#!/usr/bin/env tclsh
# copies the whole content of input PDB (first argument) except of specified atom types (third argument) to output PDB (second argument)

set input_pdb   [lindex $argv 0]
set output_pdb  [lindex $argv 1]
set input_atom  [lindex $argv 2]

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

foreach line  $indata {
    if { [regexp {HETATM.*} $line junk] || [regexp {ATOM.*} $line junk] } {
	scan $line "%6s%5d%*c%4s%*c%4s%*c%*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 != $input_atom || ( $residue != $input_atom && $residue != "IOD" && $residue != "SO4" ) } {
	    puts $output $line
	}
    } 
    if { [regexp {CRYST.*} $line junk] || [regexp {SCALE.*} $line junk] } {
    	    puts $output $line
    }
}

close $input
close $output