Nothing
"pdb2aln.ind" <-
function(aln, pdb, inds = NULL, ...) {
# get the new alignment; also check arguments internally
naln <- pdb2aln(aln=aln, pdb=pdb, ...)
if(is.null(inds))
inds <- gap.inspect(aln$ali)$f.inds
ninds <- which(naln$ref["ali.pos",] %in% inds)
ca.inds <- naln$ref["ca.inds", ninds]
if(any(is.na(ca.inds))) {
warning("Gaps are found in equivalent positions in PDB")
}
inds.a = inds[!is.na(ca.inds)]
inds.b = ca.inds[!is.na(ca.inds)]
a = list(atom=inds.a, xyz=atom2xyz(inds.a))
class(a) = "select"
b = list(atom=inds.b, xyz=atom2xyz(inds.b))
class(b) = "select"
out = list(a = a, b = b)
return(out)
}
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