I am not sure what any of this called, I got it from a lab friend. I am trying to make Keys and Values for each X, Y, and Z Coordinates for specific particles but am having problems printing what I need or calling upon the assigned coordinates.

This is my exact script:

#!/usr/bin/perl 

use strict;
use warnings;
use diagnostics;

#my $inputFile = $ARGV[0];
my $inputFile = '8ns_emb_alt_101.pdb';

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

my @array = <INPUTFILE>;

#check
#print "@array \n";
######

#### CoM of MET ####
my $met_Sulfur = 'SD';
my $met_CarbonB = 'CB';
my $met_CarbonG = 'CG';
my $met_CarbonE = 'CE';
my $met_number = '34';

my $COM_MET_Coords;

for (my $line = 0; $line <= $#array; ++$line){
   if (($array[$line] =~ m/\s+$met_Sulfur\s+/)&&($array[$line] =~ m/\s+$met_number\s+/)){
#      print "$array[$line]";
      my @splitLine = (split /\s+/, $array[$line]);
      my %coordinates = (x => $splitLine[6],
                         y => $splitLine[7],
                         z => $splitLine[8],
                         );
     push @{$COM_MET_Coords->[0]}, \%coordinates;
   }
}
foreach my $line (@{$COM_MET_Coords->[0]}){
   print "$line->{'x'}\n";

I have also tried to print by using:

print $COM_MET_Coords->[0]->[0]->{'x'};

My main problem is that I don't totally understand how and where the information I want is being stored and I am not sure what this is called. I am using perl v5.10.1. If anyone can tell me how to print X Y and Z as well as why that would be Perfect!

This is a Sample of the data:

ATOM    527  N   MET   34      -9.849  -0.893  17.835  0.00  0.00      PROT
ATOM    528  HN  MET   34      -9.231  -0.252  17.386  0.00  0.00      PROT
ATOM    529  CA  MET   34     -10.593  -1.664  16.897  0.00  0.00      PROT
ATOM    530  HA  MET   34     -11.657  -1.526  17.023  0.00  0.00      PROT
ATOM    531  CB  MET   34     -10.159  -1.300  15.525  0.00  0.00      PROT
ATOM    532  HB1 MET   34     -10.188  -2.148  14.808  0.00  0.00      PROT
ATOM    533  HB2 MET   34      -9.082  -1.050  15.637  0.00  0.00      PROT
ATOM    534  CG  MET   34     -10.806   0.010  15.045  0.00  0.00      PROT
ATOM    535  HG1 MET   34     -10.226   0.384  14.174  0.00  0.00      PROT
ATOM    536  HG2 MET   34     -10.755   0.660  15.945  0.00  0.00      PROT
ATOM    537  SD  MET   34     -12.551  -0.153  14.748  0.00  0.00      PROT
ATOM    538  CE  MET   34     -12.486  -0.712  13.101  0.00  0.00      PROT

This is what I think you want to do.

The code you have shown just builds a hash of 3D coordinates from the input file, and then prints the x coordinates from each entry. This is how I would write something to do just that.

Since you don't define $COM_MET_Coords I have used a simple array variable @coords. I also use while to read the file line by line as it is wasteful to read it into an array in its entirety and then just process the array line by line.

The output isn't very interesting as there is only one line in your data that contains both SD and 34.

By the way, please don't use capital letters in local identifiers. Numbers, lower-case letters and underscore _ are fine, but capitals are reserved for global names like packages.

#!/usr/bin/perl

use strict;
use warnings;
use autodie;

my ($input_file) = @ARGV;
$input_file = '8ns_emb_alt_101.pdb';

#### CoM of MET ####
my $met_sulfer   = 'SD';
my $met_carbon_b = 'CB';
my $met_carbon_g = 'CG';
my $met_carbon_e = 'CE';
my $met_number   = '34';

open my $fh, '<', $input_file;

my @coords;

while (<$fh>) {

  next unless /\s$met_sulfer\s/ and /\s$met_number\s/;

  my %coordinates;
  @coordinates{qw/ x y z /} = (split)[5, 6, 7];
  push @coords, \%coordinates;
}

for my $item (@coords) {
  print $item->{x}, "\n";
}

output

-12.551

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