Merge pull request #602 from RosettaCommons/roccomoretti/test_run_errorcheck Improve error handling on unit test runs. Error reporting when, e.g. the unit test applications were miscompiled, was poor. This commit provides better diagnostic output. (Error messages are no longer treated like test lists.)

• Summary

Updating performance benchmark test plot metadata so it uses ‘cycles’ instead of run_time for graphs

• Summary

Fixing performance tests, adjusting C++ code so it save results for each test into dict object instead of array. Changing benchmark.py script so it no longer tries to save results in hidden files.

• Summary

Merge pull request #589 from RosettaCommons/everyday847/performance_tests Make performance tests run for a fixed time

• Summary

Merge pull request #593 from RosettaCommons/roccomoretti/remap_pdb_atom_names_fixes Small fixes for -remap_pdb_atom_names_for Fix bug with handling multi-letter element names (e.g. Cl) Change the scoring to penalize chirality mis-matches rather than favoring chirality matches. (Changes how matches are scored when they contain different total numbers of chiral atoms.)

• Summary

Merge pull request #600 from RosettaCommons/phbradley/repeats_demo add a new pilot app that demos how to set up a tandem repeat protein for symmetrical connected-chain folding

• Summary

Merge pull request #597 from RosettaCommons/JWLabonte/PyRosetta_vector1s PyRosetta: adding vector1< Edge > This merge adds a wrapper in PyRosetta for `vector1< Edge >`. Thanks to @lyskov for showing me how to do this. Shout-outs: @mlnance @mpacella88 :rat:

• Summary

Merge pull request #598 from RosettaCommons/dougrenfrew/fix_mm_std_fa_elec_dslf_fa13_split_unfolded_score_test fixing the mm_std_fa_elec_dslf_fa13_split_unfolded_score test

• Summary

Merge pull request #594 from RosettaCommons/rhiju/fa_stack_ext Rhiju/fa stack ext Introducing potential energy function fixes for 'over-stacked' RNA conformations: • fa_stack_sol: penalty for desolvating water stacked on nucleobases • fa_stack_LR: an even more long-ranged bonus for water-mediated stacking of atoms on nucleobases. • Shape and depth of these potentials partially calibrated based on PMF of water around adenosine, computed through Amber MD calcs by @fcchou, @sripakpa, and K. Beauchamp in my lab. • Not yet checked on benchmark cases.May help 'solve' at high resolution: UUCG loop (which always overstacks the G, leaving an internal void) 1CSL rev RRE element (whose lowest energy solution brings a bulged nucleobased into the helix, leaving a weird void) T-loops, which always collapse a pocket that should accept a separate intercalating base. • Have not put in derivatives of new terms. Tests on motifs above & putting in derivs might be of interest to @calebgeniesse or @kkappel1 later in the summer.

• Summary

Merge pull request #595 from RosettaCommons/everyday847/expose_my_work_to_pyrosetta Factor out my indel modeling app into a protocol

• Summary

Merging additional deduplication into master

• Summary

Merge pull request #587 from RosettaCommons/benchmark Adding support for *.ignore files in score and integration tests. Adding examples of usage. Updating code_duplication so it now filter Simian output from line numbers and save raw logs in raw_simian_log.ignored file.

• Summary

Update hbs_dock_design.cc In the process of the pilot apps merge I had executed earlier, somehow an old version of hbs_dock_design snuck in...

• Summary

Merge pull request #584 from RosettaCommons/rhiju/residue_type_set_remove_nonconst Rhiju/residue type set remove nonconst Step along the way to more elaborate pull request (https://github.com/RosettaCommons/main/pull/591).

• Summary

Merge pull request #580 from RosettaCommons/tlinsky/ssprediction_to_protocols Move SSPrediction filter to protocols, since it is widely used and stable

• Summary

Merge pull request #566 from RosettaCommons/vmullig/reference_pose Creates a means of tracking changes to residue indices as residues are added or deleted The goal of this pull request is to create a means of tracking changes to residue indices as residues in a pose are added or deleted. The usage case is as follows: a user wants to write a protocol (e.g. in RosettaScripts) in which he or she calls a mover that appends or inserts residues in a pose, and then wants to call a mover that operates on inserted residues or downstream residues. Unfortunately, the first mover could insert a variable number of residues, making it impossible to pass exact indices to the second mover at scripting time. The solution is to implement something that can take a snapshot of a pose, then track where residues are added or removed, associating the residue indices of the modified pose with residue indices of an initial pose. This implements the following: -- Adds ReferencePoseSet class (a container for multiple named ReferencePose objects, with hooks for retrieving them by name). -- Poses now store an owning pointer to a ReferencePoseSet. This adds almost no memory overhead if reference poses are not used in a protocol. -- Adds a ReferencePose class (a class for storing the association between residues currently in a pose and residues that were in a pose at a point in the past). -- Adds unit tests for the above. -- Adds the StorePoseSnapshot mover, which creates a ReferencePose based on the current state of the pose and adds an owning pointer to it to the pose's ReferencePoseSet. -- Modifies MutateResidue to use reference pose indices should the user indicate that this should be the case (this will serve as a demo for how to modify movers to permit users to use ReferencePoses). -- Modifies the add and delete operations in the Pose class so that any mover adding or deleting residues automatically updates any ReferencePose objects that are present. -- Modifies the PDB numbering parse logic so that any Rosetta mover that takes residue numbers and parses them using the PDB numbering logic can also parse residue numbers based on a reference pose. (That is, a user could specify, "17", "5B", or "16_refpose1" to refer to residue 5 of chain B, the 17th residue of the pose, which corresponds to the 16th residue of some reference pose). -- Adds an integration test for a RosettaScript involving a StorePoseSnapshot mover, a mover that modifies pose length, and a mover that refers to a residue in the ReferencePose. -- Documents these changes, for users. -- Documents these changes, for developers. X Modify GeneralizedKIC to use reference poses. -- Put off to a future pull request.

• Summary

Legend: