Merge remote branch 'origin/master'

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further fix of bug in jump sampling for RNA denovo. output of rna_denovo filters when they are note passed. Added -extra_minimize_chi_res option to allow flexibility of ligand in RNA puzzle.

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Added cmake Werror check to integration test

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fixing bug in rna_denovo where chain_connections jumps were not sampled if connected residues were in rigid segments. big problem in rnapuzzle12 modeling!

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Fixing a bug that can cause full atom only Docking to ignore constraints. Two integration tests change as a result of caching the constraints to the pose before converting it to the full atom representation. These tests are: 1) docking_distance_constraints 2) docking_site_constraints The scores and final coordinates of the decoys that are produced by these tests remain unchanged. I observed changes in two matcher tests that resulted from swapping HIS with HIS_D. This is a weird things that seems to occur sporadically (at least on my system), and it is unlikely that these tests will change on the test server. I wonder if there is anything we can do about that because it's not great to ignore changing integration tests. Big thanks to BK for discovering and reporting this bug.

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Limited the number of allowed rotamers to pack in Splice in

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Merge branch 'master' of github.com:RosettaCommons/main

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Created TrajectoryReportToDB to enable use of the features reporter system for trajectory output TrajectoryReportToDB is a child Mover of ReportToDB, meaning most of its functionality is the same as ReportToDB (e.g. any existing features reporter can be used with it). The new behavior is that the class counts how many times each pose (identified by JD2 output tag) has been "applied" in the features reporter system. A new table, "trajectory_structures_steps", keeps track of which step iteration a particular struct_id represents. Struct_ids can be grouped from the same output by using the existing tag field. The mover has also a stride option to control how often features are reported. The mover works in Rosetta Scripts, and could be particular useful as part of a parsed protocol that is called multiple times, as in the generic monte carlo mover. In the process of creating this class, I refactored some of the other database and features code, but behavior should be unchanged. I also removed SZ_MAX from core/types.hh, as it was causing an unused variable warning/error on my system, preventing compilation. This commit merges branch kylebarlow/general_dev into master Expected test changes: features: test now uses new reporter features_database_schema: new mapping table ligand_dock_script: numerical instability

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decided to not have rna_chem_map_lores term on during fragment assembly by default, based on benchmark runs.

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Added tarcer messages to Splice.cc

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Fix signed compare errors that were breaking the build.

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Fix performance benchmark (ContextDependentGeometricSolEnergy) ContextDependentGeometricSolEnergy was using the HBondSet but not generating it. This results in issues when run in a Scorefunction with only those energy terms and no HBonding terms. Add cautious generation of the HBondSet in the setup function (along the lines of the HBond terms). No test changes expected.

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another merge from my branch rhiju/dms_score, which introduces rna_chem_map_lores score term. This allows chemical mapping data to guide fragment assembly, and is being tested in the RNA puzzles blind trials. Integration tests show changes in KIC_refine, SnugDock, antibody_H3, and a few other tests that look like floating point deviations. This has happened to me before when I update ScoreType.hh -- I will pay attention to whether there is an effect on the test server...

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Fix uninitialized variable in DdgFilter This was was giving us the intermitant DdgFilter unit test failures. No other test changes expected.

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Renaming core::scoring::getScoreFunction to core::scoring::get_score_function This function violates our naming conventions, so I'm fixing it along with getScoreFunctionLegacy. Also fixing a bug in core/membrane/io/SpanFileIO.cc which was producing unit test failures.

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