use strict;
use warnings;

sub coordinatesorter {
    my ($Ax_ref, $Ay_ref, $Az_ref, $Bx_ref, $By_ref, $Bz_ref,
        $res_to_atom, $natres, $nseg, $beginning, $ending       ) = @_;

    my $interdomaincounter = 1;
    my $counter = 0;
    my (@Axcord, @Aycord, @Azcord, @Bxcord, @Bycord, @Bzcord);

    foreach my $iseg (1 .. $nseg) {
        foreach my $ires ($beginning->[$iseg] .. $ending->[$iseg]) {
            foreach my $iat (1 .. $natres->[$ires]) {
                $Axcord[$counter] = $Ax_ref->[ $res_to_atom->[$ires][$iat] ];
                $Aycord[$counter] = $Ay_ref->[ $res_to_atom->[$ires][$iat] ];
                $Azcord[$counter] = $Az_ref->[ $res_to_atom->[$ires][$iat] ];
                $Bxcord[$counter] = $Bx_ref->[ $res_to_atom->[$ires][$iat] ];
                $Bycord[$counter] = $By_ref->[ $res_to_atom->[$ires][$iat] ];
                $Bzcord[$counter] = $Bz_ref->[ $res_to_atom->[$ires][$iat] ];

                $counter++;
            }
        }
    }
    
    return (\@Axcord, \@Aycord, \@Azcord, \@Bxcord, \@Bycord, \@Bzcord);
}