Merge pull request #4818 from RosettaCommons/jadolfbr/rabd_updates
Thanks to @rahelf and @skelow for identifying these bugs and their aid in fixing them!
Bug Fixes
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- `INCLUDE_ONLY` was not being read, and this was used in the documentation - and should be main CDRSet option.
- Fixed issue where the final cluster reported could be different than what the cluster actually was through `identify_cdr_clusters` app
- Removed the constructor that takes an ab_info object. ab_info is now always correctly initialized from pose.
- This also fixes light_chain not being correctly set from xml/pyrosetta.
Optimizations
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- High Res dock cycles have been greatly reduced to speed up integrated docking and allow more robust protocols. Options are now present to control the first and second cycles of the DockMCM (high-res) protocol in cmd-line,RS, and in code.