Description Usage Arguments Details Value Author(s) References See Also Examples
Construct a Contact Map for Given Protein Structure(s).
1 2 3 4 5 6 7 8 9 10 11 
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 
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 
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 
number of CPU cores used to do the calculation.

nseg.scale 
split input data into specified number of segments
prior to running multiple core calculation. See 
pdb 
a structure object of class 
inds 
a list object of ATOM and XYZ indices as obtained from

verbose 
logical, if TRUE details of the selection are printed. 
... 
arguments passed to and from functions. 
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.
Returns a N by N numeric matrix composed of zeros and ones, where one indicates a contact between selected atoms.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28  ## 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)
## Not run:
## Read Traj file
trj < read.dcd( system.file("examples/hivp.dcd", package="bio3d") )
## 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)

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.