Merge pull request #5360 from RosettaCommons/roccomoretti/chemistry_objects
Add "Chemistry" Objects, which are like Movers, but for ResidueTypes. This is part of the process of merging my the drug_design branch piecemeal.
The Chemisty objects come in two parts. The first is a simple core-level one, which defines the basic interface. The second is a protocols-level one which extents the interface to be XML parsable and Pose-aware. (That is, you can potentially have chemistries which are aware of the residue context in the Pose.) Chemistries occupy a new section in the input XML.
With this PR comes some simple Chemistries, such as PatchChemistry, which allows you to apply the same manipulations you could in a patch.
I also add an ApplyChemistyMover, which allows you to apply one or more Chemistries to a Pose from an XML context.
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Merge pull request #6146 from RosettaCommons/roccomoretti/fix_master_tests2
Fix clang_tidy warning in master
Be explicit about which virtual function is being called during constructor. (This is easy, as it's the most-derived class which is calling things.)
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Merge pull request #6142 from RosettaCommons/nannemdp/vicinity_sampling_by_LoopRelaxMover
Added if statement to LoopRelaxMover to bypass centroid setup when not remodeling the loop.
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