commit cb1cabafd7463ab703f6abf5efa33d2707b85924
Merge: 9dc9936 9b9dc22
Date:   Thu Feb 20 07:29:09 2020 -0800

    Merge pull request #4482 from RosettaCommons/danpf/hybrid_pmt_fix
    
    Move hybrid parse my tag pose accessing to apply

commit 9dc9936130ea42beb5b457de3e5962ceab5b43b0
Merge: 321d95b 8bf9c24
Date:   Thu Feb 20 10:23:31 2020 -0500

    Merge pull request #4516 from RosettaCommons/roccomoretti/fix_cppcheck
    
    Fix issue identified by cppcheck.

commit 321d95b6c7a2f2df9ef12360afdaf74d170ef559
Merge: 7bb3f80 e29393a
Date:   Wed Feb 19 19:48:15 2020 -0500

    Merge pull request #4509 from RosettaCommons/vmullig/fix_simple_cycpep_predict_bug
    
    Fix a bug in simple_cycpep_predict with disulfides in MPI mode
    
    The addition of the DISULFIDE variants to the native pose when predicting structures of disulfide-cyclized peptides was messed up, but only in MPI mode.  The issue was that the SimpleCycpepPredictApplication object is initialized differently in the non-MPI mode (reading directly from disk) or in MPI mode (one process reads from disk and broadcasts stuff to all other processes). The initialization of the native pose was depending on information that had not yet been received by all processes in the latter case (the sequence length).
    
    TODO:
    - [x] Check the `simple_cycpep_predict` scientific test (queued here: https://b3.graylab.jhu.edu/revision/commits/14718 ). --> Yes, this runs correctly still.

commit 7bb3f803381ea6a41699564db02b5c5d943e59d0
Merge: 286deaa 525d77f
Date:   Wed Feb 19 08:21:36 2020 -0500

    Merge pull request #4498 from RosettaCommons/JackMaguire/FixFastDesignRampLogic
    
    Fixing CST Ramping Logic in FastDesign
    
    @AJVincelli reported at Winter RosettaCON 2020 that FastDesign did not respect the -relax:ramp_constraints false flag. At the time she thought it was due to MonomerDesign2019 but it turns out this bug was present for all of FastDesign.

commit 286deaae4986f74e96d1ffcbdda130ea3221b0be
Merge: 0d16bfb 633ddc4
Date:   Wed Feb 19 07:44:18 2020 -0500

    Merge pull request #4501 from RosettaCommons/JackMaguire/FixThanhsBug
    
    Handling edge cases for the SequenceSymmetricAnnealer
    
    SequenceSymmetricAnnealer started out as a hack and slowly matured into a feature that was merged to master in #4117 and #4260. Some edge-case handling was missed during the de-hackifying process.
    
    The branch name is misleading. This is not Thanh's bug - this is my bug that Thanh found.
    
    Thanks Rocco for the review!

commit 0d16bfb5a1f4a18d84fea88ad13dd93711db809d
Merge: 7502917 25a7115
Date:   Tue Feb 18 18:02:31 2020 -0800

    Merge pull request #4435 from RosettaCommons/aloshbau/debug_params_python
    
    Aloshbau/debug params python

commit 7502917d27dea5f403fa2f065848ea926b84a38a
Merge: 2e16622 fac03e1
Date:   Tue Feb 18 19:15:31 2020 -0500

    Merge pull request #4510 from RosettaCommons/roccomoretti/fix_timing_issue
    
    Fix issue with JD2 timing code.
    
    There was a runtime assert that we weren't finishing jobs before we started them. NTP clock adjustments can make start/end times non-monotonic, so accommodate for those.

commit 2e16622e1f392beaf94e7d11eb14a58be02dd410
Merge: 16a2df6 b8275d6
Date:   Tue Feb 18 11:51:35 2020 -0600

    Merge pull request #4506 from RosettaCommons/jadolfbr/glycan_benchmarking3
    
    Fix issues identified by CPPCheck.

commit 16a2df6ce1af833ca5d006e2d08cf93075f7577a
Merge: 0ffed8f 872905e
Date:   Sat Feb 15 14:19:42 2020 -0500

    Merge pull request #4504 from RosettaCommons/sergey/binder
    
    PyRosetta update, updating Pybind11 version to address PyTorch/TensorFlow import issues.

