sub notClose{
    my $self=shift;
    my ($a1,$a2,$m)=@_;
    my %hash = %$a2;
    my $cutoff = $lengths{$a1->resName} + 7 + $hash{'r'};
    my $dist = PDB::Bond->dist($a1->x,$hash{'x'},$a1->y,$hash{'y'},$a1->z,$hash{'z'});
    my $value = $dist<$cutoff ? 0 : 1;
    return $value;
}

sub dist{my $self=shift if UNIVERSAL::isa($_[0] => __PACKAGE__);
    my ($x1, $x2, $y1, $y2, $z1, $z2)=@_;

    return numberFormat(sqrt ( ($x1 - $x2)**2 +
			       ($y1 - $y2)**2 +
			       ($z1 - $z2)**2 ),
			1,2);
}

sub numberFormat{
    my( $number, $whole, $frac ) = @_;
    return pad_left('0',$whole,'0').'.'.pad_right('0',$frac,'0')if $number == 0;
    return pad_left($number,$whole,'0') unless $number =~ /\./ || $frac; 
    my ($left,$right);
    ($left,$right) = split /\./, $number;
    $left = pad_left($left, $whole, '0');
    if(defined $right){
	$right = pad_right( substr($right,0,$frac), $frac, '0' );
	return "$left\.$right";
    }else{
	$right = pad_right( '0', $frac, '0');
	return "$left\.$right";
    }
}

sub pad_left {
    my $self=shift if UNIVERSAL::isa($_[0] => __PACKAGE__);
    my ($item, $size, $padding) = @_;	
    my $newItem = $item;
    $padding = ' ' unless defined $padding;
    
    while( length $newItem < $size ) {
	$newItem = "$padding$newItem";
    }
    return $newItem;
}
		

sub pad_right {
    my $self=shift if UNIVERSAL::isa($_[0] => __PACKAGE__);
    my ($item, $size, $padding) = @_;
    my $newItem = $item;
    
    $padding = ' ' unless defined $padding;
    
    while( length $newItem < $size ) {
	$newItem .= $padding;
    }
    return $newItem;
}