Merge pull request #1671 from RosettaCommons/vmullig/simple_cycpep_predict_features
Adding needed features to simple_cycpep_predict application
Tasks:
- Add options for torsion/angle/length space relaxation with:
- Flexible bond angles.
- Flexible bond angles and bond lengths.
- Add option for full Cartesian-space relaxation.
- Have the above options actually trigger appropriate rounds of relaxation.
- Bond angles.
- Bond angles + bond lengths.
- Cartesian-space relaxation.
- Integration tests for the above.
- Add output of number of cis-peptide bonds.
- Plus unit test for sorting by cis-peptide bond count.
- Add hard energy cutoff for output.
- Add to one integration test.
- Turn cis-pro sampling on by default. (Do this last, after confirming that above changes do not change existing behaviour of integration tests.)
- Disable cis-pro sampling explicitly in existing integration tests that did not sample cis-pro before.
- Documentation.
- Beauty.