commit 0ffed8fdc6a22988ba70661bf0a902473e383bb0
Merge: 7ebfc28 7f6bd9b
Date:   Sat Feb 15 12:32:30 2020 -0500

    Merge pull request #4505 from CyrusBiotechnology/smlewis/fix_werror_release_Debug
    
    fix some release_debug problems in FASTER's IG

commit 7ebfc28f35f8ebeffa19c6c1a0ff62fcb919ba98
Merge: 82fb3d1 c78c2eb
Date:   Sat Feb 15 10:01:50 2020 -0600

    Merge pull request #4473 from RosettaCommons/jadolfbr/glycan_benchmarking3
    
    # WaterMediatedHbondMetric
    
    
    A metric to measure hydrogen bonds between a set of residues that are water-mediated.
    
    Docs: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/SimpleMetrics/simple_metric_pages/WaterMediatedHbondMetric
    
    ## DEPTH:
    We only traverse a depth of 1 by default. Make sure to set the -ignore_waters flag to false in order to have Rosetta include the HOH residues.
    
    ## SELECTION:
    
    If one residue selector is given, will calculate bridged waters between residues of the selection and all [OTHER] residues, otherwise it will calculate bridges between one selection and another.
    
    If NO SELECTION is give, will report ALL bridged hbonds in a pose [by default without self-water-self hbonds].
    
    ## HBOND:
    
    Since these are bridged hbonds, and h-bond networks can be rather complex, the numbers
    reported here are the unique h-bond paths from sele1 to sele2.  If you give only a single residue selector, these are bridged hbonds from sele1 to OTHER residues in sele1.
    By default we do not include mediated hbonds back on itself, but this is an option.
    
    ## TIPS:
    
    It is generally recommended to repack the waters using the OptH TaskOperation before input into this metric, especially if only Oxygens were present.  Using the option -include_vrt false will keep all waters present in the resulting structure.  Use the option -corrections::water::wat_rot_sampling 10 to decrease the angle of sampling from a default of 30 to 10.  This will result in many more rotamers, but will improve networks.
    
    Hydration shells can be calculated by passing selection1 as all waters in the pose, selection2 as the protein or chain, and then reporting only a single depth (with max_depth at 0 and 1 for the first and second shell waters."
    
    # HbondMetric
    
    A metric to report the total h-bonds residues from a selection to all [OTHER] residues, or from a set of residues to another set of residues.  If No selection is given, will report ALL vs ALL.
    
    Docs: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/SimpleMetrics/simple_metric_pages/HbondMetric
    
    ## Tips:
    
    Use the SummaryMetric to get total hbonds of a selection or total number of residues having some number of hbonds. . See the WaterMediatedBridgedHBondMetric for water-mediated h-bonds.
    
    By default does not report self-self hbonds
    
    
    # Etc
    - Added unit tests for both metrics
    - Fixed glycan integration tests
    - Add deprecated warning for -1 option in `test/run.py` as it will say subtests pass even though they don't.

commit 82fb3d1ac4ee4f5a298351d0689760c9b4f6370e
Merge: aede1c1 4f6a091
Date:   Fri Feb 14 11:41:25 2020 -0800

    Merge pull request #4471 from RosettaCommons/guangfeng/galigdock_genparams
    
    Guangfeng/galigdock genparams

commit aede1c1ca1988f6091eef64db20321adc2f54098
Merge: 94921cf 9d26b69
Date:   Fri Feb 14 10:11:01 2020 -0500

    Merge pull request #4500 from RosettaCommons/roccomoretti/fix_simple_cycpep_predict
    
    Fix typos in simple_cycpep_predict script.

commit 94921cfa182447dde37180fafb46a8325856c482
Merge: db9e987 89e7c38
Date:   Thu Feb 13 17:32:50 2020 -0500

    Merge pull request #4494 from RosettaCommons/everyday847/fix_demos_failing
    
    Update demos submodule

commit db9e98799b2b7be04256ef96e1250c3d619e6d29
Merge: 3387ec4 f723e87
Date:   Thu Feb 13 12:08:09 2020 -0500

    Merge pull request #4483 from RosettaCommons/roccomoretti/restype_converter_roundtrip
    
    Promote restype_converter application to public
    
    I initially implemented the restype_converter app as a pilot application, because the output formats were a bit sketchy in their completeness.
    
    With this PR, I fleshed out the params file output, such that it should be able to output lines for each of the input lines in the params file. Theoretically, the params files should now round-trip on a functional basis, though they don't necessarily round-trip on a textual one. (Loss of comments, reorganization, different precisions & spacings, equivalent ways of writing the same thing, etc.)
    
    I think this is usable enough to promote it to public. The SDF output files aren't necessarily round-trippable, but they're usable if all you want is atoms, bonds and coordinate information.
    
    I also extended the restype_converter integration test to make sure most all of the current params file lines are represented (and output), as well as implementing a basic round-trip test for fullatom types.

commit 3387ec42a9999de15df75abf56c11a784705b6cf
Merge: feb6ebf 8df8cc9
Date:   Wed Feb 12 15:03:57 2020 -0500

    Merge pull request #4486 from RosettaCommons/roccomoretti/crash_report_server
    
    Add script for reporting crashes to the crash report server.
    
    For a while now Rosetta has been producing crash report logs. Part of the intent of having these would be to eventually collect those reports so we could see where Rosetta was having bugs or needed better error handling. -- The big limit to this so far being putting together the actual site to collect the data.
    
    Luki offered to put together such a website, and has done an awesome job of it: https://crash.rosettacommons.org/ (Submission of crash reports is open to the public, but viewing the reports needs a Github login.) There's still some open questions about how we want to summarize/organize/report the crash reports, but the actual crash report collection should be feature complete, and we have basic crash report search and summary functionality.
    
    This PR adds mention of the site into the crash report logs, as well as adding a script which can automatically collect and submit the crash reports.
    
    I also addressed a non-crash which was being reported as the most prevalent crash. (The exception raised by JD2 to report an issue with a job.) Not only will this reduce noise on the crash report server, this has the added benefit of making the tracer output look nicer in the case of errors.

commit feb6ebf6c93447cb081e3b1c7ab91a66ec91a565
Merge: 3d4081e f96cb36
Date:   Sat Feb 8 16:37:31 2020 -0600

    Merge pull request #4485 from RosettaCommons/roccomoretti/fix_broken_tests
    
    Attempt to smash a bunch of broken tests in master on the test server.
    
    I looked at the failures in master, and saw if I could make some quick technical fixes. Not treated were "scientific" failures

commit 3d4081e711726d934e392906cc1d447f4c06d09e
Merge: 8bbf20f 1f56aba
Date:   Sat Feb 8 02:21:28 2020 -0500

    Merge pull request #4474 from RosettaCommons/vmullig/no_movemap_controlling_packing_in_fastrelax
    
    Ensure more consistent default user interface for FastRelax
    
    At some point, someone added something to FastRelax that disables packing at positions where the MoveMap prohibits sidechain minimization.  This is counter-intuitive behaviour: normally, MoveMaps control minimization and task operations control packing.  This is what we teach new users, and this is what experienced users expect, so it's an unexpected side-effect to disable minimization at a position and to find that that position is no longer packing.  Worse, this is one-way behaviour: a user that sets up a task operation that prohibits packing at position 5 does not automatically disable sidechain minimization at position 5, but a user who disables sidechain minimization at position 5 _does_ prevent packing at position 5.
    
    I'm disabling this behaviour unless the user opts _in_ by turning on a suitable commandline flag, RosettaScripts option, or C++ and Python-accessible option in the FastRelax object.
    
    Tasks:
    - [x] Add commandline flag to turn _on_ the old behaviour.
    - [x] Add FastRelax setting to turn _on_ the old behaviour.
    - [x] Setters and getters for C++ and Python.
    - [x] Option accessible to `parse_my_tag()` and `provide_xml_schema()` for RosettaScripts.
    - [x] Have the option enable the old behaviour, and disable it otherwise.
    - [x] Beauty.
    - [x] Check tests.
    - [x] Update documentation.

commit 8bbf20f8097f8e458d122073211d2bc3a6d8941e
Merge: 2d8a8e2 a44d518
Date:   Fri Feb 7 15:45:31 2020 -0700

    Merge pull request #4484 from RosettaCommons/benchmark
    
    updating Benchmark release scripts, adding file locking so multiple releases could be done in parallel by multiple back-ends

commit 2d8a8e2046c7cb5453685af036327813055917c1
Merge: a77fcb8 0f927c3
Date:   Mon Feb 3 16:57:32 2020 -0600

    Merge pull request #4476 from RosettaCommons/roccomoretti/fix_cppcheck_test
    
    Attempt to fix the cppcheck test.
    
    We're having issues with cryptic errors in the cppcheck test.
    
    Part of that is that the cppcheck test script has the wrong option for grep in parsing out error lines, and part of it is that cppcheck updates (1.90 in particular) changed the behavior of cppcheck. Fix that and update the "known issues" list accordingly.

commit a77fcb8369c9b732be312cc225a0a5b984fea58f
Merge: bc2199c 8729ba5
Date:   Mon Feb 3 16:29:11 2020 -0500

    Merge pull request #4477 from RosettaCommons/smlewis/sci_tests_minor_updates
    
    Minor language changes and typographical error fixes for scientific tests.  Includes commits from Brahm so that they make it to master.

commit bc2199c8b3b45487d9b0bb67608c334c0c14dcee
Merge: aaafe23 667d629
Date:   Mon Feb 3 15:51:06 2020 -0500

    Merge pull request #4480 from CyrusBiotechnology/smlewis/GreenPacker_tests
    
    GreenPacker and GreedyOptMutationMover have ultrabasic unit tests to check that they don't segfault.

commit aaafe23d795c1705c5dc8649d7a156a040cc17de
Merge: 80fcaed 5caf2e2
Date:   Fri Jan 31 22:53:32 2020 -0800

    Merge pull request #4464 from CyrusBiotechnology/smlewis/mangle_job_id_with_HOSTNAME
    
    This adds an option (`HOSTNAME_in_jobname`) to mangle JD2 job names with $HOSTNAME.
    
    In a context where job distribution is not being done inside Rosetta, but instead being done externally, you will run into the case where the low job numbers (like 0001) recur. Instead of managing job completion by moving them around, we can make them unique by mangling them on the host on which they occur. In containerized systems $HOSTNAME is usually set; in kubernetes specifically it includes a hash unique to the problem.
    
    The option does nothing if $HOSTNAME is not set.

commit 80fcaed31d875d7a7b2ee4ca9264708cb546ab5c
Merge: 19b2b92 d1634ff
Date:   Fri Jan 31 20:27:11 2020 -0500

    Merge pull request #4436 from RosettaCommons/JackMaguire/AcceptToBestMover
    
    AcceptToBestMover
    
    I'm re-implementing FastDesign using rosetta_scripts instead of relax_scripts. People are generally more familiar with rosetta_scripts so this side-by-side comparison will hopefully be the "Rosetta Stone" of relax_scripts.
    
    The only functionality that does not currently exist in rosetta_scripts is the accept_to_best command, which updates the pose to the best one seen so far. This PR adds the AcceptToBestMover which wraps this simple logic into Mover boilerplate.

commit 19b2b9260c25038dd3215869d9a80eaf71734926
Merge: 2fa58f7 53d5b4e
Date:   Fri Jan 31 14:12:53 2020 -0500

    Merge pull request #4468 from RosettaCommons/everyday847/fix_failing_tests
    
    Fix autoDRRAFTER integration test

commit 2fa58f79ed5e5543c4574bd1dd44c405e51d43f4
Merge: b7d5f79 028a89d
Date:   Fri Jan 31 02:41:12 2020 -0500

    Merge pull request #4465 from RosettaCommons/vmullig/fix_james_helical_bundle_predict_issues_2
    
    Fix an issue with, and add some features to, helical_bundle_predict.
    
    This PR:
    - [x] Fixes a silly bug in parsing FASTA files in helical_bundle_predict.
    - [x] Adds an option to skip residues in the native structure in alignments.
    - [x] Adds an option to skip residues in the generated structure in alignments.
    - [x] Adds integration tests for the new options.
    - [x] Adds documentation for the new options.

commit b7d5f79c34f3f657f141ae0d1e8933c680f5b2d9
Merge: e584678 06199f2
Date:   Thu Jan 30 13:49:29 2020 -0500

    Merge pull request #4462 from RosettaCommons/vmullig/multithreaded_scoring_incremental_merge3
    
    Incremental merge 3 for multithreaded scoring
    
    The multithreaded scoring branch identified a major thread-safety issue with the hydrogen bonding code, in which data that were needed down a long series of function calls were cached in mutable storage in the energy method, then accessed down the chain.  This is fundamentally non-threadsafe: if different threads are trying to score different parts of the pose at the same time, one could overwrite the data that the other cached.   The proper solution is simply to pass these data down the chain of function calls.  Unfortunately, due to the complexity of the etable template classes, this means modifying a _lot_ of functions.
    
