Fixing a typo in the cis/trans torsion bin mapping that made torsion-restricted sampling crash. Also re-enabling the rama2b flag in the NGK integration test - now with the reduced memory usage (thanks Andrew!) this can be tested on the server. Torsion-restricted sampling and next-generation KIC integration tests will change. No other changes expected, other than already-failing candidates.

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Adding option superimposed to splice. Normally it is set to true. If false, the XML is expected to provide source_pdb_from_res and source_pdb_to_res during splice_out and splicing will be done between these and the template's from_res to_res. Coordinate restraints and rmsd calculations will be shut off in this case and only dihedral restraints and chainbreak will be evaluated.

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continuing fixes to compile_all_headers, gccdebug build, unit tests, etc. Helped a lot to have new commit-testing server from Sergey! In the future, that server will allow all tests to be run on branches, and should prevent these kinds of iterative fixes (which are not reproducible locally for me). There may still be an issue in pyrosetta build -- working on it.

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continuing fixes to compile_all_headers, gccdebug build, unit tests, etc. Helped a lot to have new commit-testing server from Sergey! In the future, that server will allow all tests to be run on branches, and should prevent these kinds of iterative fixes (which are not reproducible locally for me). There may still be an issue in pyrosetta build -- working on it.

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Unused parameters in Rhiju's code

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In some cases DeltaFilter doesn't need to relax the pose and record the baseline since FilterScan can do that instead. Fixing a bug that didn't allow this to happen properly in some cases. No test changes expected

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Commenting out call of ramp_score_function in the refactored loops code, since it breaks the KIC_with_fragments integration test. The following list of integration tests were failing before and are not affected by this commit: centroid_disulfide_scores membrane_relax2 torsion_restricted_sampling app_exception_handling No other test changes expected.

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trying to fix build, and also I want to test new SHA-based test server

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a testing server for branches and pull requests would prevent this -- checking in fixes for unit tests and linux debug build

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CCD: fixing severe rama check bug

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trying to remove unused parameter warning/error from debug build.

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Pushing Kale's attempt to fix the header-only build.

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cleanup/reorganization of stepwise code to prepare for rosetta dev meeting. merge from branch rhiju/swm_cleanup. integration tests checked -- all changes cosmetic or recurrent floating point deviations on my mac (e.g. in match).

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This commit adds a new loop modeling protocol to the Rosetta code-base, KIC with fragments, which combines the power of kinematic closure with sampling coupled degrees of freedom from protein fragment data. In the KIC with fragments protocol, coupled phi/psi/omega torsion angles from consecutive residues in protein fragments are used to sample all but 6 torsional degrees of freedom. Those remaining 6 phi/psi torsions are solved analytically by KIC. This combination allows for rapid sampling of large conformational spaces. The protocol is based on Kale Kundert's refactored KIC code, which provides a more flexible and more easily extendable framework than its legacy counterpart. Our current benchmark results, using the 45 12-residue loops KIC benchmark set, indicate that KIC with fragments retains the sub- Angstrom loop reconstruction accuracy of the next generation KIC protocol, while considerably outperforming previous methods in the sampling of sub-Angstrom models (median fraction of sub-Angstrom models = 33% (without using homologs during fragment generation), compared to only 13% for next generation KIC, 6% for legacy KIC and 1% for CCD). KIC with fragments can be activated for the centroid (perturb) and fullatom (refine) stages using the following flags: -loops:remodel perturb_kic_with_fragments -loops:refine refine_kic_with_fragments Fragment data can be loaded using the standard flags -loops:frag_sizes and -loops:frag_files A comprehensive documentation for KIC with fragments, incl. algorithmic details, protocol usage (such as necessary input files and available options) and a quick-start example can be found at https://www.rosettacommons.org/docs/wiki/application_documentation/KIC_with_fragments This commit also contains a subtle bugfix by Kale in KicMover that was causing chain breaks during initial loop building. That bug only affected the refactored loop modeling framework and in most cases led to reduced performance (in one benchmark case it caused the initial loop build to fail). The newly-added KIC_with_fragments integration test is expected to change. The following integration tests have already failed before and are not affected by this commit: torsion_restricted_sampling centroid_disulfide_scores No other test changes expected. NEWS: Adding a new loop modeling protocol, KIC with fragments, which combines the power of kinematic closure with sampling coupled phi/psi/omega degrees of freedom from protein fragment data.

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Updating PyRosetta dependency calculation algorithm

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Fixing Windows build

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