This is code for the new application RosettaAMRLD.

The framework is based on the Monte Carlo Drug Design branch (PR #282) by Rocco Moretti (@roccomoretti)

The algorithm use Monte Carlo Metropolis methods and similarity-guided sampling to iteratively optimize molecules within a combinatorial library.

The changes are primarily new Filters and Chemistries added to `src/protocols/drug_design/` and modifications to the DrugDesignMover for RosettaAMRLD related functionalities and Simulated Annealing options.