#!/usr/bin/perl

use strict;
use warnings;

# the script creates links to all models adding the extension pdb

my $INDIR = "/local/CASP13/MODELS";

my $OUTDIR = "/local/CASP13/MODELS_PDB";

if (! -d $OUTDIR){
   system("mkdir -p $OUTDIR && chgrp users $OUTDIR && chmod 775 $OUTDIR");
}

# read targets
my @targets;
opendir D, $INDIR;
while(defined(my $d = readdir(D))){
    if ($d =~ m/^T\.*/){
	if (! -d "$INDIR/$d") {next;}
	push @targets, $d;
    }
}
closedir D;

@targets = sort(@targets);

foreach my $t (@targets){
     if (! -e "$OUTDIR/$t"){
	system("mkdir -p $OUTDIR/$t && chgrp users $OUTDIR/$t && chmod 775 $OUTDIR/$t");
     }
     opendir D, "$INDIR/$t";
	my @models = ();
	while(defined(my $m = readdir(D))){
		if ($m !~ m/^T/ ){next;}
		my $src = "$INDIR/$t/$m";
		my $dest = "$OUTDIR/$t/$m.pdb";
		if (!-e $dest){
			my $command = "ln -s $src $dest ";
			system("$command");
		}
	}
     closedir D;
}