Merge pull request #3913 from RosettaCommons/jadolfbr/glycan_no_inner
This merge holds a few changes and bug fixes for glycan modeling, antibody work, and simple metrics. Nothing too major.
1) Remove `AntibodyDesignProtocol`; make AntibodyDesignMover's parser interface more feature-complete with the command line. This simplifies the antibody design code into a single main mover, instead of two of them. Features from the protocol that were useful are added to the mover. Support for `get_additional_output` functionality is added. Removed some unused options.
2) Remove inner bb sampling from glycan modeling. This resulted in better energies, but reduced control of sampling time. Removing it.
3) Adding author tags to my parsable classes as we are moving towards full XSD documentation of most classes.
4) Make the `TotalEnergyMetric` work for different size reference poses as was originally intended.
5) Make a few carbohydrate tools into public apps as they are tested and now have public-facing documentation.
6) Simplify/Clean up Mover interface. No code changes, only the presentation and organization of Mover.hh as it was a mess. I can now read it. We really should remove the JD1 stuff from the base-class at some point. Perhaps through integrated DataMap functionality in the Mover base class?
7) Add better documentation for reference_pose XSD, instructing the user that this is created via a `SavePoseMover`.
8) Fix `RestrictToCDRsAndNeighbors` task op for camelid antibodies. Add unit tests for this and other antibody task ops for camelid antibodies.
Merge pull request #3870 from RosettaCommons/roccomoretti/silence_recon_mpi
Fix recon_design_mpi.
Add the appropriate flags such that it's no longer a permanent diff.
Merge pull request #3797 from RosettaCommons/jadolfbr/sm_in_pyrosetta
This Address #3777 - getting SimpleMetrics to work seamlessly in PyRosetta
This PR makes `pose.scores` work by accessing the `ScoreMap` 'class' directly instead of individual extra scores functions. Unit tests for this functionality are added to the PyRosetta unit testing framework, as well as additional tests for SimpleMetrics in C++ testing framework. The `ScoreMap` itself is now unit tested to work with SMs and an additional clear function has been added to the `SimpleMetricData` class.
This PR also deprecates the old-style PyRosetta score file, which was ALWAYS bad and too different from C++ Rosetta scorefile output to be of much use in general protocols. If one tries to use the old-style format, we exit with a helpful message.
Merge pull request #2468 from RosettaCommons/JWLabonte/PDB_IO
PDB IO: Title Section IO
Following an idea/request from @cdbahl at RosettaCON 2017, I have added functionality for automatically adding a time stamp and Rosetta version number to all output `.pdb` files. The default output uses proper/standard/PDB-defined records, _e.g._:
```
HEADER 21-FEB-19 XXXX
EXPDTA THEORETICAL MODEL
REMARK 220
REMARK 220 EXPERIMENTAL DETAILS
REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING
REMARK 220 DATE OF DATA COLLECTION : 21-FEB-19
REMARK 220
REMARK 220 REMARK: MODEL GENERATED BY ROSETTA
REMARK 220 VERSION 2019.04.post.dev+165.HEAD.646026d
```
This way, one will always know whence a `.pdb` came, and it will lead to better reproducibility of results.
One could also easily adapt this system, using JD2 or JD3, to automatically include specific protocol information to the file.
This merge will also allow input and output of `AUTHOR` records:
```
HEADER 21-FEB-19 XXXX
EXPDTA THEORETICAL MODEL
AUTHOR LABONTE
```
To include a list of authors, simply use the option flag `-set_pdb_author` with a comma-delimited list of names, according to the PDB format:
```
-set_pdb_author "I.M.A.JUNIOR JR.,I.HYPHENATE-MY-SURNAME,LABONTE"
```
If integration tests are running, the system automatically outputs the date as `xx-MMM-xx` and the version number as `INTEGRATION TEST` to ensure that integration tests do not fail every time from the changing date and version output.
This merge also corrects some bugs in `HeaderInformation`.
All unit tests pass.
Almost every single integration test changes, as every `.pdb` file now has a default title section prepended. I have looked through about 10% of the >400 tests and did not find any unexpected changes.
Likewise, 5 score tests are changed and 2 mpi integration tests.
Merge pull request #3819 from RosettaCommons/vmullig/fix_bg_yet_again
Fixing Blue Gene compilation. Minor change to an included file's path. Might fix compilation on certain other systems, too. (Note that this is not a BG-specific change. This corrects an incorrect path; other systems were largely _robust_ to the incorrect path, but some might not be.)
Merge pull request #3799 from RosettaCommons/jadolfbr/iam_bugfix
General bug fix from an email - IAM is now chain order independent as of sometime not too long ago. This is now reflected in both `RosettaAntibodyDesign` and Antibody Modeling to protect against failures arising from chain order.
Merge pull request #3742 from RosettaCommons/sergey/f2
Refactoring main unit test script, adding time measurements for TestSuites, removing mentioning of `YAML` to reduce confusion