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.

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Merge pull request #1373 from RosettaCommons/sergey/binder Fixing Mac PyRosetta build

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Merge pull request #1381 from RosettaCommons/everyday847/pass_by_reference_where_appropriate Pass by reference cppcheck issues

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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.

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Merge pull request #1378 from RosettaCommons/hssnzdh2/crick_files adding crick_params for PPII and 3_10 helix

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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.

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Merge pull request #1338 from RosettaCommons/laurafulton/cdr_cluster_bug_fix fix null pointer crash (when cdrs are not identified) by adding exception

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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<bool>```) 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_

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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.

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Adding command.mpi.sh to ignore list so it will not show up in regression test diff

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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.

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Fixing divide-by-zero edge case in AACompositionEnergy.

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Merge pull request #1366 from RosettaCommons/hahnbeom/residue_depth Adding residue depth filter

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Merge pull request #1365 from RosettaCommons/vmullig/fix_rama_uninit Trying to fix uninitialized var issue flagged by Valgrind. Turns out that it was a couple of new variables that were initialized in the default Ramachandran constructor, but not in an alternative constructor.

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Merge pull request #1367 from RosettaCommons/rhiju/magnesium_in_stepwise Code updates needed for modeling RNA residues around magnesium ions for ERRASER and stepwise modeling. Includes code for optimizing water locations and orientations around Mg(2+) during stepwise. No tests change, except for floating point issues & minor output changes to mg_modeler & number_of_residue_types, which are expected.

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Adding measurement units to profile test graphs legends

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Legend: