commit 6dc40c1f5316b6b996e46326015a29753c09cc76
Merge: 56d7835 22ec427
Date: Sun Apr 22 20:27:40 2018 -0700
Merge pull request #3118 from RosettaCommons/fordas/cmake_extern_extras
Update cmake build configuration to disable extras-enabled-externals.
commit 56d7835560f1ff19cbe847f756dfbaa708db5b59
Date: Thu Apr 19 15:30:00 2018 -0400
RosettaAI: Setting pyrosetta_scripts submodule to latest origin/master version.
commit 32367fe0473d0b8c0afe9686e1e68310f5dde863
Merge: c2997f6 ecd6bcf
Date: Wed Apr 18 09:26:48 2018 -0600
Merge pull request #3129 from RosettaCommons/sergey/binder
PyRosetta update: porting Binder PR44 to `build.py` so LLVM is now installed from source-download instead of Git-clone (this should save ~3Gb of disk space). Thanks to @asford for prototyping this!
commit c2997f6a23cbb5cc3269aec7860661c31cc84746
Merge: 034378f e0de4ef
Date: Tue Apr 17 23:51:31 2018 -0700
Merge pull request #3124 from RosettaCommons/kkappel1/benchmark_RNP
RNA-protein ddG calculations. All integration test changes are expected due to new score terms and a new energy method option.
commit 034378f153c9528d1adbeeb386770a453fc0135a
Merge: 7eb68bf dda1ed1
Date: Tue Apr 17 10:46:37 2018 -0500
Merge pull request #3119 from RosettaCommons/jadolfbr/simple_metrics
Fix SimpleMetric integration tests
Fix the simple_metric_filter and simple_metric_features integration tests.
Remove the IntegerMetric code after Rocco's excellent points.
commit 7eb68bf83829435f3b3d3ff1a517800f7a9e5bf8
Date: Mon Apr 16 18:49:45 2018 -0400
updating mpi_fraction_outputters default
commit a476c8ad359dbf959aed76d7087e585112a1af84
Merge: 874151f 18b1232
Date: Mon Apr 16 13:07:10 2018 -0400
Merge pull request #3111 from RosettaCommons/MelanieAprahamian/HRFMSLabeling
burial_measure_centroid Integration Test fix
commit 874151f1b92297c4da52783df566e5a76619bc44
Date: Sun Apr 15 20:46:10 2018 -0400
RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.
commit 20f7dd5e99235fc7c90979f0db167faa56a9d23e
Merge: 38d3500 f68618a
Date: Sun Apr 15 13:58:05 2018 -0600
Merge pull request #3123 from RosettaCommons/benchmark
Fixing Python-3.* local install issues in Benchmark scripts
commit 38d3500a798f694848c6747a07f7419877869e17
Merge: 7f8c35c ff67908
Date: Sat Apr 14 13:53:23 2018 -0600
Merge pull request #3122 from RosettaCommons/everyday847/reduce_default_outputter_fraction
Reduce default on -jd3:mpi_fraction_outputters. @vmullig i am tagging you in case you used this option default during Blue Gene runs.
commit 7f8c35c9d7adf8483c35a025e123650df04f1e3f
Merge: 4efedae ce27190
Date: Fri Apr 13 00:02:07 2018 -0700
Merge pull request #3117 from RosettaCommons/everyday847/noncanonical_bp_constraints
Base pair constraints for noncanonical residues
commit 4efedaea87dba1e56c4739b48992e65c67df1cf4
Merge: d03d37f d210c7d
Date: Fri Apr 13 00:01:36 2018 -0700
Merge pull request #2950 from RosettaCommons/everyday847/erraser2_wip
More erraser2 stuff
commit d03d37f790f1f27558deece0467d4efc83f9485c
Merge: 7af6bf7 d37823a
Date: Thu Apr 12 14:10:37 2018 -0700
Merge pull request #3108 from RosettaCommons/danpf/static_fix
Danpf/static fix
commit 7af6bf748d149b72f985d82cb1314cf1cf70a3f5
Merge: 4942466 14c394f
Date: Thu Apr 12 15:16:34 2018 -0400
Merge pull request #3091 from RosettaCommons/JackMaguire/MCHBNetCorrection
Removed overkill utility_exit_with_message() from MC HBNet
When writing MC HBNet, I apparently thought that the reasonable way to handle the lack of results from a single instance of the mover is to kill the user's entire rosetta_script run. This PR changes this so that the mover just prints a message and returns 0 results, letting the other trajectories continue.
Thanks to Vikram for reviewing!
commit 4942466c12fa0449db59899c52aa52b1bdb30a0d
Date: Thu Apr 12 01:17:04 2018 -0400
beautifying
commit d3e04ebaf4c972e77cdfdde12e8cb3c8d6441a83
Merge: e00b011 8071e7d
Date: Wed Apr 11 23:04:56 2018 -0600
Merge pull request #3115 from RosettaCommons/benchmark
fixing release and code_quality scripts
commit e00b011a5b6139907878d4444dd2515cf5b37526
Merge: 951fe3c c8926b9
Date: Wed Apr 11 21:06:00 2018 -0700
Merge pull request #3112 from RosettaCommons/everyday847/update_lores_potential
Initial merge from a branch for updating the lores potential -- just cleans up code
commit 951fe3cecceeacebd33fe09dc156a30ed26cdea2
Merge: a2a2ad6 513e6f9
Date: Wed Apr 11 15:07:31 2018 -0600
Merge pull request #3077 from RosettaCommons/benchmark
Upgrading Benchmark testing scripts to Python-3.6
commit a2a2ad66dd3af596abb787dc21880d8320d9d90b
Merge: bae7fc5 4696fa9
Date: Tue Apr 10 16:11:53 2018 -0700
Merge pull request #3105 from RosettaCommons/vmullig/goto_killer
Remove a bunch of unnecessary gotos.
The only gotos remaining in Rosetta after this are in pilot apps (which we won't touch) and in `numeric/linear_algebra/rgg.cc` (which is an incomprehensible mess of gotos that nobody will ever dare to change).
commit bae7fc5e2f497d74b4d92f8acb911b233e764102
Merge: 8bf3dc5 207369e
Date: Tue Apr 10 18:18:15 2018 -0400
Merge pull request #3102 from RosettaCommons/BYachnin/global_SetupForSymmetry_option
Add option to disable setting symmetry globally during SetupForSymmetry parse_my_tag
This adds a new option, `set_global_symmetry_at_parsetime`, to the `` mover. By default (true), the current behaviour is maintained. If set to false, the global option `symmetry_definition` is NOT set, which provides greater "safety" and flexibility for when symmetry should be used. This option is not backwards compatible with all symmetric protocols, however, necessitating the need to switch back and forth.
The following integration tests are expected to fail due to new tracer output. This is entirely the expected behaviour:
integration.mpi: threefold_symm_peptide_design
integration.release_debug: crosslinkermover_tma_symm, homodimer_fnd_ref2015_memb, make_symmdef_file, minimize_with_elec_dens, mirror_symm, oligourea_design, repack_with_elec_dens, resource_database_locator, symm_disulfidize, symm_rotamer_boltzmann, symmetry_data_resource, threefold_symm_peptide_design, threefoldlinkermover_tbmb_symmetric, voids_penalty_energy_symmetry
integration: crosslinkermover_tma_symm, homodimer_fnd_ref2015_memb, make_symmdef_file, minimize_with_elec_dens, mirror_symm, oligourea_design, repack_with_elec_dens, resource_database_locator, symm_disulfidize, symm_rotamer_boltzmann, symmetry_data_resource, threefold_symm_peptide_design, threefoldlinkermover_tbmb_symmetric, voids_penalty_energy_design_symmetry
commit 8bf3dc5b1239734fc90492819d4870ab24cde743
Date: Tue Apr 10 18:00:47 2018 -0400
beautifying
commit 4441cacd03a9ff917d732a5dd48be95a7c499624
Merge: f9e0cf8 e591f11
Date: Tue Apr 10 10:51:20 2018 -0500
Merge pull request #3080 from RosettaCommons/jadolfbr/simple_metrics
SimpleMetrics for analysis, filters, and features
This PR adds **SimpleMetrics** to Rosetta, which I'm hoping will be the way we write metrics and filters going forward.
