Merge pull request #1152 from RosettaCommons/kwikwag/peptiderive-integration-test-fix Peptiderive: remove Rosetta version from integration test Expected integration test changes: `peptiderive`

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Merge pull request #1143 from RosettaCommons/jadolfbr/antibodies/remove_creators_from_headers This moves (my) antibody task operation creators to their own file. Also makes files for sewing creators. As @aleaverfay has pointed out, TaskOp creators should be in their own file to decrease compile time of init.cc. A note has also been added to init.TaskOperationCreators.ihh

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Merge pull request #1151 from RosettaCommons/vmullig/fixbetanov15 Trying to fix failing beta_nov15 unit tests. There was a call to oneletter_code_from_aa() that didn't first check whether the AA enum passed to it was an L- or D-amino acid. This adds a check.

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Merge pull request #1150 from RosettaCommons/dimaio/fix_beta_for_d_aas A few fixes to beta_nov15 to ensure: a) L- and D-AAs are scored equivalently, and b) symmetric_gly_tables is respected for bb-dep omega.

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Merge pull request #1067 from RosettaCommons/orlypolo/peptiderive-report-reformat This adds / fixes some features in `PeptideDeriverFilter` and `DisulfideInsertionMover` - change PeptideDeriver report file format - information of peptides with cyclization potential now appears in a table of its own. - If best linear peptide has cyclization potential but is not the best cyclic peptide, will be added to the (new) cyclic peptides table - add Rosetta version info - fix a few bugs: - far away chains cause segfault - specifying partner chain which appears before a receptor chain would reverse the order - remove internal energy filtering of cyclized peptide - add `peptiderive` integration test - `DisulfideIntersionMover` unit test coverage: test `determine_cyclization_viability` - `PeptideDeriverFilter` unit test coverage: edge case of far away chains Expected integration test changes: `peptiderive` (new integration test!)

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Merge pull request #1145 from RosettaCommons/vmullig/add_betanov15_tests Add beta_nov15 tests to the sfxn_fingerprint test suite. If I'm going to start fixing problems in the beta_nov15 scorefunction, I need to be sure that I'm not introducing scorefunction changes by accident. This adds a test for the beta_nov15 scorefunction to the sfxn_fingerprint test suite.

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Merge pull request #1147 from RosettaCommons/roccomoretti/cmake_linker Make CMake builds slightly faster This cherry picks two efficiency improvements from pull request #958 1. Convert from using the python script smart_symlink.py to using the CMake-internal symlinking facility. 2. Adjust version.py not to re-write the version header if it hasn't changed. On my machine, these improvements speed up a no-change rebuild by about a factor of 3 or so. (Symlinking now takes less than a second.) The speedups also (slightly) help with normal rebuilds.

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Merge pull request #1144 from RosettaCommons/vmullig/add_betanov15_tests Add symmetric gly, symmetric scoring, and cyclic permutation unit tests for the beta_nov15 energy function **Note: this deliberately adds unit tests that fail. This is to illustrate current scorefunction failures that need to be addressed.** Talaris is now fully symmetric (i.e. mirror-image poses consisting of L- and D-amino acids score identically), fully consistent with cyclic permutations (i.e. cyclic peptides core identically no matter where residue 1 is), and has a mode in which glycine behaves perfectly symmetrically (favouring left- and right-handed conformations equally). Unit tests already enforce this for talaris and for whatever the default scorefunction is at any given time. However, the beta_nov15 scorefunction is seeing increasing use, and these unit tests do not cover this scorefunction. This pull request adds these unit tests for this scorefunction. Since the beta_nov15 scorefunction has introduced asymmetries, they currently FAIL, and will continue to do so until this is fixed. (That is, they are illustrating a current failure of Rosetta, not introducing a new one.)

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Fixing the Mac PyRosetta build.

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Merge pull request #1139 from RosettaCommons/roccomoretti/reb_pdbnum Add PDB numbering to residue_energy_breakdown and per_residue_energies output Integration test changes to residue_energy_breakdown and per_residue_energies expected (extra columns in output).

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Merge pull request #1134 from RosettaCommons/jadolfbr/sugars/debug_valgrind Fix issues identified by valgrind for (de)glycosylation Fix issue identified in carbohydrate util Unit Test Fix issue identified in simple glycosylate mover integration test

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Merge pull request #1022 from RosettaCommons/tjbrunette/fast_forward_folding Tjbrunette/fast forward folding this code introduces code to: A. Generate a structural profile fast. B. Fix the structure of short loops. C. Score centroid models with Will's motif score term. -The integration test errors are expected and due to the new energy functions -Most of the new code uses an hdf5 database so there are no integration tests to protect it because hdf5 needs a different compile then is currently being done.

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Merge pull request #1073 from RosettaCommons/aleaverfay/pose_builder_tests Rosetta will now read ACE and NME residues without needing any special flags. Changing the variant types given to the AcetylatedProteinNterm and MethylatedProteinCterm patches so that they register as LOWER_TERMINUS and UPPER_TERMINUS variants, which they are. The effect is to enable some code in the PoseFromSFRBuilder that has been laying in wait. Now, when Rosetta encounters an ACE residue on the Nterm of a chain, it will take the atoms for that residue and append them to the next residue, which will end up patched with the AcetylatedProteinNterm patch. NOTE: we have two ACE patches in rosetta when we should really only have one. "N_acetylated" and "AcetylatedProteinNterm". The more commonly used patch is "N_acetylated". It, however, has a different set of backbone torsion angles than the one defined by "AcetylatedProteinNterm". The same applies for the "C_methylamidated" and "MethylatedProteinCterm" pair. We should rapidly decide how we are going to eliminate one of the two ACE patches and one of the two methylamidadtion patches, as duplication is the devil.

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Merge pull request #1112 from RosettaCommons/aleaverfay/fix_sp3acc_discontinuity Reformulating the chi penalty for sp3 acceptors to fix a discontinuity. The "chi" dihedral for sp3 acceptors is defined by the four atoms: Hdon -- Acc -- Acc Base -- Hacc where "Hacc" is the hydrogen chemically boudn to the acceptor (but which is not participating in the hydrogen bond). On serine, for example, Acc would be "OG", Acc Base would be "CB" and Hacc would be "HG". With the Talaris2013 score function, we added a penalty based on chi for sp3 hybridized acceptors that had not been present in score12. In score12, the "BAH" angle was measured with respect to Hacc, and it was assumed that the lennard-jones term would push the Hdon atom away from the Acc Base atom. This resulted, however, in rather funky geometries if you looked at the Acc Base--Acc--Hdon angle. What measuring the BAH angle wrt the Hacc atom did accomplish, however, was avoiding geometries where Hdon and Hacc were very close. In the Talaris2013 score function, we define the BAH angle wrt the Acc Base atom. To make sure that Hdon and Hacc did not get too close, I also added in a penalty that dependend on chi and only chi. Of course this penalty had a discontinuity when the BAH angle hit 180; I was aware of the discontinuity, but thought it would not be disruptive. After Talaris2013 became the default score function, the degree of its disruptiveness became apparent. To remedy this problem, I worked with Frank off and on with a "soft-max" function to take the worse of two scores: one defined by the BAH angle and one defined by the Hdon -- Acc -- Acc Base angle, but we have not smoothed out all of the edges on this formulation. The fix in this commit defines the "chi" penalty for sp3 hybridized acceptors to also respect the BAH angle in order to avoid a discontinuity at BAH=180. It is not necessarily the best formulation, but it does fix the discontinuity and the derivative discontinuity, and thus should fix the common cases of "inaccurate G!" that shut down minimization. This is a stopgap. The softmax potential will be much more useful and smooth and generally better than this ugly thing. It's a work in progress, however, and this is easy to bring online. This will effect everyone who is using talaris2013 and talaris2014. I am bumping the score function revision ID so the "score function fingerprint" test will change. You should note that the score function in master is changing.

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Merge pull request #1140 from RosettaCommons/vmullig/fix_macrocycles Trying to fix the macrocycles integration test The app has a while( !closed ) loop that can potentially loop forever. I think that my changes didn't actually break the app -- they just altered the trajectory so that it no longer converges in the time limit for the integration test. This is a temporary workaround that causes the app to break out from that loop if a maximum number of iterations for loop closure is passed. (Incidentally, please don't ever close a loop like this in a real instance! Use GenKIC, CCD, or anything else -- it'll definitely be faster!) @everyday847

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Merge pull request #1137 from RosettaCommons/vmullig/fix_resarrayannealeval Adding an escape check to the initialize() function of the ResidueArrayAnnealingEvaluator so that it doesn't try to do expensive rotamer setup steps if nothing is going to use them.

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