Merge pull request #1045 from RosettaCommons/raemisch/fix_remodel Remodel Fixes A few fixes for various things in remodel from Sebastian Raemisch (@raemisch) and I. Heres the list: 1) Remodel should work on the first chain of the pose or the chain given in -run:chain. However, (in some instances) you must pass run:chain even if you only have a single chain in the PDB. This fixes that, and by default will use the first chain of the PDB. 2) If you use Alanine's instead of any other aa for centroid-stage backbone fragment building using the -remodel::generic_aa option, you would seqfault. This fixes that. 3) Lets say you have an option, _design_neighbors_, that you explicitly set to false on the command-line. Remodel would design those neighbor residues and baffle you. The bug is that for boolean options all over remodel code, instead of accessing the option itself, it accessed the use of the option. This fixes it in every file that used the remodel options. In most instances (as these were default false or were intended to be default false), this is OK. However, this is an interface bug, and one should generally __NEVER__ do this as it can (easily) lead to wrong results. Remodel integration test will change - It was tested as is (in the PR) and then updated to use -out:prefix in order to run its 3 tests and have good comparisons for the future.

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Merge pull request #1049 from RosettaCommons/xrw_enzdes_refactor_test Who says you have to be at an XRW to overhaul a major system in Rosetta? Integration test changes are either cosmetic, those irksome 18-ish, or understood (inverse_rotamer_remodel) and desired.

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Merge pull request #1078 from RosettaCommons/GlycanRelax/master Glycan Relax Protocol Add a new Glycan Relax application, add updates to Jason's RosettaCarbohydrate framework and add a generalized framework for backbone dihedral sampling. Code by @jadolfbr and @JWLabonte mainly during an intense collaborative coding week in SD. Thanks Jason! Glycan Relax aims to sample potential conformational states of carbohydrates, either attached to a protein or free. It is extremely fast. Currently, it uses a few strategies to do so, using statistics from various papers, the CHI (CarboHydrate Intrinsic) energy term, and a new framework for backbone dihedral sampling. Conformer statistics adapted from Schief lab Glycan Relax app, originally used/written by Yih-En Andrew Ban. Algorithm ======= Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. The overall total number of rounds is scaled linearly with the number of residues to sample. Currently uses a random sampler with a set of weights to each mover for sampling. The packing of OH groups is currently disabled for speed and memory. Weights are currently as follows: .20 Phi Sugar BB Sampling .20 Psi Sugar BB Sampling .20 Linkage Conformer Sampling .30 Small BB Sampling - equal weight to phi, psi, or omega -> .17 +/- 15 degrees -> .086 +/- 45 degrees -> .044 +/- 90 degrees .10 MinMover Framework Updates =============== Enable Optimization of glycan linkages during creation of glycans to ideal values @labonte - Fixed packer to disable packing of residues with SC_BRANCH_POINT variant, which would cause breakage of polymer residues coming off of amino acid side chains. Refactor CHI (CarboHydrate Intrinsic) energy term, enable creation of Sugar BB sampling data from the energy term, handled by the ScoringManager, and only done once. LinkageConformerMover: ``` ///@brief This code changes all of the dihedrals of a particular glycosidic linkage based on database info, /// esentially sampling carbohydrate dihedral conformers of two residues. /// ///@details The linkage conformers are carbohydrate residue type and (and linkage oxygen) dependant ie MAN-MAN /// If data is not known here, by default we sample from restype-independant data. /// If there are multiple conformers for a given linkage, will randomly select from them. /// /// 3 Main Conformer Sampling Strategies: //// 1) Mean + uniform in X standard deviations (Default) //// ->Build conformers using the means of dihedrals + or - some amount within X standard deviations of the mean. //// //// See Also: //// LinkageConformerMover.set_x_standard_deviations //// //// 2) Mean + probability in X standard deviations //// //// 3) Idealize //// -> Use only means when building linkage conformers. //// //// See: //// LinkageConformerMover.set_idealize_torsions ///// ``` Other ==== Added proper enums for the 3 main dihedrals to core/types (MainchainTorstionType). Eventually, these need to be reconciled with the numerical bb dihedral types that already exist, but aren't quite typed enums. Add functions to deal with these in pose/util. Since the numbers of the enums and the named integers match, these work with either. Add BBDihedralSampler base class and derived types for 1 dimensional, 2 dimensional, etc. sampling of BB data. Recapitulate SmallMover using this framework. Can use a general mover (BBDihedralSamplerMover) to use any BBSampler derived class. With a factory class, this could have RS Support. Code in protocols/simple_moves/bb_sampler and protocols/simple_moves/BBDihedralSamplerMover. Clean up MoverContainer. Add FAIL enum to MoverStatus. Fix/clean up some Code Templates. Add function to PyMolMover to set the model name. Clean up documentation for BackboneMover (turns out I've been using it wrong for 5 years. yay). Clean up documentation for MinMover

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Merge pull request #1100 from RosettaCommons/hahnbeom/bugfix Fixing stability issue in cartesianMD Mover.

