cmap.Rd
Construct a Contact Map for Given Protein Structure(s).
cmap(...) # S3 method for default cmap(...) # S3 method for xyz 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, ...) # S3 method for pdb cmap(pdb, inds = NULL, verbose = FALSE, ...) # S3 method for pdbs cmap(pdbs, rm.gaps=FALSE, all.atom=FALSE, ...)
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. 
pdbs  a ‘pdbs’ object as returned by 
rm.gaps  logical, if TRUE gapped positions are removed in the returned value. 
all.atom  logical, if TRUE allatom coordinates from 
...  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.
Grant, B.J. et al. (2006) Bioinformatics 22, 26952696.
Barry Grant
## 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)if (FALSE) { ## 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") }