Merge pull request #1402 from RosettaCommons/dimaio/ptconway_rotlib_corrections This PR merges in Patrick Conway's rotamer library corrections, and moves the app used to generate these corrections into public. Documentation on the application has been added. Finally, a few pilot apps are updated.

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Merge pull request #1401 from RosettaCommons/hahnbeom/beta_nov15_soft Updates on beta_nov15_soft

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Merge pull request #1396 from RosettaCommons/lqtza/lhoc_script Make LHOC plotting script public and minor bug fixes/enhancements.

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Merge pull request #1397 from RosettaCommons/hahnbeom/cen_hb_soft Adding hb_cen_soft

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Merge pull request #1394 from RosettaCommons/JWLabonte/sugars/branching This merge is a quick, one-line fix to a warning output only in cases where the minimizer was setting up the DoF map for MoveMaps allowing BRANCH TorsionIDs to move. Tagging @fdimaio

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Merge pull request #1382 from RosettaCommons/roccomoretti/cppcheckfixes Assorted Cppcheck fixes I had a branch hanging around with assorted cppcheck fixes that should probably get merged ... and now it is. (This brings us from 529 to 329 remaining issues.)

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Merge pull request #1389 from RosettaCommons/antibody Updates and Bug Fixes for Antibody.cc

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Merge pull request #1388 from RosettaCommons/orlypolo/FPD_PhiPsi_check Allow FlexPepDock to do rigid body sampling of a pose containing a ligand

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Merge pull request #1391 from RosettaCommons/vmullig/avoid_iplus1 In SimpleCycpepPredictApplication, prevent the countng of hydrogen bonds to adjacent residues. This is a common pathology that inflates the hydrogen bond count. Tasks: - Add an option for preventing counting of hydrogen bonds to adjacent residues (default true). - Have this option set up ResidueSelectors based on the pose geometry. - Documentation. - Beauty.

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Merge pull request #1377 from RosettaCommons/hahnbeom/fastdesign_beta_patch changing hardcoded nrepeats to use input value for the beta_nov15-pat…

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Merge pull request #1385 from RosettaCommons/JWLabonte/sugars/loops CCD: Locking main-chain torsions that are also ring torsions If the main chain runs through a ring, it cannot be allowed to move during backbone minimization, (which is really a misnomer currently,) or during CCD. This merge generalizes code that I had used to lock main-chain torsions that were also internal ring torsions, which was specific to carbohydrates, to apply to any cyclic system where the ring atoms are also part of the main chain, and uses the new function in the CCD and torsion minimizer code. Carbohydrate CCD test changes expected. All tests pass.

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Merge pull request #1387 from RosettaCommons/dimaio/denstools_fix This PR fixes a few small bugs with density_tools as well as outputting more information when run in -perres mode.

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Merge pull request #1376 from RosettaCommons/lqtza/snugdock_auto_kink SnugDock: auto kink!

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Switching some irritating output to debug output.

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Merge pull request #1384 from RosettaCommons/vmullig/fix_disulfidize_2 Fixing another rare segfault in the DisulfidizeMover Disulfides weren't being broken before mutating the cysteine residues to alanine.

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Merge pull request #1380 from RosettaCommons/revert-1379-revert-1359-vmullig/design_cycpep_app_2 Re-merge "Add design capability to the simple_cycpep_predict application" Reverts RosettaCommons/main#1379 Tasks: - [x] Figure out cause of integration test instabilities. (OK, I think it was a line I commented out in the constructor for the ReadResfile TaskOperation.) - [x] Fix this. - [x] Double-check that simple_cycpep_predict in MPI mode runs without repeated disk reads.

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