    I've done the work for this, now, and want to make it a separate pull request to ensure that it only improves performance and has no effect on accuracy.  Note that I've tried to do this in a way that involves a subclassed container class, so that we can add additional data in the future if we so wish _without_ having to refactor all of these dozens of template functions, simply by adding new subclasses of the container class.
    
    Note also that this might fix rare thread safety issues with multithreaded packing, so it benefits multi-threading even before we enable multithreaded scoring.
    
    - [x] Pull request #4460 must be merged before this one.

commit e584678417d867cf66325de0cdce68bad0bad399
Merge: f01b52b 18c3c74
Date:   Tue Jan 28 18:32:36 2020 -0500

    Merge pull request #4469 from RosettaCommons/vmullig/another_xyz_vector_uninitialized
    
    Fix another uninitialized xyzVector error.

commit f01b52ba4dead724a6a62fa5b312fd1b0ff3cdbb
Merge: dbfc681 02d1094
Date:   Tue Jan 28 15:21:52 2020 -0500

    Merge pull request #4460 from RosettaCommons/vmullig/multithreaded_scoring_incremental_merge2
    
    Incremental merge 2 for multithreaded scoring
    
    This PR relaxes some of the locking of the global options system.  I was overdoing it, and it was hurting multithreaded performance and performance scaling a bit.
    
    (Note that the full locking can be restored by defining `OPTIONS_COLLECTION_FULL_THREAD_SAFETY`.  This is not defined by default.  When `MULTI_THREADED` is defined, as it is when building with `extras=cxx11thread`, only the necessary locking occurs.)
    
    - [x] Pull request #4459 must be merged before this one.
    
    @bcov77

commit dbfc6818e16b4df972b322d2349b63d84890674c
Merge: 531813a 2ceb9f5
Date:   Mon Jan 27 09:52:49 2020 -0800

    Merge pull request #4463 from RosettaCommons/danpf/fix_csts_blank_bs
    
    fix constraint file io if blank header

commit 531813ae494df1ec1ae67dd202ef04de5f53d4cc
Merge: 3f087db c632aae
Date:   Mon Jan 27 12:14:28 2020 -0500

    Merge pull request #4461 from RosettaCommons/vmullig/fix_maybe_uninitialized_errors
    
    Fix a couple of compilation errors in gcc/7.
    
    The gcc/7 compiler on Ubuntu 18 was complaining about uninitialized or potentially uninitalized variables in a devel protocol. This may be a false warning, since other compilers don't seem to complain, but initializing the vars shushes the warnings, and is unlikely to have any significant impact on performance given the complexity of the other stuff that these classes do.

commit 3f087db07b24815cd458c23e003478c7964b11b9
Merge: ae05cc5 0dd4769
Date:   Sun Jan 26 04:53:13 2020 -0500

    Merge pull request #4459 from RosettaCommons/vmullig/multithreaded_scoring_incremental_merge1
    
    Incremental merge 1 for multithreaded scoring.
    
    This pulls the changes to the RosettaThreadManager into its own pull request, to keep everything nicely compartmentalized and easy to review. See pull request #4342 for details.

commit ae05cc5c462f8507065fd9066bddc4f483ecc7dd
Merge: 4fcf800 1c29e75
Date:   Fri Jan 24 11:13:56 2020 -0600

    Merge pull request #4450 from RosettaCommons/roccomoretti/clang_tidy_4
    
    Clang tidy: modernize-use-nullptr
    
    Another in the series of adding additional clang-tidy tests. This one is pretty much purely mechanical.
    
    The big change was to fixedarray1/fixedarray0. These were changed to default initialize instead of zero initialize. This had the knock-on effect of requiring me to convert their internal store from a C-style array to a std::array, as well as changing a few places where there were fixedsizearrays of xyzVectors (which behave differently for zero vs. default initialization.)

commit 4fcf80033aebbcdf7c379387df97fd3d51a2c079
Merge: 2246d00 f86dd00
Date:   Fri Jan 24 11:08:55 2020 -0600

    Merge pull request #4456 from RosettaCommons/roccomoretti/no_apply_to_pose
    
    Remove APPLY_TO_POSE usage in integration tests
    
    APPLY_TO_POSE is deprecated, and we should hopefully be removing support for it in the (nearish?) future.
    
