That can still be helped by better formatting rules. The way I write complex conditionals that would be too long to fit on one line is to treat the parens like curlies and line them up the same way, indenting the content.

See what your mistake would look like then:

if(
    ( $flag1 or $flag2 )
    and ( length( $string )
) {
    # ...
}
[download]

It still isn't perfectly obvious, but it's much easier to see now.

It also helps to have an editor that will match brackets/parens/curlies for you; go through your delimiters one by one and check that there is a matching one where you expect it.