cmap. bio3d 2.3-0

Usage

cmap(...)
"cmap"(...)
"cmap"(xyz, grpby = NULL, dcut = 4, scut = 3, pcut=1, binary=TRUE, mask.lower = TRUE, collapse=TRUE, gc.first=FALSE, ncore=1, nseg.scale=1, ...)
"cmap"(pdb, inds = NULL, verbose = FALSE, ...)

Arguments

xyz: numeric vector of xyz coordinates or a numeric matrix of coordinates with a row per structure/frame.
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 cutoff distance value below which atoms are considered in contact.
scut: a cutoff neighbour value which has the effect of excluding atoms that are sequentially within this value.
pcut: a cutoff probability of structures/frames showing a contact, above which atoms are considered in contact with respect to the ensemble. Ignored if binary=FALSE.
binary: logical, if FALSE the raw matrix containing fraction of frames that two residues are in contact is returned.
mask.lower: logical, if TRUE the lower matrix elements (i.e. those below the diagonal) are returned as NA.
collapse: logical, if FALSE an array of contact maps for all frames is returned.
gc.first: logical, if TRUE will call gc() first before calculation of distance matrix. This is to solve the memory overload problem when ncore > 1 and xyz has many rows, with a bit sacrifice on speed.
ncore: number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
nseg.scale: split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.
pdb: a structure object of class "pdb", obtained from read.pdb.
inds: a list object of ATOM and XYZ indices as obtained from atom.select.
verbose: logical, if TRUE details of the selection are printed.
...: arguments passed to and from functions.

Description

Construct a Contact Map for Given Protein Structure(s).

Details

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

Function "cmap.pdb" is a wrapper for "cmap.xyz" which selects all ‘notwater’ atoms and calculates the contact matrix grouped by residue number.

Value

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

References

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

Examples


##- Read PDB file
pdb <- read.pdb( system.file("examples/hivp.pdb", 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.cmap(ref.cont)

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


 NATOM = 198 
 NFRAME= 117 
 ISTART= 0 
 last  = 117 
 nstep = 117 
 nfile = 117 
 NSAVE = 1 
 NDEGF = 0 
 version 24 
Reading (x100)
  |======================================================================| 100%

## 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")

Author

Barry Grant

Contact Map