Nothing
pdbfit <- function(...)
UseMethod("pdbfit")
pdbfit.pdb <- function(pdb, inds=NULL, ...) {
if(!is.pdb(pdb))
stop("Input 'pdb' should be of class 'pdb', e.g. from read.pdb()")
if(nrow(pdb$xyz)<2)
stop("nothing to fit. < 2 frames in pdb object")
if(is.null(inds)) {
inds <- atom.select(pdb, "calpha")
cat(" no indices provided. using all", length(inds$atom), "calpha atoms\n")
}
if(length(inds$xyz)<3)
stop("insufficent atoms to superimpose")
return(fit.xyz( fixed=pdb$xyz[1,], mobile=pdb$xyz,
fixed.inds=inds$xyz, mobile.inds=inds$xyz))
}
pdbfit.pdbs <- function(pdbs, inds=NULL, outpath=NULL, ...) {
##
## Quick Fit Fitter for PDBs
## was called 'fit.pdbs()' in model.R
##
if(!inherits(pdbs, "pdbs")) {
stop("Input 'pdbs' should be of class 'pdbs', e.g. from pdbaln() or read.fasta.pdb()")
}
full <- ifelse(is.null(outpath), FALSE, TRUE)
if(is.null(inds)) { inds <-gap.inspect(pdbs$xyz)$f.inds }
if(is.list(inds)){ inds=inds$xyz }
invisible( fit.xyz( fixed=pdbs$xyz[1,], mobile=pdbs, fixed.inds=inds,
mobile.inds=inds, outpath=outpath,
full.pdbs=full, ... ))
}
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