A couple of random remarks ...
- The article you linked to is published in the Journal of Chemical Information and Modeling. Only very few of us will probably have online access to this ACS publication, so refering to the algorithm described there is difficult to impossible.
- If you are able to describe what the alogrithm is supposed to accomplish, maybe somebody can point you to an existing implementation of this alogrithm. We have a number of bioinfo-savvy monks here and there are a number of modules available on CPAN.
- Indenting your code properly helps with reading and understaning it, take a look at perltidy.
-- Hofmator
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