They are easy to write, easy to use and (IMO) powerful - as you can use them to analyze data, use all of them for filtering, and/or create features reporter databases. I have not rewritten all of the filters, as they do some really crazy stuff. Additionally, we can use this to revive the scientific benchmarks. These have all been tested.
Extras:
- MinMover now works with new the new MoveMapFactory in RS
- utility to define/limit RS option xsd as a vector of strings
- All simple metrics have code_templates
ToDo:
- [x] Test all code
- [x] Write integration tests
- [x] Write unit test suite
- [x] Write Documentation
# SimpleMetrics
Base Class: **SimpleMetric**
Main SubClasses:
**RealMetric**: Returns `Real`
**StringMetric**: Returns `string`
**CompositeRealMetric**: Returns `map< string, Real >`
**CompositeStringMetric**: Returns `map< string, string >`
## SimpleMetric code
- `core/simple_metrics`
- `core/simple_metrics/metrics`
- `protocols/analysis/simple_metrics`
The two main methods of these classes are ` calculate( const & pose ) const` which returns a value (listed above), and `void apply( & pose, prefix="", suffix="") const`, which runs calculate and adds data to the pose.
- `calculate( const pose )` : The calculate method is basically the only method you will need to code in your derived simple metric. The value depends on the type of subclass you are deriving from.
- `apply( pose, prefix="", suffix="")` : This method adds the data to the pose as setPoseExtraScore so EVERY metric can be easily output into the score file. This apply method is defined in each main class, **so you do not need to write it and can always rely on it**. The metric name that is output as the score tag is `prefix+metric()+suffix`. Additionally, each metric from a composite metric is named (the key from the map).
## Implemented SimpleMetrics
### Main
**RMSDMetric**:
- Calculate the RMSD between an input (native) or reference pose to the current pose. Accepts a `ResidueSelector`. Works for protein/ligands/glycans/etc. Can accept TWO `ResidueSelector`s in order to compare non-matching areas. More options code-wise. Many options accepted as a string to determine HOW the calculation is done. Default is to be robust against non-matching atoms in a residue, allowing comparison of post-traslational modifications and similar mutations (option `robust`). **DOES NOT SUPERIMPOSE ** (and nor should it)
RMSD Types (`rmsd_type` rosetta_script option)
```
rmsd_protein_bb_heavy,
rmsd_protein_bb_heavy_including_O,
rmsd_protein_bb_ca,
rmsd_sc_heavy,
rmsd_sc,
rmsd_all_heavy,
rmsd_all,
```
**DihedralDistanceMetric**:
- Return the normalized BB dihedral angle distance from directional statistics in degrees. This was used for North/Dunbrack CDR clustering, but can be useful for comparing loops or regions of interest. A good internal comparison of structural change - as lever-arms do not effect measurement too much, so natural fluctuation is compared well. This also does not require a superposition. Accepts a `ResidueSelector`. Works for proteins and glycans.
**TotalEnergyMetric**
- Returns the total energy of the score function. Can set a `ResidueSelector` to limit to only those residues (yes, the hbond-energy is decomposed). Can set input structure or reference pose to get **DELTAS**
**CompositeEnergyMetric**
- Returns the energy of each nonzero score term in a score function. Can set a 'ResidueSelector' to limit to only those residues (hbonds decomposed). Can set input structure or reference pose to get **DELTAS**.
**SasaMetric**:
- Calculate the SASA of the pose or set of residues from a `ResidueSelector`
### Utility
**TimingMetric**
- Safely output the time passed from construction till calculate/apply in minutes. Options for hours. Useful for getting runtimes or averaging runtimes for protocols. Using two between movers or sets of movers can allow you to calculate time between them.
**SelectedResiduesMetric**
- Output residues selected by a `ResidueSelector`. Either pose or PDB numbering. Useful to get at the pose-numbers of residues of interest.
**SelectedResiduesPyMOLMetric**
- Output residues selected by a `ResidueSelector` as a PYMOL selection. Useful for very complex selections such as Layer Selection.
# RunSimpleMetrics
Run the metrics defined in the the `` block (or defined as sub tags) (or set via code). The RunSimpleMetrics (mover) takes a list of metrics and runs them, adding the data to the pose for direct output into the score file using any set prefix/suffix. In this way, we can use them to show differences between movers or sets of moves if desired. Recommended to use json-format score files.
# SimpleMetricFilter
Takes a single metric from to run as a filter (including strings and composites).
## General Use
You are required to give a `cutoff` value and `comparison_type` (eq, ne, lt, gt, lt_or_eq, gt_or_eq) to control the behavior of the filter (basically, when to return True). We do not define the cutoffs within the metrics - as filters currently work. If you want to write a filter that does this, write a `SimpleMetric` and use it within a classic filter with a cutoff.
Comparison is done as `value comparison_type cutoff`. So if your `cutoff=4.0` for RMSDMetric and your` comparison_type` is lt, we return true if the value is less than 4.0.
## StringMetrics
String metrics only work with eq and ne and this is checked. Instead of cutoff, StringMetrics require a `match` option to be set, which is simply a string. In this way, you can filter unwanted SS, sequence changes, or some other metric.
## CompositeMetrics
Composite metrics require an additional option, `composite_action`. This can be `any`, `all`, or a specific composite type. For example, the `CompositeEnergyMetric` can return the energy value or delta energy between an input pose for each energy term. If we set this to `any`, then we return TRUE if ANY composite matches. ALL only returns TRUE if all of the metrics match our filter criteria. Additionally, we can give, for example, 'chainbreak' to filter specifically on the chain break term.
# SimpleMetricFeatures
The SimpleMetricFeatures simply takes a list of metrics. You can control the table that they get written to and can run the same set multiple times. If the table columns do not match on subsequent runs, we will exit with an informative error message.
## Documentation:
https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/RosettaScripts#rosettascript-sections_simple_metrics
https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/SimpleMetrics/SimpleMetrics
commit f9e0cf84fc444a6c05ca5d840c0b54bbda2c03b6
Merge: 8dd9fff 6806bcb
Date: Mon Apr 9 19:15:52 2018 -0400
Merge pull request #3107 from RosettaCommons/roccomoretti/only_for_extras_dummy
Add dummy cc file for 'only_for_extras' build.
It appears the static build doesn't like an empty source list when an 'only_for_extras' library isn't active. Add a dummy source file which will be used for that purpose. Should fix the mac.clang.static.build.release test on the test server
commit 8dd9fff3c41e0f77dc5397e967d8ca4fdcfab05f
Merge: 3c2e9cb a20bb05
Date: Sat Apr 7 09:04:25 2018 +0200
Merge pull request #3104 from RosettaCommons/jaumebonet/expandWriteSSEMover
WriteSSEMover add phipsi output
commit 3c2e9cb43351da5401421ab630e57dff19b7028e
Merge: 3bfd6ef 322c76c
Date: Fri Apr 6 08:49:04 2018 -0600
Merge pull request #3067 from RosettaCommons/sergey/zeromq
Adding ZeroMQ as external library via Git submodule
commit 3bfd6ef7200bafb742785b84a9694083b36f70ab
Merge: bfdb5e4 e095abf
Date: Fri Apr 6 00:49:57 2018 -0700
Merge pull request #3090 from RosettaCommons/vmullig/fix_sidechain_conjugation
Just fix SIDECHAIN_CONJUGATION patch.