    There are, however, two integration tests which make (non-trivial) use of it. This PR adjusts those integration tests not to use it, using the suggested replacement instead.

commit 2246d009395deacac3a0f84e26b039c5d7576ac5
Merge: adf10ee 7b5a53c
Date:   Fri Jan 24 01:07:27 2020 -0500

    Merge pull request #4458 from RosettaCommons/vmullig/fix_james_helical_bundle_predict_bug
    
    Fix two bugs in helical_bundle_predict
    
    Thanks to @jameseastwood for finding these.  This PR fixes:
    - [x] The `TryDisulfidePermutations` mover would segfault for poses with only one disulfide-forming residue.
    - [x] The `helical_bundle_predict` application was not ignoring comment lines in FASTA files.

commit adf10ee355f45deb3535b0885e69702daeda4832
Merge: e3dc1d8 4961ba1
Date:   Wed Jan 22 15:23:00 2020 -0500

    Merge pull request #4326 from RosettaCommons/JWLabonte/sugars/modifications
    
    Carbohydrates: Adding two more families of modified sugars
    
    This merge adds support for phosphorylated and thio-sugars into Rosetta.
    
    auto-drrafter_setup_run_R1 is broken. All other tests pass.

commit e3dc1d862146de1aff035116f12acad962231b76
Merge: 1ae3d1f e950c6e
Date:   Mon Jan 20 15:17:36 2020 -0800

    Changes to get the libraries building on windows - Merge pull request #4448 from RosettaCommons/solberg/minirosetta_windows
    
    In src/protocols/jd3/JobGenealogist.hh, the hash function for some custom classes (which themselves didn't seem to be much more than pointers) could not be found since they're in another namespace, (and then not part of the custom class itself and only included via using), so I put in explicit hash functions for the unsorted_sets.
    In src/protocols/jd3/util.cc and /src/core/io/mmtf/util.hh there were some ambiguous types for which I had to guess at which one was intended, hopefully I guessed correctly.
    Had to add in lot of #includes which were probably forgotten due to gcc's order of compilation happening to include them from elsewhere before needed, or something like that (owning_ptr.hh was the most common)
    Had to remove direct usages of std::make_shared- I believe we are intended to be using utility::pointer::make_shared, and directly calling std::make_shared causes mixture between boost and std shared pointers.
    Removed an exit "status" variable that I couldn't find the definition for in src/utility/exit.cc . Just replaced it with "1" since it seemed to be used for exit failures.
    Fixed a naming collision in src/utility/pointer/deep_copy.hh
    S_ISREG and S_ISDIR are linux-only things. Replaced them with boost is_directory in src/protocols/docking/DockingEnsemble.cc
    In src/protocols/boinc/boinc.cc, reverted a change from Oct 31st 2018 which caused (I think) a partially specialized template

commit 1ae3d1ffee7e562cbbf214aec9fbf239ce9e045f
Merge: 37923f1 53ba3be
Date:   Mon Jan 20 14:30:05 2020 -0600

    Merge pull request #4445 from RosettaCommons/roccomoretti/packer_palette_restype_tests
    
    Delay ResidueTypeSet usage in PackerPalettes
    
    For the vHTS protocols, the introduction of PackerPalettes caused crashes due to the way they were implemented with respect to the protocols::ligand_docking::HighResDocker mover.
    
    This PR attempts to fix that issue by deferring the use of the ResidueTypeSet until the Palette is actually used (rather than encoding it at Palette creation time). A side benefit of this is that this makes PackerPalettes better compatible with mixed-mode Poses (e.g. where some residues are fullatom and some are centroid.)
    
    The way this was accomplished is by removing the RTS member value from the PackerPalette object, and instead passing it as a function parameter from the ResidueLevelTask object. This does mean that the creation of the base type list is deferred until the RLT, and thus happens multiple times (though can happen for different RTS for a single Palette, and the results for a single RTS is cached for faster lookup).
    
