my @candidates;  # should use a hash instead, if 
my $c_id;        #   the numbering has lots of big gaps

while (<>) {
    if ( /CANDIDATE\s+(\d+)/ ) {
        $c_id = $1;
    }
    elsif ( /DNA\s+.Note.\s*(\S*.*)/ ) {
        my $proteins = $1;
        my @p_set = ();
        while ( $proteins =~ /\[(NP\s+\d+)\]/g ) {
            push @p_set, $1;
        }
        $candidates[$c_id]{proteins} = [ @pset ];
    }
    elsif ( /R-score\s*=\s*([.\d]+)/ ) {
        $candidates[$c_id]{rscore} = $1;
    }
}