Merge pull request #1695 from RosettaCommons/vmullig/eccentricity2
Add a parameter to the Crick parameters to allow lateral sqash of bundles or beta-barrels
The old pull request branch was branched off of master with the toxic commit. I've re-pulled (removing the toxic commit), created a new branch, and cherry-picked all of my changes from the old.
Tasks:
- Add the parameter to functions in numeric.
- Add arclength correction factor (t->t' s.t. int(0->t')(|f'(x,epsilon)|dx) = int(0->t)(|f'(x,epsilon=1)|dx)) This is very hard to compute, but as it turns out, the correction factor is negligibly small.
- Add correction factor in numeric to normalize the path tangent vector.
- Update protocols/helical_bundle/util.cc/hh.
- Update MakeBundleHelix mover.
- Update PerturbBundleHelix mover.
- Update MakeBundle mover.
- Update PerturbBundle mover.
- Update BundleGridSampler mover.
- Update BundleGridSamplerHelper class.
- Update BundleParameters class.
- Update BundleParametersSet class. Nothing to update.
- Update PerturbBundleOptions class. Nothing to update.
- Update test_makebundle_mover pilot app.
- Integration test.
- Documentation.
- Beauty.
(Note: at some point, I'll properly set things up so that the parametric movers don't need to be updated whenever a new parameter is added to the generating equations. When I initially implemented this, I failed to anticipate the need for this.)
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Merge pull request #1719 from RosettaCommons/vmullig/reinstante_mainchainscoretable
Reinstate the merge of the MainchainScoreTable class
I think I solved the gcc/release issue. A call to ceil and a cast from float to int were occasionally resulting in the wrong bin being chosen (e.g. 180.0 -math-> 18.0 -ceil-> 19.0 -static_cast-> 19 instead of 18); I don't know why this created an issue only with gcc and only in release mode. But in the context, round made more sense than ceil, and this resolves the scoring issue and preserves old scoring behaviour.
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Merge pull request #1707 from RosettaCommons/roccomoretti/no_using
Dis-ab-using Rosetta headers
Our coding conventions state that we shouldn't use `using namespace` in the top level of header files. There's a good reason for this: `using namespace` in a header file doesn't just affect that header file, it also affects all subsequent header files and cc files. (Even if the two headers don't directly include each other, but are instead mutually included in a third file, the using declaration from one can change how the other header is parsed.) I'd even go one further: a non-namespace `using` directive in headers is also a bad idea, unless you're explicitly attempting to hoist a symbol from one namespace to the other. (So no using declarations just because you don't want to type "core::" in front of everything.)
This pull request removes all `using namespace` from the headers in src, as well as all the convenience `usings` (usings which looked to me to be namespace hoistings were left.) A new integration tests was added, which should fail upon the introduction of a `using namespace` or `using` in the top level of headers. (There's an ignore mechanism for the hoisting usings.)
`using`s and `using namepace`s are still permitted in *.cc file, as well as within classes and functions within header files (as the effect is scope limited). I also did not touch the apps/pilot/ or devel/ directories, and the integration test ignores those.
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Merge pull request #1716 from RosettaCommons/vmullig/split_ppi
Split the ppi_v3 integration tests to prevent test server failure
The ppi_v3 integration test has been failing to complete for months, which trains developers to ignore integration test failure-to-run errors. I'm splitting this test up into several tests, each of which runs in a reasonable amount of time.
(To clarify: ppi_v3 applies a few movers, than tests a large number of reporter filters, some of which take a while to calculate what they measure. I'm splitting this into ppi_v3_suiteA, ppi_v3_suiteB, etc., and ensuring that each suite applies all of the movers and a subset of the filters, so that all of the filters are tested, albeit in several small integration tests instead of a single large one.)
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Merge pull request #1718 from RosettaCommons/vmullig/temporarily_revert_mainchainscoretable
Temporarily reverting merge of MainchainScoreTable class while we debug gcc release build
Reverting merge of MainchainScoreTable class temporarily while I figure out what the gcc issue is.
Details: It seems that there's a gcc-specific scoring bug that crept in, possibly with this merge. It does NOT alter scoring in debug mode or in any clang release compilation. Only the gcc 4.8 release-mode compilation is affected, and it results in RamaPrePro returning NaN for most poses. It's some sort of weird compiler optimization thing that we haven't yet tracked down, but in the interests of keeping master functional, I'll do the detective work in a branch.
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Merge pull request #1715 from RosettaCommons/JWLabonte/sugars/PyRosetta_scripts
Carbohydrates/PyRosetta: fix to PyRosetta demo/test for carbohyrdates
If this doesn't work, we'll try something else....
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Merge pull request #1701 from RosettaCommons/tlinsky/tomponents_multi_bulge
Add BuildDeNovoBackbone mover support for multiple bulges per strand
The cyclic peptide integration tests failed upon testing, but should be fixed now that Vikram has reverted a commit that broke them.
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Merge pull request #1712 from RosettaCommons/vmullig/revert_cart_breakages
Reverting pull request 1699 due to breakages of simple_cycpep_predict tests.
@BrandonFrenz: Fix these test breakages in your branch, test on the test server, and then re-merge with master.
And the community as a whole needs to start paying more attention to the test server. We had green lights across the board for some time, but now we're starting to ignore breakages. It is NOT a developer's responsibility to keep re-fixing his or her features that someone else has broken, IF those features are covered with tests. It is the rest of the community's responsibility to make sure that they don't break tests.
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Merge pull request #1635 from RosettaCommons/JWLabonte/sugars/scoring
Carbohydrates: Updating sugar_bb term to score additional linkage types
This merge introduces two new CHI Energy Functions (from http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00834) to the `sugar_bb` scoring term for the scoring of exocyclic ψ angles. It also adds two simple parabolic functions to the `sugar_bb` term for the scoring of exocyclic ωs, depending on whether the gauche effect is in play or not. These changes should improve the scoring of sugars.
This merge also refactors some lengthy code to remove code duplication, adds some C++11 simplifications, and has fixed several silent bugs. A whole bunch of integration and unit tests were added.
carbohydrates, vancomycin, and simple_glycosylation integration test changes are expected.
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