Merge pull request #4399 from RosettaCommons/jadolfbr/fix_rmsd_metric
Fix bug in RMSDMetric different residue types in pose vs ref_pose
The code would fail if robust was set to true and side chains are being used for to create the atom_id_map of different residues.
Identified and originally fixed by Hope - @woodsh17
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Merge pull request #4351 from RosettaCommons/dimaio/glycan_chiral_volume
Fixes to the glycan chirality constraints in cart_bonded.
- Previous code was special-cased for only a couple sugars and required manual curation of params files
- this version has automatic logic to set chirality constraints
- constraints have been tuned to match molprobity's chiral volume check
Note on integration test changes:
- Most due to an informational message on # of cart_bonded parameters
- Carbohydrate integration test failures expected
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Merge pull request #4388 from RosettaCommons/roccomoretti/backtrace_tracer_option
Add an option to display the backtrace on the console.
Right now, when Rosetta crashes it only prints the backtrace to the ROSETTA_CRASH.log file.
This PR adds a (currently default false) option -run:crash_to_console which will cause the crash reporter system to also print the backtrace to the console.
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Merge pull request #4392 from RosettaCommons/dimaio/update_symmdef_script
A collection of updates for make_symmdef_file.pl. The major change is to add support for apolar helical symmetries (that is, those that include 2-fold symmetry axes perpendicular to the helical axis)
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Merge pull request #4383 from RosettaCommons/vmullig/fix_gcc_9_unit_tests
Fix gcc 9 unit tests.
The gcc 9 unit tests revealed a silly float-float comparison that could fail stochastically. Fixing.
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Merge pull request #4197 from RosettaCommons/vmullig/add_options_to_simple_cycpep_predict
Adding a few features to simple_cycpep_predict and helical_bundle_predict.
This pull request adds:
- The ability to automatically calculate RMSD to the lowest-energy structure encountered to `simple_cycpep_predict` and `helical_bundle_predict`.
- The ability to calculate various metrics related to solubility and membrane permeability for each sample, and to compute the Boltzmann-weighted ensemble average for these metrics.
- Support for sampling bond lengths and angles.
I'll flesh this out more as I go along.
<u>TODO:</u>
- [x] Pull request #4216 should be merged before this one.
- ~~Pull request #4220 should be merged before this one.~~ --> Merged into this one and closed that one, since this one fixes some bugs that persist in that one.
- [x] Add the options.
- [x] Register them as relevant to `simple_cycpep_predict`.
- [x] Register them as relevant to `helical_bundle_predict`.
- [x] Write the ensemble lowest-energy RMSD calculator.
- [x] Output.
- [x] Integration test.
- [x] Add to scientific test.
- [x] Document new flag.
- [x] Write the ensemble SASA calculator.
- [x] Total, polar, and hydrophobic SASA.
- [x] Compute ensemble average.
- [x] Output.
- [x] Integration test.
- [x] Add to scientific test.
- [x] Document new flag.
- [x] Add support for sampling bond lengths and angles.
- [x] Add options.
- [ ] Document new options.
- [x] Add GenKIC bond angle and bond length perturbers.
- [ ] Document new GenKIC features.
- [x] Register with `simple_cycpep_predict` (but _not_ `helical_bundle_predict`).
- [x] Have the options do something.
- [x] Integration test.
- [x] Check scientific test with new features: queued here (https://b3.graylab.jhu.edu/revision/commits/14270).
- [x] Beautify.
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Merge pull request #4380 from RosettaCommons/JackMaguire/quietTF
Reducing Noise in TF Tests
The tensorflow integration tests are noisy when comparing output from different processors.
This is an example from PR 4359's merge with master:
```diff
< [DATESTAMP]: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA
---
> [DATESTAMP]: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
```
This PR simply adds that line to the `ignore_list`
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Merge pull request #4382 from RosettaCommons/JackMaguire/fixsubmodule
Updating scientific tests submodule
I've been tripping over submodules recently and accidentally merged in a change to tests/scientific/data. This PR reverts that change.
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