#!/bin/sh
#
eval "exec perl -x $0 $*"
#
#!perl -w
#
# script to convert a nucleic acid coordinate file from the PDB
# to a format closer to CNS
#
# written by: Paul Adams 25-06-99
#
# copyright Yale University
#
# =========================================================================
#

while ( <> ) {
    if    ( /^(ATOM  |HETATM)/ ) {
	substr($_,17,3) = resconv(substr($_,17,3));
	s/(\D\d)\*/$1\'/;
	s/C5M T/C5A T/;
    }
    elsif ( /^END   / ) {
        $_ = "END\n";
    }
    print;
}

sub resconv {
    local ($resname) = @_;
    local (%map);

    my $rn = $resname;
    $rn =~ s/^ +//;
    $rn =~ s/ +$//;

    %map = ( "A" => ADE, 
	     "C" => CYT, 
	     "G" => GUA,
	     "T" => THY,
	     "U" => URI );

    if ( $map{$rn} ) {
	$resname = $map{$rn};
    }

    return $resname;
}

__END__