Since pull request #3089 generated controversy, I'm cherry-picking out the changes that actually seem to fix the problem that I'm seeing and leaving the others for later. This pull request corrects the SIDECHAIN_CONJUGATION patch, and fixes a few little things in the Patch and PatchOperation classes. It does not alter the Conformation class in any way. Cosmetic integration test changes are expected from the Patch tracer name correction, and some trajectory changes in those integration tests involving sidechain-conjugated ASP or GLU are expected too (e.g. the simple_cycpep_predict isopeptide tests).
commit bfdb5e490e47e1efd380dc51f8950f94082df1f7
Merge: c44882c 6532172
Date: Thu Apr 5 23:47:47 2018 -0700
Merge pull request #3098 from RosettaCommons/vmullig/fix_nterm_proline_error
Fix bug in simple_cycpep_predict with N-terminal prolines and isopeptide bonds.
The issue was that the app is trying to sample the cis conformation of the peptide bond preceding the proline, which it can't do in the isopeptide case with proline at the N-terminus. Fixed.
commit c44882c4944c6198ff061b6aa4e951b4a65ea6da
Merge: d9519a2 ac4d806
Date: Thu Apr 5 16:34:51 2018 -0700
Merge pull request #3097 from RosettaCommons/everyday847/odd_error
Allow rna_minimize to 'remember its place' for big silent files
commit d9519a2ad8cddad8f58d3bc05d56b6c65da0f887
Merge: 15ef52a 3150bbb
Date: Thu Apr 5 11:52:17 2018 -0700
Merge pull request #3095 from RosettaCommons/JacobOConnor/SimpleCycPepPredictPermute
Fixing Bug in SimpleCycPepPredict
commit 15ef52adc03631dadcb7d7d3e7b018cf36c6dbcd
Merge: 7f5547c dd897b3
Date: Thu Apr 5 11:23:26 2018 -0400
Merge pull request #3094 from RosettaCommons/roccomoretti/RotamerSetFactory_symmetry
Fix RotamerSetFactory
How RotamerSetFactory was handling symmetry was sub-optimal. I've removed SymmetricRotamerSetFactory and consolidated logic in RotamerSetFactory in a non-options-system dependent way.
commit 7f5547cfafbffb3b629f5cb641d3a7ca8d539c62
Merge: aac1205 19398df
Date: Tue Apr 3 12:46:37 2018 -0400
Merge pull request #3085 from RosettaCommons/MelanieAprahamian/HRFMSLabeling
Melanie aprahamian/hrfms labeling
commit aac1205592ae8fa35cd1b35d7aff79adc654d1d7
Merge: a6620ab ecea5f0
Date: Mon Apr 2 07:40:04 2018 -0400
Merge pull request #3075 from RosettaCommons/aleaverfay/fix_jd3_outputter_for_job_confusion
Fixing output-filename specification for silent files in JD3. Also fixing an issue with -out:path:all for score files in JD3
commit a6620ab8ca890f04ad457c9ea3ef061fd27a7f6c
Merge: 81cc7be b05d1c0
Date: Sun Apr 1 18:30:43 2018 -0600
Merge pull request #3062 from RosettaCommons/sergey/f2
Adding C++ MessagePack library to source/external as Git submodule
commit 81cc7bec2c4ccbd9f1a5eaed700777cb367ec796
Merge: 02146c8 5666479
Date: Sat Mar 31 14:50:42 2018 -0700
Merge pull request #3086 from RosettaCommons/vmullig/fix_betanov16_metals_issue
Fix issue with beta_nov16 scorefunction and -auto_setup_metals
This pull request addresses issue #3066. The problem is that when -auto_setup_metals strips off a proton from a residue that coordinates a metal, the hydroxyl torsional potential chokes because it expects that proton to be there. This adds a simple check that all the relevant atoms are, indeed, present.
