store.atom {bio3d} | R Documentation |
Not intended for public usage
store.atom(pdb)
pdb |
A pdb object as obtained from read.pdb |
This function was requested by a user and has not been extensively tested. Hence it is not yet recommended for public usage.
Returns a matrix of all-atom data
This function is still in development and is NOT part of the offical bio3d package
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## 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)