In this case, it would certainly serve you well to have posted a simplified version of your code - you could certainly remove 5 elements from your call list and have the same structure.

I cannot replicate your issue. Perhaps if you included a wrapping script that fed your subroutine some sample data and included information on how you were attempting to print out the values from your arrays. Your naming scheme is not great either - it took me a minute to figure out Axcoord and Axcord, etc. were different. And you probably shouldn't be using typeglobs for array passing. The following code should replicate your code's behavior. Note I've swapped to Foreach Loops to prevent syntax traps and all the code conforms to the strict/warnings pragmas. I'd also suggest replacing three independent arrays by hashes of arrays to reduce the number of variables.

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
+);
}

[download]

If this code still doesn't perform to spec, please provide some sample data.

In reply to Re: Can call array but not index of an array in subroutine?! by kennethk
in thread Can call array but not index of an array in subroutine?! by fraizerangus

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