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while (@parts) {
        my $part = shift @parts;
...
        $parent->{_name_} = $protein;
    }

while ($wIndex < @words && exists $parent->{$words[$wIndex]}) {
        @best = ($parent->{_name_}, $wIndex) if exists $parent->{_name
+_};
        $parent = $parent->{$words[$wIndex++]};
    }