#! perl -slw
use strict;

my $reTokenise = qr[\s*(\S+)(?:\s+((?i:and|or)))?];

sub parseExpr {
    my $expr = shift;
    my @tokens = $expr =~ m[$reTokenise]g;
    pop @tokens unless defined $tokens[ $#tokens ];
    return '[' . join( '.', @tokens ) . ']';
}

while( <DATA> ) {
    chomp;
    warn "Unbalanced parens '$_'" and next unless tr[(][] == tr[)][];
    s[ \( ( [^()]+ ) \) ]{ parseExpr( $1 ) }xe while m[[()]];
    $_ = parseExpr( $_ ) if m[\s];
    print;
}

__DATA__
((A or B)
(A) or B)
((A) or B)
A or B or C and D
( ( this OR that ) AND other )
( A or ( B and (C or D) ) or (E and F) )
(A or (B or C) or (D and E))

##</code><code>##

c:\test>junk5
Unbalanced parens '((A or B)' at c:\test\junk5.pl line 15, <DATA> line 1.
Unbalanced parens '(A) or B)' at c:\test\junk5.pl line 15, <DATA> line 2.
[[A].or.B]
[A.or.B.or.C.and.D]
[[this.OR.that].AND.other]
[A.or.[B.and.[C.or.D]].or.[E.and.F]]
[A.or.[B.or.C].or.[D.and.E]]