Neither BioPython nor BioRuby have a native module for this task.

Depending on the enzyme, digest from the EMBOSS package may be of use. It can locate sites for 8 enzymes/reagents, including trypsin, chymotrypsin and CNBr.

BioRuby does not have an EMBOSS module, but I believe that BioPython has a wrapper for EMBOSS applications. It's generally quite simple to call and parse EMBOSS from a script, since the EMBOSS tools are command-line with well-defined parameters and ASCII, often delimited, output.

While it may not be python or ruby specific the destination of all knowledge and information (wikipedia) has a nice article on restriction enzyme cutting sites: http://en.wikipedia.org/wiki/List_of_restriction_enzyme_cutting_sites

It has a list of all nucleotide recognition sites (hundreds by the looks of it). All you really need to do is scrape the info off of there and just create regular expressions in your preferred language.

Hope that helps,

Will

Edit: After re-reading I realized that you wanted protein digests, not NTs. The ELM database actually has a nice collection of protein cleavage recognition sites. The link is here: http://elm.eu.org/browse.html .. just look at the ones started with CLV_ (for cleavage related). The nice thing is that they are all regular expressions as well.