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Revisions №59804

branch: master 「№59804」
Commited by: Vikram K. Mulligan
GitHub commit link: 「f44f45d89d204553」 「№2398」
Difference from previous tested commit:  code diff
Commit date: 2017-10-23 15:28:39

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).