making arrays from data in files and subtracting them

Question

I am trying to find the distance between objects in 3D from a Protein Data Base file (PDB). A PDB file looks like this.

Example:

ATOM      1  N   GLU    1     -19.992  -2.816  36.359  0.00  0.00      PROT
ATOM      2  HT1 GLU    1     -19.781  -1.880  35.958  0.00  0.00      PROT
ATOM      3  HT2 GLU    1     -19.713  -2.740  37.358  0.00  0.00      PROT
ATOM      4  HT3 GLU    1     -21.027  -2.910  36.393  0.00  0.00      PROT
ATOM      5  CA  GLU    1     -19.344  -3.944  35.652  0.00  0.00      PROT
ATOM      6  HA  GLU    1     -19.817  -4.852  35.998  0.00  0.00      PROT
ATOM      7  CB  GLU    1     -19.501  -3.795  34.119  0.00  0.00      PROT

I am trying to take the first row of 5 digit numbers the x coordinates and make them into an array. The Final column that says PROT changes to MEM1 later in the PDB file. I am trying to subtract all the MEM1 x coordinates from the Prot x coordinates by putting them into two arrays.

I currently have:

#!/usr/bin/perl

use warnings;

my $inputfile = '8ns_emb_alt_101.pdb';

open( INPUTFILE, "<", $inputfile ) or die $!;

my @array = <INPUTFILE>;

$protein = 'PROT';

for ( $line = 0; $line <= $#array; ++$line ) {
    if ( $array[$line] =~ m/\s+$protein\s+/ ) {
        chomp $array[$line];
        @splitline = ( split /\s+/, $array[$line] );
        @protx = $splitline[5];
    }    #if 1
}    # for 1

print "@protx \n";
print "$splitline[5] \n";

The only thing that @protx and $splitline[5] prints is the last x coordinate of the PROT section of the PDB. I need all of them printed. My overall objective is to find the distance between each atom of the protein PROT against each atom of the membrane MEM by using d = sqrt((deltaX)^2+(deltay)^2+(deltaz)^2). Then when d < 5 it will print the resID, which is 1 in this case and corresponds with GLU.

Make sure you always have `use strict;` at the top of your script to eliminate errors (you will need to declare your variables with `my`). Unless you need to know the line number, it is much easier to iterate through arrays using `for (@array)`; `$_` will be set as the current array element. — i alarmed alien, Oct 06 '14 at 14:57
You will also need to think about storing the unique identifier from each line -- is that col 3, N / HT1 / HT2 / HT3, etc? — i alarmed alien, Oct 06 '14 at 15:01

score 0 · Accepted Answer · answered Oct 06 '14 at 14:50

0

Instead of assigning a value to the array (which in fact assigns it to its first element, overwriting the previously assigned value)

@protx = $splitline[5];

push the value into it:

push @protx, $splitline[5];

answered Oct 06 '14 at 14:50

choroba

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making arrays from data in files and subtracting them

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