#!/usr/bin/perl -w
use strict;

my $line;

while ($line = <DATA>)
{
   if ($line =~ m/while\s*\(/) #perhaps m/^\s*while/ ? 
                               #think about "while in a comment". 
                               #other border cases...
   {
      process_while();
      next;
   }
   print $line;
}

sub process_while
{
   my $i =1;
   while (1)   #normally while(1) not a good idea, but
               #I figure its ok here.
   {
      $line =~ s/(\w+)(\s*)(&&|\|\||\s*\))/ $i++." $1$2$3" /ge;
      print $line;
      return if $line =~ m/{/;
      $line = (<DATA>);
   } 
}

=Prints:
 some statement;
 while( ( 1 condition1 && 2 condition2 && 3 condition3 ) || 
 ( 4 condition4 || 5 condition5 && 6 condition6 ) { #statements; }
 while( ( 1 condition1 ) || 
 ( 2 condition2 || 3 condition3 && 4 condition4 ) { #statements; }
 while(  1 condition1 &&  2 condition2 ||  3 condition3 ) 
 { #statements; }
 more statements;
=cut

__DATA__
some statement;
while( ( condition1 && condition2 && condition3 ) || 
( condition4 || condition5 && condition6 ) { #statements; }
while( ( condition1 ) || 
( condition2 || condition3 && condition4 ) { #statements; }
while(  condition1 &&  condition2 ||  condition3 ) 
{ #statements; }
more statements;