.cont, typ="l")
## End(Not run)

[Package bio3d version 1.0-6 Index]