#!/usr/bin/env tclsh
# copies all atoms from input PDB (second argument) to the end of the output PDB (first argument)

set output_pdb   [lindex $argv 0]
set input_pdb    [lindex $argv 1]
set temp_pdb     temp.pdb

set input  [open $input_pdb r]
set input0 [open $output_pdb r]
set output [open $temp_pdb w]
set indata  [split [read $input]  "\n"]
set indata0 [split [read $input0] "\n"]

foreach line  $indata0 {
    if { (![regexp {END*} $line junk]) && (![regexp {^$} $line junk]) } {
	    puts $output $line
    } 
}
foreach line  $indata {
    if { [regexp {HETATM.*} $line junk] || [regexp {ATOM.*} $line junk] } {
	scan $line "%6s%5d%*c%4s%*c%*c%*c%*c%2s%*c%*c%*c%*c%*c%*c%*c%*c%*c%*c%8f%8f%8f%6f%6f" label number atom residue x y z occ b 
	if { $atom != "" } {
	    puts $output $line
	}
    } 
}

close $output
close $input
close $input0

file copy -force $temp_pdb $output_pdb
file delete -force $temp_pdb