Store all-atom data from a PDB object

Description

Not intended for public usage

Usage

store.atom(pdb)

Arguments

Details

This function was requested by a user and has not been extensively tested. Hence it is not yet recommended for public usage.

Value

Returns a matrix of all-atom data

Note

This function is still in development and is NOT part of the offical bio3d package

Author(s)

Barry Grant

References

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

See Also

read.fasta.pdb

Examples

## Not run: 
sel <- c("N", "CA", "C", "O", "CB", "*G", "*D",  "*E", "*Z")
pdbs <- read.all(aln, pdb.path = pdb.path, pdbext = ".ent", sel=sel)
core <- core.find(pdbs, rm.island=TRUE)

##-- Core indices
atm <- rep( rep(sel,each=3), ncol(aln$ali))
ca.ind  <- which(atm == "CA")
core.ind <- c( matrix(ca.ind, nrow=3)[,core$c0.5A.atom] )

##-- Core Fit
xyz <- fit.xyz(fixed=tmp[1,],
             mobile = tmp,
             fixed.inds  = core.ind,
             mobile.inds = core.ind)

##-- Examine all-atom data
colnames(tmp) = atm

gap.ind <- unique(which(is.na(tmp),arr.ind=T)[,2])
nogap.ind    <- c(1:ncol(tmp))[-gap.ind]
#ca.nogap.ind <- intersect(ca.ind, nogap.ind)

##-- PCA 
xray.pca <- pca.xyz( xyz[,nogap.ind] )

plot(xray.pca)
## End(Not run)