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.