    On a subclass level, this means that the new get_base_residue_types() member function is the key function to overload, taking the place of the previous set_residue_type_set() member function.
    
    This still only works if the type being packed/designed is in the PoseRTS. Testing this actually revealed an issue where the pose loading functionality is clearing the pose without properly (re)setting the PoseRTS, when applicable. This PR also contains a patch to fix that.

commit 37923f1e8060844555174c6409094ca87169f362
Merge: 9c2e2d5 887825d
Date:   Mon Jan 20 09:40:40 2020 -0800

    Merge pull request #4454 from RosettaCommons/dimaio/fiber_symmgen
    
    Updates to a pilot app. Small output fix in make_symmdef_file.pl

commit 9c2e2d50289580e523ae948312e9c3496e485676
Merge: d96aa13 3ec88d5
Date:   Fri Jan 17 20:36:53 2020 -0500

    Merge pull request #4453 from RosettaCommons/vmullig/fix_andy_genkic_bug
    
    Turn a segfault into an informative error message.
    
    Andy identified a crash bug in a GeneralizedKIC perturber. I'm turning this into an informative error message.

commit d96aa1311025ed6a88d6ef92bf9c7aa56d5df4dc
Merge: 763f794 be7301e
Date:   Fri Jan 17 14:15:09 2020 -0500

    Merge pull request #4451 from RosettaCommons/aleaverfay/add_prefix_for_intana_scorefile_reporting
    
    Add prefix for reporting intana stats to the score file
    
    If you want to look at more than one interface in a structure
    or to look at the evolving properties of that interface over
    the course of a trajectory, then InterfaceAnalyzer will now
    let you use different prefixes to label the pose-extra-scores
    that it calculates and stores in the pose. Without the prefix,
    the 2nd use of the InterfaceAnalyzer would overwrite the
    results of the 1st use.

commit 763f7940ff4c1c5747df0d04fa8f1de19f5ee055
Merge: e8f09ca6 41a035f
Date:   Fri Jan 17 10:57:48 2020 -0600

    Merge pull request #4368 from RosettaCommons/jadolfbr/glycan_benchmarking2
    
    General
    =====
    
    - Fix `Or_combine` and `And_combine` functions
    - Fix `get_score_function` to correctly use the local options collection
    - Fix `set_weight_if_zero` by comparing the 0 delta instead of actual 0.
    - Fix `extract_asymmetric_unit` to be much more robust, using `create_subpose` as a guide but keeping the additional functionality.
    - Fix `RMSDMetric` to extract the asymmetric unit if the pose is symmetric and the ref/native is not.  This works fine for RMSD but failed for superposition.  The fixes here and with `extract_asymmetric_unit` now allow glycans poses to be properly extracted and superimposed.
    - Add options to allow RMSDMetrics to use a different set of residue_selectors for superposition vs RMSD.
    - Add a warning to `superimpose_pose` that warns when a user is trying to superimpose a symmetric pose with an asymmetric pose (even with a correct `AtomID_map`).  It won't crash, but it will give you a garbage superposition.
    - Fix flip of HNQ for residues across a side-chain branch point
    
    Glycans
    =====
    
    - Add option to force `sugar_bb` 0 (if using get_score_function)
    - Add ability to control `kT` properly
    - Add conformer probability option for root of glycan only
    - Allow `sugar_bb` to be set on cmd-line or through score functions without overriding to 1.0 - only set to 1.0 if it had not been set manually
    - Add `match_window_one` option for glycans that is used for benchmarking so that the total number of rounds is the same for various sampling techniques.
    
    Beta Scorefunction
    ==============
    
    - Make -beta score function work for JD3 apps
    - Add serialization methods to core beta energy classes that are stored in the pose

commit e8f09ca683fe2cfe0dacad2f7cf6ed14289e934c
Merge: 85a2059 72e8794
Date:   Thu Jan 16 14:38:48 2020 -0700

    Merge pull request #4449 from RosettaCommons/benchmark
    
    updating timelimit.py so on timeout it also terminate all child processes

commit 85a205900572b8933103a2a2208cf3ddf086c502
Merge: f1c7e97 8e65d03
Date:   Wed Jan 15 13:13:33 2020 -0800

    Merge pull request #4447 from RosettaCommons/rpavlovicz/control_rmsd_simpleddg
    
    turn off default calculation of rmsd