PHP - preg_replace how to add an extra "]" and an extra "["

SELECT  TOP 25
        tblClient.ClientCode,
        tblRegion.Region
FROM    (tblClient LEFT OUTER JOIN
            tblRegion ON tblClient.RegionCode = tblRegion.RegionCode)
ORDER BY tblRegion.Region, tblClient.Client

$oldstr1='/\<span style="font-family: Times New Roman; font-size: 12pt;"\>/';
$oldstr2='/\<\/span\>/';

RewriteCond %{QUERY_STRING} ^view=article&id=(?:[0-9]{1,3}|1000)(&|$) [OR]
RewriteCond %{QUERY_STRING} ^view=article&id=(668)&action=synopsis [OR]
RewriteCond %{QUERY_STRING} ^view=person&id=1
RewriteRule ^(?:index\.php|)$ http://www.innovateonline.info? [R=301,L]

RewriteCond %{QUERY_STRING} ^id=1149(&|$) 
RewriteRule ^extra\.php$ http://www.innovateonline.info? [R=301,L]

foreach $element (keys %dist){ ...

foreach $element (keys %dist){
    $HoA{$element}[3]++;
    my $newKey=scalar (keys %HoA);
    if($newKey!=($PolymerSize-1)){
        push @{$HoA{$newKey}}, $coordsNeighbors[0];
        push @{$HoA{$newKey}}, $coordsNeighbors[1];
        push @{$HoA{$newKey}}, $coordsNeighbors[2];
        push @{$HoA{$newKey}}, $coordsNeighbors[3]+1;
        push @{$BondHoA{$element}}, "$newKey";
        push @{$BondHoA{$newKey}}, "$element";
       #here I add a last to break out and go to the next do-while iter.
        last
    }

#!/usr/bin/perl;
use strict;
use warnings;
use Data::Dumper;
my $PolymerSize=8;
my $maxNeighbors=3; #each monomer/node can bond upto 3 times
my %HoA; #Store coordinates and number of neighbors for each monomer/node (in C would be an array of structs)
my %BondHoA; #who are my neighbors
my @coordsNeighbors;
my $element; #Iteration dummy variable
my %dist; #temporary distance hash
my $selected;
$coordsNeighbors[0]=0; #Xcoord
$coordsNeighbors[1]=0; #YCoord
$coordsNeighbors[2]=0; #ZCoord
$coordsNeighbors[3]=$maxNeighbors; #How many bonded neighbors?
my $tempx;
my $tempy;
my $tempz;
my $tempL1;
#Intialize origin (first node/monomer)
push @{$HoA{0}}, $coordsNeighbors[0];
push @{$HoA{0}}, $coordsNeighbors[1];
push @{$HoA{0}}, $coordsNeighbors[2];
push @{$HoA{0}}, $coordsNeighbors[3];
my $iter=0;
#Generate new nodes/monomer and "grow" polymer
do{
 #print "$iter\n";
 # $iter++;
  undef(%dist);
        for(my $j=0;$j<3;$j++){
             $coordsNeighbors[$j]=int($PolymerSize*rand()); #generate coords of potent. monomers/node
         }
             $coordsNeighbors[3]=$maxNeighbors;
        foreach $element ( keys %HoA) { #loop through existing monomers/nodes
                $tempx=int($HoA{$element}[0])-int($coordsNeighbors[0]);
                $tempy=int($HoA{$element}[1])-int($coordsNeighbors[1]);
                $tempz=int($HoA{$element}[2])-int($coordsNeighbors[2]);
                $tempL1=abs($tempx)+abs($tempy)+abs($tempz);
                  if($tempL1==1){
                        $dist{$element} .= $tempL1;
                  } elsif($tempL1==0){
                        undef(%dist);
                        last;
                  }
         }
        foreach $element (keys %dist){
                 if ( ($HoA{$element}[3]>0)){ #potential monomer is good, so add to HoA and update bonds
                        my $newKey=scalar (keys %HoA);
                        if($newKey<=($PolymerSize-1)){
                         $HoA{$element}[3]--;
                         push @{$HoA{$newKey}}, $coordsNeighbors[0];
                         push @{$HoA{$newKey}}, $coordsNeighbors[1];
                         push @{$HoA{$newKey}}, $coordsNeighbors[2];
                         push @{$HoA{$newKey}}, $coordsNeighbors[3];
                         push @{$BondHoA{$element}}, "$newKey";
                         push @{$BondHoA{$newKey}}, "$element";
                         last;
                        }
                 }
              }
} while((scalar (keys %HoA))<=$PolymerSize-1);
foreach $element (keys %HoA){
        print "$element \t $HoA{$element}[0] \t $HoA{$element}[1] \t $HoA{$element}[2]\n";
}

$content = preg_replace('/-1(?!-1)/','',$content);