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Merge pull request #1102 from RosettaCommons/vmullig/fix_helix_fit Fixing issues with fit_helixparams app. Some code in the numeric libraries for superimposing structures and calculating RMSDs is throwing off my fit_helixparams app. A small value (1.0e-7) is currently added to certain numbers to avoid a zero determinant in edge cases. This small value is resulting in a skew to the transformation matrices in some cases, and it turns out that it's because it's TOO small. I won't take it out, but I'll add a pass-through to let a specific protocol override it with a larger value. Initial tests indicate that this greatly improves the behaviour of the fit_helixparams app. @hssnzdh2 @everyday847 Tasks: - Modify the rmsfitca2() function in numeric/model_quality/rms.cc/hh to take a double-precision float for the offset value. (Defaults to 1.0e-7 -- preserve the old behaviour). - Modify calling functions similarly. - Modify the fit_helixparams app to pass "1.0e-5" to rmsfitca2(). - Add option for user to set the offset value to pass to rmsfitca2(). - Beauty.

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Merge pull request #1099 from RosettaCommons/hahnbeom/bugfix merged.

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Merge pull request #1097 from RosettaCommons/tlinsky/denovo_util_fix Fix DeNovoUtilTests problem identified by Rocco

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Merge pull request #1096 from RosettaCommons/roccomoretti/valgrind_fixes A bundle of fixes for Valgrind issues. 1. Don't access off the end of a string in PoseFromSFRBuilder, for mmcif_IO 2. Better checking of out-of-range access in DeNovoUtilTests 3. (slightly) Better input checking in residue_io, to catch badly formatted params files, for ProteinUpstreamBuilderTests 4. Don't wrap a stack-allocated object into an OP, for AntibodyDesignOptions 5. Increase stack size, for fragment integration tests (At some point we may want to figure out what's taking up so much stack space in these tests, and see if we can flatten the call stack, or move some object allocation to the heap.) I turned off the bulk of DeNovoUtilTests:test_bulge_strandpairing, as there was a hidden bug that, once properly checked for, makes the unit test now perma-fail. (The ss parameter given is not long enough to cover the segment.) Someone who knows the test should probably look into why that is, and what should be done to properly correct it.

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Merge pull request #1094 from RosettaCommons/roccomoretti/reenable_atoms Re-enable the atom types we commented out in the XRW due to unit test issues. Andrew has fixed the bug associated with them, so there is no reason to keep them commented out. Trajectory changes for integration tests, due to the added number of atom types.

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Merge pull request #1064 from RosettaCommons/vmullig/nicer_conect_behaviour2 XRW -- Make dumping of CONECT records default for noncanonicals/nonsolvent This changes the default behaviour of CONECT records in PDB files, dumping them for all noncanonicals by default (the PDB standard). Unfortunately, this is another one that changes a lot of integration tests. Details: - [x] Turn CONECT record writing on by default. - [x] Set default distance cutoff to 0. - [x] Add concept of CANONICAL_AA to database. - [x] Add concept of CANONICAL_NUCLEIC to database. - [x] Add concept of SOLVENT to database. - [x] Add logic to only write internal bonds if the current residue is not a CANONICAL_AA, CANONICAL_NUCLEIC, or SOLVENT. - [x] Add logic to only write inter-residue bonds if one of the residues involved is not a CANONICAL_AA, CANONICAL_NUCLEIC, or SOLVENT. - [x] Add option to dump <i>all</i> CONECT records if one so wishes. - [x] Add option to prevent CONECT record dumping, if one so wishes. - [x] Documentation. This is part of the 2016 Chemical XRW. It should be tested and merged AFTER pull request #1060 and AFTER pull request #1066.

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Merge pull request #1053 from RosettaCommons/everyday847/remove_extra_pcs Removed old versions of pseudocontact shift code no longer in use as of 2010 Do let me know if you've got plans to add a new PCS implementation to Rosetta! Since they haven't changed in like five years, you'll have no deficit of SHA1s to benchmark against.

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Merge pull request #1090 from RosettaCommons/aleaverfay/fix_enzdes_bug_generating_RTs_w_variants Changing RTS::generate_residue_type() to avoid calling RTS::name_map(), which will throw an exception when the requested name does not exist. This is important because generate_residue_type is used by RTS::has_name(), which really should just return "false" when the answer is "no", instead of quitting. This fixes a bug in the (soon to be obsoleted) enzdes code when trying to create connectivity variants for RTs that themselves have patches (e.g. PHE:NtermProteinFull). Thanks, Sophia, for finding this.

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Merge pull request #673 from RosettaCommons/smlewis/pose_mover_file_itest In the spirit of merging old PRs, here's an integration test I wrote on the van back from RosettaCON last year. The comment from its command file explains its purpose: This test is not an integration test in the traditional sense: it is not testing a run of the code. Instead, this test just examines the code itself for a few important central classes. These are important base classes used by everyone, and modifications to those classes should be approved by the community (or, let's be serious, Andrew). Failing this integration test does NOT mean something is wrong - just that you've changed a file it watches and should be prepared to justify your change. itests will break because a new itest is added. No code changes.

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Merge pull request #234 from RosettaCommons/aleaverfay/mean_for_daf Adding a 'mean' function that can be used to describe a fitness function...

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Merge pull request #70 from RosettaCommons/kalngyk/calibur 18 month old PR: merged. Bring it on!

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fixing cyclization integration test

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