Merge pull request #2398 from RosettaCommons/vmullig/energy_based_clustering
Make "bettercluster" (now "energy_based_clustering") into a public app in anticipation of publication
Tasks:
- [x] Move to public apps.
- [x] Rename to "energy_based_clustering" (internally, too).
- [x] Add copyright info.
- [x] Correct tracer names.
- [x] Move bulk of functionality to protocols.
- [x] Trim app down to a bare-bones thing that calls functionality in protocols.
- [x] Move options to `options_rosetta.py`.
- [x] Add to options_rosetta.py.
- [x] Remove from app.
- [x] Update app to take an options object, with option to set from global options system.
- [x] Disable PCA analysis for now.
- [x] Check generality -- there may be old hard-coded assumptions about mainchain torsion names, _etc_.
- [x] Unit tests.
- [x] Cyclic alpha/oligourea peptide, Cartesian-based clustering.
- [x] Cyclic alpha/oligourea peptide, dihedral-based clustering.
- [x] Cyclic alpha/oligourea peptide, with symmetry, Cartesian-based clustering.
- [x] Cyclic alpha peptide, Cartesian-based clustering with cyclic permutations.
- [x] Cyclic alpha peptide, dihedral-based clustering.
- [x] Integration test -- cyclic peptides.
- [x] Integration test -- torsion-based clustering.
- [ ] Documentation.
- [x] Beauty.
Note: the `vmullig/oligourea` branch has been merged into this branch. As such, pull request #2528 must be merged before this one -- DONE.
For the future:
- Check that this works for Jacob's test cases (fragments of proteins).
- Check that this works for Christine's test cases (linker-containing peptides).
- Check that this works for Parisa's test case (which caused a segfault before).
- Check that this works for Tim's test cases (N-methyl amino acids).