Merge pull request #2513 from RosettaCommons/vmullig/peptoid_struct_predition Add support for peptoid macrocycle structure prediction This pull request fixes a number of bugs and issues related to general noncanonical design, and peptoid design in particular. It also enables peptide macrocycle structure prediction with the simple_cycpep_predict application, and restores support for N-methylation. - [x] This pull request is branched off of pull request #2309, and must be merged after that one. (OK, done -- that one is merged.) - [x] This pull request also requires that pull request #2308 be merged first. (The `xrw_dunbrack_unification` branch was merged into this one.) - [x] This pull request also requires that pull request #2975 be merged first. - [x] This pull request will ultimately require that pull request #3477 be merged first. Tasks: - [x] Update chiral (600-series) peptoid params files as described in the comments below. - [x] Update simple_cycpep_predict to allow peptoid residues. - [x] Update cutpoint handling to use the refactored cutpoint energy instead of the current kludge (constraints). Tasks: - [x] Remove redundant sarcosine params files. - [x] Add sarcosine rama table to params files for remaining peptoids. - [x] Add properties for `ACHIRAL_SIDECHAIN`, `L_PEPTOID` (for peptoids with chiral side-chains that are in the database), and `D_PEPTOID` (for peptoids with chiral side-chains that are the mirror image of what's in the database). - [x] Ensure that terms like `omega` and `ramaprepro` are updated to correctly mirror their potentials for `D_PEPTOID` residues. - [x] Add check that Dunbrack file read was successful. (Currently, it segfaults without an error message if the peptoid rotamer libraries are missing.) - [x] Unit test for scoring (current default energy function -- currently `ref2015`). - [x] Unit test for scoring (current `beta` energy function -- currently `beta_nov16`). - [x] Unit test for minimizing (current default energy function -- currently `ref2015`). - [x] Unit test for minimizing (current `beta` energy function -- currently `beta_nov16`). - [x] Unit test for minimizing with N-methylation (current default energy function -- currently `ref2015`). - [x] Unit test for minimizing with N-methylation (current `beta` energy function -- currently `beta_nov16`). - [x] Unit test for cyclic geometry. - [x] Unit test for mirror symmetry. - [x] Test peptoid with chiral side-chain (e.g. 601 -- like phenylalanine, but with extra methyl on beta-carbon creating a chiral centre). - [x] Test peptoid with achiral side-chain (e.g. 001 -- phenyl ring side-chain). - [x] Solve asymmetry issue with achiral side-chain peptoids. I think this a problem with the interpolation, which might be addressed by Andy's pull request #2851. **Edit:** Confirmed. Pull request #2851 addresses this. The `core:SymmDL_peptoid_Tests:test_symm_DL_fa_dun` unit test passes after merging pull request #2851 into this branch. **Edit2:** But my simpler polylinear interpolation scheme (#3477) does _not_ seem to fix this. Hmm... - [x] Integration test -- simple_cycpep_predict - [x] The majority of the current unit test failures in this branch are due to a problem with the cutpoint variant and peptoids. Debug this. - [x] Problem remains with Dunbrack scoring. This is caused by small asymmetries in rotamer libraries for achiral peptoids. Adding automatic symmetry correction on peptoid rotamer library load. - [x] GAH! Dunbrack unit test failures remain mysterious. Debug this. - Found it. Corrected by pull request #2975. - But it does _not_ seem to be resolved by pull request #3477. Hmm. I need to debug this still. - OK, we're good, now. The problem was inconsistently-numbered rotamer wells from one backbone bin to another. The wrong rotamer centres were often interpolated. This is fixed, now. - [x] Resolve `core:CyclicGeometry_beta_peptoid_TwoChainTests:test_cyclic_permutation_fa_dun_rot` unit test failure. - [x] Resolve `SingleNCAARotamerLibraryTests:test_peptoid_001_rotamer_well_scoring` unit test failure. - [x] The `polycubic_interpolation()` function was also apparently introducing asymmetry. This was actually due to spikes in the landscape caused by improper identification of the rotamers over which to interpolate, due to inconsistent rotamer numbering in the Dunbrack library. I think I've fixed this, now. - [x] Remove temporary `std::cout` lines in `RotamericSingleResidueDunbrackLibrary.tmpl.hh`. - [x] Decide whether to uncomment the special-case rotamer spline setup code for N=3. - [x] Fix Dun02 unit test failures that my fix to the asymmetry issue introduced. - [x] Fix bug in peptoid clustering. (This was actually due to the virtual atoms introduced by the cutpoint variant.) - [x] Fix integration test failures that I caused. - [x] Address further issues: 601/602 design not working. - ~~Ensure that peptoid design from sarcosine works. (This will probably fail without special-casing due to variant type matching.) This is likely something in `ResidueLevelTask_.cc`.~~ --> Will be fixed in PackerPalette branch (pull request #1047). - [x] Ensure that peptoid/amino acid design works. (_e.g._ I should be able to say, "Allowed residues at this position are 601, 602, proline, sarcosine, glycine, or alanine."). This is also likely something in `ResidueLevelTask_.cc`. - [x] Address further issues: design not working with peptoids due to "interchangability group" error (at least, with peptoid 303). - [ ] Add rotamer libraries for peptoids 631, 633, 332, 333. - [x] Address issues with design not working with N-methyl amino acids. - [x] Fix peptoid params files that don't depend properly on LOWER connection. - [x] Documentation. - [x] Add note about "GLY:N_Methylation" being considered "SAR" for purposes of design. - [x] Beauty. Also: - [x] This pull request restores N-methylation support, and should address the N-methylation bug. - Update: this fixes several N-methylation bugs. The N-methyl libraries likely suffered the same spikiness in Dunbrack maps from inconsistently-assigned rotamer wells and from Voronoi boundaries crossing backbone bins. Addresses issue #2133. Note: - [x] I should cherry-pick whatever I can salvage from pull request #2134 and close that pull request. Put off to a future pull request: - Add params file for @twcraven's new peptoid. - Add mainchain potential. - Add rotamer libary to LFS repository.

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