Merge pull request #909 from RosettaCommons/vmullig/energyparse
Adds RosettaScripts parsing of the aa_composition setup
This pull request lets the user set up the aa_composition energy from RosettaScripts on a per-scorefunction basis. (Previously, this was only possible globally, from the command line). This also cleans up some of the inner workings of aa_composition, making it easier to define new sets of things to be counted.
Tasks:
- Add parsing of one or more aa_composition setup file name to the "Set" subtag in scorefunction tags in RosettaScripts.
- DOCUMENT the "Set" subtag somewhere -- I don't think it's in the RosettaScripts documentation. (Update: it's documented, but the list of commands is woefully out of date.)
- Document the aa_composition setup stuff.
- Integration test.
A bunch of integration tests show cosmetic changes due to the addition of another variable to the EnergyMethodOptions, which gets reported whenever the show() function is called.