Merge pull request #3325 from RosettaCommons/vmullig/update_his_p Tweaking HIS_P.params to allow confirmational sampling and peptide structure prediction at low pH Adding Ramachandran information. At some point, we really should make the protonated variants into patches instead of separate params files. For now, this is a very minor tweak. Update: I'll update all of the protonation params files while I'm at it. This was an old pull request approved some time ago, so I re-tested it (with the latest master merged into the branch) before merging it into master.

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Merge pull request #5692 from RosettaCommons/roccomoretti/update_cmake_build Update CMake build Don't die if an only-with-extras external library isn't present on disk. (This fixes an issue I'm seeing on my machine with the bcl external library.)

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Merge pull request #5696 from RosettaCommons/vmullig/add_tyka_et_al_reference Add Tyka, Keedy, et al. 2011 JMB reference for FastRelax. The omission of this citation was an oversight. Thanks to @AJVincelli for pointing out that this should be included.

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Merge pull request #5652 from RosettaCommons/roccomoretti/atomistic_energy_ouput Add interface to get atomistic energies from EnergyMethods Energies in Rosetta are officially residue-based: all the main interfaces give the energies decomposed at the residue level. This makes things efficient for general usage, but sometimes it's nice to be able to get energy information for individual atoms. (For example, the LJ energies are defined on the atom level, not the residue level.) This PR adds an interface to the EnergyMethod class which allows subclasses to hook into a common interface for providing such atom-level energies. In deference to the fact that not all energies are necessarily going to be atomistic, the implementation of these functions is optional, and there's a has_atomistic_energies() function which allows you to query the method about whether it supports the interface. The "standard" terms from ref2015 have been hooked into this framework, or at least those terms which have sensible atomistic energies. Terms like ref and fa_dun aren't really atomistic, and so they do not support the interface. (Existing residue-based implementations should be unchanged, so there shouldn't be an execution speed concern.) A atom_energy_breakdown utility (mirroring the residue_energy_breakdown utility) has also been created to provide a command line interface to the data, and utility functions in src/core/scoring/util.hh provide C++/PyRosetta-level access.

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Merge pull request #5684 from RosettaCommons/roccomoretti/update_ccd Update the CCD components definitions On Slack, it was mentioned that the CCD definitions in the database are about 2 years out of date at this point, and that's causing issue with the read-all-the-PDB tests. Thanks to the scripts, it's relatively easy to update the components definitions, so we have. We've also updated the PDB_diagnostic test metadata to account for the new components.

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updating integration tests ignore list to filter out kernel version

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Merge pull request #5685 from RosettaCommons/roccomoretti/fix_master_tests Fix tests in master. * Virtual/override issues in FaMPAsymEzCBEnergy * Update tracer registration issue with simple_cycpep_predict output in scientific tests * Update dgdp_script integration test to be compatible with the Valgrind testing framework.

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Merge pull request #5683 from RosettaCommons/guangfeng/galiganddock_update2 GALigandDock update

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Merge pull request #5681 from RosettaCommons/guangfeng/galiganddock_update2 GALigandDock update

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Merge pull request #5671 from RosettaCommons/BYachnin/add_pyrosetta_interface_CMS Add getters and setters to ContactMolecularSurfaceFilter The ContactMolecularSurfaceFilter has a number of member variables that cannot be accessed or set except during construction or using parse_my_tag. Furthermore, the selectors, which are required for compute to work, can only be set by parse_my_tag. This makes using the filter cumbersome in PyRosetta. I've added getters and setters for all private member variables in the class, and also added a constructor that allows setting of the selectors directly.

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Merge pull request #5668 from RosettaCommons/vmullig/fix_t900_distributed Fix the T900_distributed PyRosetta test Tasks: - [x] Removing thread index from T900 test. - [x] Confirm that this does fix the Linux PyRosetta tests.

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Merge pull request #5666 from RosettaCommons/brownbp1/bcl_repair_mac_release_10-2021 Updated bcl_rosetta branch to include <algorithm> include in bcl_sour…

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Merge pull request #5634 from RosettaCommons/JackMaguire/InverseKin Inverse kinematics utility for calculating jumps. This PR adds a tool in core/kinematics/inverse that computes what value a given jump needs to hold in order for a set of user-defined atoms to be placed in desired coordinates

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Merge pull request #5013 from RosettaCommons/guangfeng/galiganddock_bugfix Small bugfix and updates for GALigandDock

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Merge pull request #5637 from RosettaCommons/yhsia/mergepdbmover_selector add residue_selector capability for mergePDBmover.

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Merge pull request #5602 from RosettaCommons/jadolfbr/design_restrict Bug fixes, filter logic, disulfidize improvements, etc. # Bunch of stuff in this PR, listed below: - `NamedDihedralConstraint` bug fix - Bug fix and additions to `GlycanSequonSelector` - Bug fix for excluding germlines in RAbD - Added `sort_scorefxn` option to Disulfidize - actually sort them and not just give you random ones that were found. Added option to _actually_ _keep_ current disulfides. Fix a bug so that without this option, actual random ones are given using shuffle. Update docs. - Added `TrueFalseFilter` to enable control-flow of RosettaScripts using script_vars - which is true or false on-the-fly - Added `logic` option to `CompoundStatement` to use instead of subelements. Simplifies use. - Enable filter logic across RosettaScripts through the `find_filter_or_die` function. This is similar in nature to Selector logic across RosettaScripts. - Add `detect_disulfides` option to `DeleteRegionMover` which when false will not 'redetect and probably destroy' designed disulfides. - Add `logic` option to IfMover to allow more complex behavior: -- Parse logic as `if x : y else z` This corresponds to filter_name,true_mover_name,false_mover_name. Use null for do nothing. not is also accepted so - if not x : y else z -- Added control-flow directly within IfMover using a 'value' option that interprets a '0' or '1' as a TrueFilter or FalseFilter to allow script_vars control flow (awesome idea from @ajasja 's to save some declaration of the TrueFalseFilter.) - `SequenceMover` is now RosettaScriptable. `RandomMover` now has the option of repeats for each mover, allowing probabilistic repeats. - Add `dir` option to dumpPDB mover. Use the PDBInfo name if set to prefix the output PDB that is dumped - this enables it to be a lot more useful. - Add a few functions here and there that are tested and will be used in future PRs. # Tests An integration test covers parsable logic, rosetta-scripts parsable components, parsable control-flow.

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