I'd like to play around applying a set of assitance rules based on recognition of 3D motifs. To acheieve this we'd need an API to expose position of backbone residues and side chains and mechanism for enumerating, creating and modifying bands.

It's seems to me that exposing an automation API (preferaly with java api or webservice) would offer a much greater bang for your development bucks than pushing the cookbook which is effectively another DSL.