commit 8ecab77aa50ac1301efe53641e07e09ac91fee3b
Merge: a3330b8 bc4988a
Date:   Tue Jul 7 16:41:06 2020 -0600

    Merge pull request #4833 from RosettaCommons/sergey/binder
    
    fixing PyRosetta build on Ubuntu-20.04

commit a3330b83973c2189fea138ff691abff6f2a90945
Merge: fabdc32 a765edc
Date:   Tue Jul 7 09:48:27 2020 -0400

    Merge pull request #4787 from RosettaCommons/BYachnin/bonusmap_for_ResidueTypeLinkingConstraint
    
    Allow more complex behaviour with ResidueTypeLinkingConstraints
    
    This class previously applied a bonus/penalty to scoring if two residues were the same identity. Reviewing the code, it looks like the intention was to expand this to allow for alternative pairing options, but this was never implemented. There were constructors that appeared to be unused and untested in the code base that had behaviour that didn't seem to be working.
    
    We've updated this class to allow apply a custom bonus/penalty applied for any of the 400 possible residue pairs. A fully customized option is obtained by passing a std::map. The "legacy" behaviour is maintained by constructing this map based on user-supplied options.
    
    All existing tests pass, and new unit tests have been added to test the new (and previously untested) functionality. Getters and setters have also been added to improve PyRosetta interface.
    
    Thanks to @roccomoretti for the review!

commit fabdc3234b134baaf033a642bc5efaefbe097e3a
Merge: 28f338a b295ef9
Date:   Mon Jul 6 19:27:13 2020 +0200

    Merge pull request #4794 from RosettaCommons/SamuelSchmitz/FavorDirectMover
    
    Adding FavorCouplingTensor mover

commit 28f338acfb3bfd87048b38a04772486975dc83fa
Merge: f7f9ecb 75f0b8c
Date:   Thu Jul 2 13:04:25 2020 -0700

    Merge pull request #4828 from RosettaCommons/dimaio/restrict_packing_in_cart_ddg
    
    Limit repacking in cartesian ddg

commit f7f9ecb9d8a59728a961ec47b39e07a939a5d125
Merge: cd4c8de 572a7d4
Date:   Tue Jun 30 11:33:27 2020 -0600

    Merge pull request #4823 from RosettaCommons/benchmark
    
    updating how Python virtual environment is setup and fixing Python virtual environment issues on Mac

commit cd4c8de0d49b3a523091f756785370c2adf91ff4
Merge: c17fd4d f304ab3
Date:   Mon Jun 29 13:41:46 2020 -0700

    Merge pull request #4761 from RosettaCommons/vmullig/all_to_all_pnear_analysis
    
    Add PNear analysis for many states.
    
    I'm using peptide structure prediction to train ML models that can recognize peptides that fold well.  A single structure prediction run actually generates far more data than I'm using.  It would be useful to compute and output PNear to all of the negative states in addition to PNear to the state that I'm designing for, to give me more data for training.  This PR adds this functionality.
    
    Tasks:
    - [x] Add new option.
    - [x] Register new option.
    - [x] Have the new option do something:
         - [x] Add a new step to the `HierarchicalHybridJDApplication` class for this computation:
              - [x] Sends a request for each state in turn from the emperor node to all slave nodes.
              - [x] Each slave node broadcasts that state to all other slave nodes.
              - [x] All slave nodes compute RMSD to that state.
              - [x] Emperor collects RMSDs up the hierarchy and carries out PNear calculation.
              - [x] Repeat for each relevant state.
              - [x] Write out PNear list at end.
    - [x] Error if used with `-compute_rmsd_to_lowest option.`.
    - ~~Check and address issue #4738~~ --> separate pull request.
    - [x] Documentation.
    - [x] Integration test.
    - [x] Beauty.

commit c17fd4d9e06b525d81295db6b05db4abdaada8c2
Date:   Fri Jun 26 10:04:03 2020 -0700

    Add UDPSocketClient access to pymolMover (#4753)
    
    This pr adds getters/setters for the address/port of the pymolmover (or internally the UDPSocketClient)
    
    the expected usage is shown in the test that have been added -> specifically the new set_link function.

commit 26505c553176aba7fbaaf1abae8e6b2f143a4ca8
Date:   Tue Jun 23 18:07:53 2020 -0400

    beautifying

commit b2bcaec52b2266317641f24dcb8ffd10e9282dea
Merge: e0f41a7 cd78cbce
Date:   Mon Jun 22 20:25:22 2020 -0400

    Merge pull request #4805 from RosettaCommons/smlewis/fix_lemmin
    
    Update rosetta_citations.txt
    fixing Gordon's name
    
    this will probably cause cosmetic itest changes if anything uses this code in the itests

commit e0f41a746dbf6570d0f94fa2bbdd6cf033615477
Merge: d2d9f90 1f83a53
Date:   Mon Jun 22 14:00:31 2020 -0400

    Merge pull request #4756 from RosettaCommons/jonpliu-patch-3
    
    Carbohydrates: adding lactyl sugars to the database