__UPDATE____

dear all

I've started a 'profile' on one of my biggest files (15 chains!) and here's the most telling results:

%Time    Sec.     #calls   sec/call  F  name
17.79 1043.2695  10727535   0.000097     PDB::Bonds::notClose
14.88  872.6432  14509596   0.000060     PDB::Writer::numberFormat
10.52  616.7291  14509596   0.000043     PDB::Bond::dist
 6.89  403.8085  14509597   0.000028     PDB::Writer::pad_left
 6.40  375.5808        1  375.580791  ?  HighPDB::parse
 6.39  374.5854  14509596   0.000026     PDB::Writer::pad_right
 5.54  325.1066  43586508   0.000007     UNIVERSAL::isa
 4.89  286.5572  1881489   0.000152     PDB::Bond::new
 3.49  204.5796  18291657   0.000011     PDB::Atom::x
 3.42  200.8238  18291657   0.000011     PDB::Atom::y
 3.23  189.6586  18291657   0.000010     PDB::Atom::z
 3.14  184.3266  1881489   0.000098     PDB::Bond::isHydphb
 3.14  184.2096  1880381   0.000098     PDB::Bond::isElcsta
 2.24  131.0808        1  131.080769     WhatIf::doWhatif
 1.91  111.7546  10730691   0.000010     PDB::Atom::resName

The code for the first three subroutines are shown here:

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 $nu
+mber == 0;
    return pad_left($number,$whole,'0') unless $number =~ /\./ || $fra
+c; 
    my ($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;
}
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I had totally forgotten that I use numberFormat to manipulate the result of the sqrt function. (This is essential for the DB) I'm now going to move this to the DB part, so that it only gets called when adding 'real' bonds to the DB.

I'm also going to remove the UNIVERSAL::isa calls, and just try to ASSUME $self whenever I can.

Thanks for all the help, and I'm still investigating mr. Delauney.

Cheers
Sam