Merge pull request #3406 from CyrusBiotechnology/delucasl/write_seqres
From @decarboxy at Cyrus:
optionally output SEQRES lines in PDB files
This PR extends the pdb outputter to produce SEQRES records.
This feature is off by default and can be turned on with -out:file:write_seqres_records
also added a test that exercises the feature. No integration test changes expected.
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Merge pull request #3410 from RosettaCommons/smlewis/PR_patterns
At PRC Day 2, I promised that @weitzner and/or I would write up our standards for PR review. We said we'd put it in the README. We changed our minds, because the README is an obvious target for end users looking for compiling and use documentation, so instead I added it to the https://www.rosettacommons.org/docs/wiki/internal_documentation/GithubWorkflow page and improved the link from here.
I am going to go ahead and merge this on the expectation that most further modifications are to the wiki not the README - but edits here are cheap, so feel free to open another README PR as necessary if there is further comment.
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Merge pull request #3405 from RosettaCommons/roccomoretti/IG_size_debug
Switch interaction graph size output to debug tracer level.
There's little a non-expert user can do with the raw size value. Make it available with a debug-level tracer, but put a more user-actionable message for high IG memory usage. (Set arbitrarily at 25 MB)
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Merge pull request #3403 from CyrusBiotechnology/indigo/argobody_fix_outlier_bug
Antibody grafting, database blast outlier exclusion list, add H3 and orientation
This add 2 lines of code to protocols/antibody/grafting/scs_functor.cc
For the antibody grafting app, blast search of pdb templates can be modified by giving an input list of "oulier" pdbIDs to ecvlude for the search of templates to graft from. The ability to exclude outliers for H3 and orientation was left out of the code (not sure if this was an accident). With this PR, H3 and orientation graft outliers are excluded if and only if you add the corresponding H3 and orientation -specific lines to your outlier list file. This does not change any defaults, but adds the ability to exclude templates for H3 grafting too.
From Cyrus from @indigogo
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BindingSiteConstraint bugfixes
1. site_constraint is an orphaned ScoreType. BindingSiteConstraint is a functioning constraint that uses atom_pair_constraint as its ScoreType, but optionally uses whichever ScoreType you request. I have added site_constraint to the list in ConstraintsEnergy so that you may use site_constraint with BindingSiteConstraint.
2. BindingSiteConstraint's Tracer was mislabled (copy paste error)
3. BindingSiteConstraint's clone() function was missing an argument in its dispatch to the copy ctor and thus forced cloned copies into the default ScoreType instead of an assigned ScoreType.
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Merge pull request #3375 from RosettaCommons/smlewis/fix_noe_assignment
should fix unstable noe_assignment itest by grepping out the offending log lines
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Merge pull request #3381 from RosettaCommons/vmullig/eliminate_std_rand
Removing an instance of std::rand in protocols, and updating a function signature to pass a vector by const reference instead of by copy.
Flipping tests flip (the same integration tests that changed in the revision in which I did nothing but beautify). No other test changes observed.
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Merge pull request #2573 from RosettaCommons/vmullig/refactor_parametric_code
Refactor the Parametric code
Merged from my phone. This somehow feels wrong...
This will simplify the code considerably, and make it easier to add additional parameters or new parameterizations. It will also simplify the parameter-space minimizer that I have working in a branch (and which I really need to get back to at some point).
Tasks:
- [x] Add a Parameter abstract base class.
- [x] Derived classes for Real, Size, or Boolean-valued Parameters.
- [x] Store parameter name, type, value.
- [x] Setters and getters for these.
- [x] Value-parsing functions.
- [x] XSD functions.
- [x] Serialization.
- [x] Ensure that default values can be specified (e.g. 1.0 for `epsilon`).
- [x] Add means of copying parameters.
- [x] Have this do something.
- [x] Override the default "copies_from" to say "copies_helix" (_e.g._ "r0_copies_helix").
- [x] Special case of omega -- add means of copying pitch.
- [x] Means of converting degrees->radians.
- [x] Ensure that sampling and perturbing options are reset before storing in the Conformation.
- [x] Add a ParametrizationCalculator abstract base class.
- [x] Add a BundleParametrizationCalculator class.
- [x] Tie in to MakeBundleHelix mover.
- [x] Tie in to MakeBundle.
- [x] Add default BundleParametrizationCalculator, and have it parse its options.
- [x] Have the individual helix BundleParametrizationCalculators start off as clones of the default one (with cloning _after_ setup).
- [x] Have them then override their options by parsing sub-tags.
- [x] Check MakeBundle function (existing tests).
- [x] Think about non-RosettaScripts interface, too. (What if defaults are set _after_ individual
helices?)
- [x] Fix the helical_bundle_nonideal integration test. (The second pose should be identical to the first. There's currently a problem with the bundle symmetry option in degrees mode.)
- [x] Tie in to PerturbBundle.
- [x] Deprecate PerturbBundleOptions class.
- [x] Simplify PerturbBundleHelix mover.
- [x] Simplify parse_my_tag().
- [x] Simplify apply().
- [x] Simplify perturb_values().
- [x] Check tests.
- [x] Simplify XSD function.
- [x] Tie in to BundleGridSampler.
- [x] Check tests.
- [x] Update parametric design GUI.
- [x] Refactor the BundleParameters class to reduce the hardcoding of parameters.
- ~~Maybe deprecate the BundleParametersSet class, too.~~ --> No, I like having a specialized class for this. _Right now_ it's not doing anything special, but it could conceivably in the future, and I don't want to have to subclass at that point.
- [x] Fix integration test failures-to-run.
- [x] Debug pitch copying with perturbation. It's currently not working.
- [x] Check pitch copying with the BundleGridSampler.
- [x] Check integration test changes.
- [x] Debug changes seen when delta_t is nonzero.
- Caused by ambiguity in rotation direction for beta-strands with omega1 ~ 180 degrees. Not a big cause for concern, though integration tests have been updated.
- [x] Fix unit tests.
- [x] Check `perturb_helical_bundle` integration test failure. It was the only one showing a real failure, and I think I've fixed it, now.
Put off to another pull request:
- Fix the longstanding residue vector problem in the Parameters object.
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