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;
}