#!/usr/bin/perl -w

# Create a CASP TS file from a PDB file in stdin.
# usage:
#	pdb2casp T0132 -author xxxx-xx-xxxx -model 1 -method foo.method < decoys/T0132.try999-opt.pdb

sub process_command_line();
sub absolute($);

process_command_line();

print "PFRMAT TS\n";
print "TARGET $target\n";
print "AUTHOR $author \n";

if (defined $method)
{    open METHOD, "<$method";
    while (<METHOD>)
    {    print "METHOD $_";
    }
    close METHOD;
}

print "MODEL $model_num\n";
print "PARENT N/A\n";

while ($line=<STDIN>)
{   next if $line !~ /^ATOM/;
    # change the chainID to " "
    print substr($line,0,21). ' '. substr($line,22);
}

print "TER\n";
print "END";


sub process_command_line()
{
    # Set default values
    $model_num=1;
    undef $method;
    $author = "Some SAM method---should be passed as -a";
    undef $target;

    # Get user specified values
    local ($i)=0;
    while ($i <= $#ARGV) 
    {
        $_ = $ARGV[$i++];
	if (/^-a/)	{$author  =  $ARGV[$i++]; }
	elsif (/^-model/) {$model_num  =  $ARGV[$i++]; }
	elsif (/^-method/) {$method  =  absolute($ARGV[$i++]); }
	elsif (! defined($target)) {$target = $_;}
	else 	{ die "Argument $_ not understood\n";
		}
    }

    defined($target) || die "You must provide a target name.";
    
    print STDERR "target=$target model_num=$model_num author=$author";
    print STDERR " method=$method" if defined($method);
    print STDERR "\n";
    
    return;
}

sub absolute($)
{    my ($file) = @_;
    return $file if ($file =~ /^\/.*/);
    my $wd = `pwd`;
    chop($wd);
    if ($wd=~/\/auto(.*)/) {return "$1/$file"};
    if ($wd=~/\/export(.*)/) {return "$1/$file"};
    return "$wd/$file";

}