Bug found independently by @senord25 and @aroy10.
Tasks:
- [x] Fix the bug.
- [x] Unit test.
- [x] Beauty.
commit 02146c8167f2afac8014575feebab07c09b2dd04
Merge: 2b4b948 777a84a
Date: Sat Mar 31 14:06:19 2018 -0700
Merge pull request #3006 from RosettaCommons/vmullig/tweak_fit_helixparams_restype_access
Small tweak to a pilot app.
In older code, I had a bad habit of using pose.residue(i).type() instead of pose.residue_type(i). This, unfortunately, can trigger a refold, which is computationally expensive if you just want to interrogate the residue type for some information. This pull request updates a pilot app that others might be using for reference to avoid doing this.
commit 2b4b9485da60c20908a33afbcd5691eb3047ef1f
Merge: ef4144e 18130cc
Date: Sat Mar 31 14:05:24 2018 -0700
Merge pull request #3000 from RosettaCommons/vmullig/lariats_for_kris
Add support for isopeptide-bonded lariats to simple_cycpep_predict
This pull request adds support to `simple_cycpep_predict` for peptides in which a D/L-aspartate or D/L-glutamate side-chain is connected to the N-terminus. Requested by @deiblerk.
Tasks:
- [x] Add sidechain conjugation patch for D/L-aspartate.
- [x] Add sidechain conjugation patch for D/L-glutamate.
- [x] Add `SET_NET_FORMAL_CHARGE` patch operation.
- [x] Add flags to `simple_cycpep_predict` for specifying lariat closure.
- [x] Have them do something internally.
- [x] Add flags to `simple_cycpep_predict` for specifying sidechain isopeptide closure.
- [x] Have them do something internally.
- [x] Integration tests:
- [x] N-terminal lariat.
- [x] Debug alignment code.
- [x] C-terminal lariat.
- [x] Sidechain isopeptide bond.
- [x] Sidechain isopeptide bond - reverse direction.
- [x] Documentation.
- [x] Include note about ASX and GLX not being used in `simple_cycpep_predict`.
- [x] Beauty.
Also:
- [x] Deprecate the old carboxy sidechain-conjugation patch.
- [x] ~~Update code that called it~~ --> I don't think there was any.
- [x] Add unit tests for isopeptide bonded peptide scoring.
- [x] ~~Fix `rama`~~. --> Not necessary. Not fully compatible with NCAAs in any case, and `rama_prepro` is its replacement.
- [x] Fix `rama_prepro`.
- [x] Note: I found a little bug in rama_prepro that's also fixed in this pull request. This creates a number of minor trajectory changes in integration tests.
- [x] Remove debug output from unit test.
- [x] Update `ResidueType` and `Conformation` to allow easy, efficient updating of coordinates that depend on nonpolymeric connections (or on other atoms that depend on non polymeric connections).
commit ef4144e777de1ddf71165b8c9ac3143a4e0380c5
Merge: e0d8674 b2b0225
Date: Sat Mar 31 12:51:33 2018 -0600
Merge pull request #3082 from RosettaCommons/sergey/f3
Refactoring PyMOLMover, thanks to @smlewis for his feedback!
commit e0d86740ed30e28fc16f36793f608bbc5ce7eaf9
Merge: cf1b88f 286c462
Date: Sat Mar 31 08:07:21 2018 -0700
Merge pull request #2509 from RosettaCommons/bcov/DumpMinimizerFrames
Dumping Minimization Trajectories
commit cf1b88f5b4d7b881217e7697e6734a533bb814f4
Merge: 48a5744 d088c85
Date: Fri Mar 30 23:45:20 2018 -0700
Merge pull request #3081 from RosettaCommons/vmullig/fit_jorge_structure
Adding support for fitting Crick parameters from a repeating unit defined by an input pose.
