Nothing
"var.xyz" <- function(xyz, weights=TRUE) {
## Calculate pairwise distances
natoms <- ncol(xyz) / 3
all <- array(0, dim=c(natoms,natoms,nrow(xyz)))
for( i in 1:nrow(xyz) ) {
dists <- dist.xyz(xyz[i,])
all[,,i] <- dists
}
## Calculate variance of pairwise distances
all.vars <- apply(all, 1:2, var)
if(weights) {
## Make the final weights
wts <- 1 - (all.vars / max(all.vars, na.rm=TRUE))
wts[is.na(wts)] <- 1
return(wts)
}
else {
return(all.vars)
}
}
"var.pdbs" <- function(pdbs, ...) {
xyz <- pdbs$xyz
return(var.xyz(xyz, ...))
}
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