Rosetta automated reaction-based ligand design (RosettaAMRLD) (#403)
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.
Other changes include:
* Added a python script that plot the distribution of (RDKit) metrics (by RM)
* Added an edge case handling when removing charges in RDKit utils (by RM)
* Modified the recompute function in `source/src/core/pose/metrics/simple_calculators/InterfaceDeltaEnergeticsCalculator.cc` to handle multiple chains. (calculate energies between the first and second chains -> between all chains and the last chain)
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Co-authored-by: Rocco Moretti <rmorettiase@gmail.com>