Feature needed for @jfv1812.
commit 48a5744c5dde197cf8d83de8e167ca0cb9b0628a
Merge: 2c3224b 384333b
Date: Fri Mar 30 11:01:14 2018 -0700
Merge pull request #3083 from RosettaCommons/basantab/fix_StrandCurvatureByLevels
Fix to StrandCurvatureByLevels filter
commit 2c3224b58389e4ab050a067015a9be47c8f7a2a5
Merge: 023bf2b cb339c1
Date: Thu Mar 29 10:09:18 2018 -0700
Merge pull request #2876 from RosettaCommons/everyday847/protocols_3_split
More protocols.3 splitting
Integration test changes only in logfile. I'm glad PyRosetta folks are prepared to shim, and I am prepared to help them out. This just couldn't wait any longer or it would die entirely.
commit 023bf2be7f93cff335d82769912a4cd4cb91af3f
Merge: a1c4547 e824aad
Date: Tue Mar 27 18:34:05 2018 -0700
Merge pull request #3023 from RosettaCommons/vmullig/add_metal_csts
Adding `metalbinding_constraint` to weights files in database that have constraints turned on
The -auto_setup_metals flag turns on the metalbinding_constraint score term in the default scorefunction, but if a user specifies a custom scorefunction (or uses Sharon's very useful SetupMetalsMover in RosettaScripts with a script-defined scorefunction), this is not on by default. To make it a bit easier for users, I think it makes sense to turn on the metalbinding_constraint term in all of the scorefunctions that are defined with *_cst.wts files in the database. (All other constraint types are on in these scorefunctions.)
Integration test changes are due to extra column in score line in tests that use the *_cst.wts files. This is exactly the expected behaviour. Merging.
commit a1c45475c34c568c8a8884474d4d4b91a30a5786
Merge: cc67c78 6780d7b
Date: Tue Mar 27 17:23:18 2018 -0700
Merge pull request #3071 from RosettaCommons/vmullig/better_mc_error_message
Trying to make some error messages in the GenericMonteCarloMover more informative.
commit cc67c78f1b37cc4a39ae5aeedbaebff47a0a4053
Merge: 18cee4c 39e8d3a
Date: Tue Mar 27 16:53:12 2018 -0400
Merge pull request #3063 from RosettaCommons/BYachnin/symmetric_SimpleThreadingMover
Make SimpleThreadingMover symmetry aware. Also adds additional user input checking.
commit 18cee4c30530034000170ff3c8c8ca6b64a17e61
Merge: 1e536db 6114696
Date: Tue Mar 27 12:31:19 2018 -0700
Merge pull request #3068 from RosettaCommons/everyday847/bug_omnibus
A few clang analysis bugs
commit 1e536db287cade34663c16bb4a0d8d8804fecd2e
Merge: 7ae1b44 74f09e1
Date: Mon Mar 26 11:31:02 2018 -0400
Include last residue of constraint chain in setup_csts method in SiteConstraint
SiteConstraint did not include last residue of constraint chain due to an off-by-one error when iterating through residues
commit 7ae1b4433846007b5bdaba3bf29460cd359c6481
Merge: 5ecebca 15cdf85
Date: Fri Mar 23 16:03:04 2018 -0700
Merge pull request #3057 from RosettaCommons/vmullig/fix_integration_test_using_score12
Switching rotamer_recovery integration test back to score12.
The rotamer_recovery integration test used to use the -correct flag. I took this out when I added an error message / failure for using -correct with talaris or later, since the test was not set to use a pre-talaris scorefunction (i.e. it was using ref2015 with -correct). However, this has revealed aberrant behaviour that was being masked by the spurious use of the -correct flag. Since the test is clearly testing something that's not supported post-score12, and since I don't know the original intent of the test, I'm switching it back to use score12 for now.
@everyday847 @aleaverfay