ATOM      1  N   GLY A   1      43.202  54.570  86.432  1.00 44.15           N
ATOM      2  CA  GLY A   1      44.109  54.807  85.249  1.00 45.94           C
ATOM      3  C   GLY A   1      44.984  56.034  85.443  1.00 43.20           C
ATOM      4  O   GLY A   1      45.070  56.527  86.578  1.00 46.54           O
ATOM      5  N   SER A   2      45.617  56.538  84.378  1.00 38.14           N
ATOM      6  CA  SER A   2      46.461  57.710  84.544  1.00 33.00           C
ATOM      7  C   SER A   2      46.057  59.017  83.842  1.00 29.38           C
ATOM      8  O   SER A   2      46.522  60.071  84.270  1.00 32.21           O
ATOM      9  CB  SER A   2      47.972  57.377  84.387  1.00 29.10           C
ATOM     10  OG  SER A   2      48.326  56.931  83.084  1.00 25.44           O
ATOM     11  N   HIS A   3      45.172  59.000  82.838  1.00 24.08           N
ATOM     12  CA  HIS A   3      44.778  60.271  82.173  1.00 20.59           C
ATOM     13  C   HIS A   3      43.299  60.425  81.787  1.00 18.87           C
ATOM     14  O   HIS A   3      42.664  59.463  81.375  1.00 16.14           O
ATOM     15  CB  HIS A   3      45.597  60.514  80.897  1.00 17.13           C
ATOM     16  CG  HIS A   3      47.060  60.648  81.145  1.00 20.02           C
ATOM     17  ND1 HIS A   3      47.596  61.677  81.887  1.00 20.09           N
ATOM     18  CD2 HIS A   3      48.099  59.855  80.797  1.00 21.10           C
ATOM     19  CE1 HIS A   3      48.904  61.516  81.989  1.00 19.86           C
ATOM     20  NE2 HIS A   3      49.233  60.417  81.333  1.00 18.86           N

##</code><code>##

 open (FILE, "< ".$file ) or die "\ncouldn't open FILE: ".$file.": $! ";
    my $i=0;
    while(<FILE>){
	if($_ =~ /^ATOM/){
	    $temp = new PDB::Atom('-line' => $_, '-number'=>$i);
	    addToMemory($self, $temp, $i);

	    ########bond detection ################# 
            ###iterate through chains###
		foreach my $ch (sort {$a <=> $b} keys %{$self->{'contacts'}){
            next if $temp->chain eq $ch; #skip same chains

            ###iterate through residues###
		foreach my $r (sort {$a <=> $b} keys %{$self->{'contacts'}{$ch}}){
		    next if notClose($temp,self->{'contacts'}{$ch}{$r});
			foreach my $a (sort {$a <=> $b} keys %{$self->{'residues'}{$ch.$r}}){
			    			    $bonds->newBond($temp,$self->{'all'}{$a});
			}
		    }
		}
	    }
    }
    close(FILE);

sub addToMemory{
    my ($self, $atom, $numb) = @_;

    $self->{'all'}{$numb}=$atom;
    unless($atom->proton){
	$self->{'atoms'}{$numb} = 1;
    }else{
	$self->{'protons'}{$numb} = 1;
    }
    
	$self->{'contacts'}{$atom->chain}{$atom->resNumber}=residualAverage($atom, $self->{'contacts'}{$atom->chain}{$atom->resNumber});
	$self->{'residues'}{$ch.$atom->resNumber}{$numb}=1;
}