commit e348527827798eaa60f0185d11d0d898527e3089 Merge: 5e09b31 9b15222 Date: Tue Jun 7 17:37:31 2016 -0700 Merge pull request #1377 from RosettaCommons/hahnbeom/fastdesign_beta_patch changing hardcoded nrepeats to use input value for the beta_nov15-pat… commit 5e09b31ab60bdbc138dec718fa6d17ac0c194d3a Merge: ab567a1 1af30e9 Date: Tue Jun 7 14:26:40 2016 -0400 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. commit ab567a149be6436afe8205ffa154e89fbf345603 Merge: 99349bb cfae319 Date: Mon Jun 6 14:53:00 2016 -0700 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. commit 99349bb9da5033aad88332f3b196d2037d3b7a61 Merge: 01a39b6 097a5c8 Date: Mon Jun 6 17:43:14 2016 -0400 Merge pull request #1376 from RosettaCommons/lqtza/snugdock_auto_kink SnugDock: auto kink! commit 01a39b67aeea45279193b8a548fd37b9015911e1 Date: Mon Jun 6 11:54:20 2016 -0700 Switching some irritating output to debug output. commit 3f835d08cb1a1d6b67e61b8f91b95cf227bfe76a Merge: 996224f 48e75b9 Date: Sun Jun 5 23:04:25 2016 -0700 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. commit 996224fbebc1326c4fdc9df30fedaf2f2610a27b Merge: 75fcb7e c5ce02c Date: Sun Jun 5 03:56:49 2016 -0700 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. commit 75fcb7efe0eda15c76de59915e99f744964a98c3 Merge: 38dcd38 0149374 Date: Sun Jun 5 03:41:07 2016 -0700 Merge pull request #1383 from RosettaCommons/vmullig/fix_disulfidize_segfault Trying to fix segfault in Disulfidize when mutating a disulfide positionion to ala. The code wasn't properly calling core::conformation::break_disulfide(), resulting in a dangling disulfide partner that still thought that it was bonded to the mutated residue. At least, I think this is the problem. commit 38dcd38d55591b28f8e81858842866a3237ac1b9 Merge: 8ea8c55 042e7f1 Date: Sat Jun 4 17:49:27 2016 -0600 Merge pull request #1373 from RosettaCommons/sergey/binder Fixing Mac PyRosetta build commit 8ea8c5526be93edbefe96f2d7476e4d8e025c6d4 Merge: a071e52 771f365 Date: Sat Jun 4 12:02:55 2016 -0700 Merge pull request #1381 from RosettaCommons/everyday847/pass_by_reference_where_appropriate Pass by reference cppcheck issues commit a071e5285177f3ebc7a9b8a5880956a99627062d Merge: e8d13fa 8ac71c9 Date: Sat Jun 4 02:51:40 2016 -0700 Merge pull request #1379 from RosettaCommons/revert-1359-vmullig/design_cycpep_app_2 Temporarily revert "Add design capability to the simple_cycpep_predict application" Reverts RosettaCommons/main#1359 There are a lot of weird instabilities in the integration tests that seem to have crept in with this merge, for reasons that I don't understand. I'm reverting this until I work this out. commit e8d13faeeddd37176b1dc3a5b3de06d931acb074 Merge: 0354ef1 af7f797 Date: Fri Jun 3 18:41:50 2016 -0700 Merge pull request #1378 from RosettaCommons/hssnzdh2/crick_files adding crick_params for PPII and 3_10 helix commit 0354ef1bb541f0052a5dd263f47f008186cd230a Merge: 22f785e 2315715 Date: Thu Jun 2 15:23:33 2016 -0700 Merge pull request #1334 from RosettaCommons/jadolfbr/pyrosetta_toolkit/fix_mutate PyRosetta Toolkit GUI: ================= Finally fixes the neighbor packing shell with mutate in the FullControlWindow that has been broken for sometime. Disables redirection of std::out to the terminal. The window looks nice, but the output in the terminal is way more useful. PyRosetta ======== Reinstate MutateResidue and separate how packing is done for neighbor residues into new function. Enable import of toolbox in rosetta ```__init__.py``` to re-inable default use of mutate_residue without imports. This has been requested by users on the forums, as well as used in various PyRosetta apps. commit 22f785ed0a9e53ce08f34390392704e5b7379756 Merge: a3e7328 51aae5e Date: Thu Jun 2 10:12:59 2016 -0400 Merge pull request #1338 from RosettaCommons/laurafulton/cdr_cluster_bug_fix fix null pointer crash (when cdrs are not identified) by adding exception commit a3e7328121bcf7877eb54b11237e21809761a5af Merge: 2901de5 a6230f8 Date: Wed Jun 1 16:33:27 2016 -0700 Merge pull request #1368 from RosettaCommons/jadolfbr/carbohydrates/glycan_relax This PR covers some general code, bug fixes, and new code for antibodies, carbohydrates, and GlycanRelax. General ====== - _NeighborhoodResidueSelector_ completely refactored. Cleaned up. Simplifiied. Code that loop modeling used for getting neighbor residues, generalized and moved to core/select/util. This is now integrated with the _NeighborhoodResidueSelector_ to speed up neighbor calculation immensely (if scoring). - _ResidueSelector_ code_template cleaned up, fixed where needed. - Can now set a _ResidueSubset_ (```vector1```) in addition to a _ResidueSelector_ for the _OperateOnResidueSubset_ TaskOp - Can set an option in _OperateOnResidueSubset_ to flip the subset. So, for example, if your Selector chooses neighbor residues on each apply, you can operate on everything else. Bug Fixes ======== Disulfide link records properly skipped during read-in if output. This was causing a number of issues in being able to re-read in PDBs with disulfides that were output by Rosetta when using -write_pdb_link_records, which we use for carbohydrates Carbohydrates =========== - Adds a _GlycanResidueSelector_ to core. This can be used to both get ALL carbohydrates in a pose, or the glycans from specific root residues, like the carbohydrates given a particular ASN, or the branching residues from a particular carbohydrate residue in a tree. - Adds support for Side-Chain packing to GlycanRelax, with the default to pack all glycan residues and neighbors within the MC protocol, and at our final optimization step. Resfile support also given, as well as TF support through RosettaScripts. This enables OH group packing now that @JWLabonte has optimized this, as well as design of protein side-chains during the protocol. Antibodies ======== - Adds a _CDRResidueSelector_ for selecting residues of particular CDRs. @aleaverfay - Adds an _AntibodyRegionSelector_ for selecting residues of particular antibody regions, such as the antigen, framework, or CDRs Unit Tests ======= Added for all new _ResidueSelectors_ commit 2901de5732899211c36b21e9bd5e8155bfbf917d Merge: e054830 bbdd570 Date: Wed Jun 1 12:11:54 2016 -0700 Merge pull request #1359 from RosettaCommons/vmullig/design_cycpep_app_2 Add design capability to the simple_cycpep_predict application This allows the simple_cycpep_predict application to design every conformation that it samples. Tasks: - Add option for design. - Add option to read in file allowing specification of allowed residues by position. - Add options for prohibiting D-amino acids in negative-phi region of Ramachandran space, and prohibiting L-amino acids in positive-phi region. - Have the above options actually set up the SimpleCycpepPredictApplication's settings. - Read per-residue options from a file. - Unit test for this. - Override file read by slave processes in MPI mode. - Have the above options actually DO something -- i.e. add design to the SimpleCycpepPredictApplication::genkic_close() function. - Set up design TaskOperations. - Unit test. - Debug problems revealed by unit test. - Eliminate/refactor anything in SimpleCycpepPredictApplication that would cause repeated reads from disk. - Check that this also results in no disk reads in beta_nov15 mode. - Double-check this at the end. - Integration test. - MPI-mode integration test. - Documentation. - Beauty. - Test on Jojo. - Test on Cetus (Blue Gene/Q test nodes). - Performance benchmarks on Mira (Blue Gene/Q production nodes). - Fix broken unit tests. Also: X Add option to exclude i - i+1 hydrogen bonds from hydrogen bond count. --> Separate pull request. - Add option to stop sending jobs after a certain amount of execution time has elapsed (and just collect whatever has completed). - Add timer, to facilitate benchmarking. - Add support for external constraints file. (Would need to handle circular permutations, though). --> Separate pull request. - Add support for separate .comp files for L-alpha, L-beta, D-alpha, and D-beta regions of Ramachandran space. - Add the options. - Have these files be read in. - Add them to the parsed protocol for design (with a SequenceConstraint and a suitable ResidueSelector). - In MPI mode, have the master process read these data from disk and transmit them to the slaves, to avoid repeated read-ins. (This means setting comp_file_contents_L_alpha_, comp_file_contents_D_alpha_, comp_file_contents_L_beta_, comp_file_contents_D_beta_, and abba_bins_). - Have global aa_composition setup files cache their data, rather than being re-read from disk whenever the score type is instantiated. - Test this. commit e054830eb86735bc864b2b2a71ecae22e37e4897 Date: Wed Jun 1 00:10:38 2016 -0400 Adding command.mpi.sh to ignore list so it will not show up in regression test diff commit 551a71c407c5ed0db0cdc301e44511b83a69ee94 Merge: 0dbd094 f2d4792 Date: Tue May 31 18:21:06 2016 -0700 Merge pull request #1370 from RosettaCommons/dimaio/symmmult_fix Change score_multiply in SymmInfo to Real-valued (was Size). Symm test failures are expected, they are either numeric noise (from Size->Real conversion), or bugs fixed. commit 0dbd0947f9c960f29b4c4034fc1628fe1ff24e58 Date: Fri May 27 20:26:58 2016 -0700 Fixing divide-by-zero edge case in AACompositionEnergy.