commit 231d1f370a51db6959d3da57afc5f0ec93f6c6fd Date: Fri Aug 3 15:45:06 2018 -0400 beautifying commit e8f0fd1d3dfb5cc5e6ae8aab9a670f039d3d7ece Merge: e47495a c0f17e1 Date: Fri Aug 3 14:47:56 2018 -0400 Merge pull request #3315 from RosettaCommons/hdanderson/protac_stuff Hdanderson/protac stuff Converted UBQ_Gp_LYX-Cterm application into a mover compatible with RosettaScripts. Made some modifications to the mover code so that it supported a ResidueSelector for choosing the lysine to which the ubiquitin would bind. Also updated the application so that it calls UBQ_GTPaseMover from protocols. The output of UBQ_GP_LYX-Cterm is expected to change as part of this merge. There were also some changes in the integration test for cycpep, but I expect that this is just noise. I am open to reverting if the cycpep change turns out to be real. commit e47495a7f51129bebbbfe8441a8893ea1d280b6c Merge: def0738 036ed4f Date: Thu Aug 2 21:16:16 2018 -0700 Merge pull request #3362 from RosettaCommons/weitzner/clang_conda_cpp Enable C++ conda builds (for Mac) commit def0738ea758872476b9bf85b9d78fe578537b6f Merge: ecf20c7 a8f2e2c Date: Thu Aug 2 22:13:16 2018 -0600 Merge pull request #3361 from RosettaCommons/sergey/binder Refactoring PyRosetta, adding Pybind11 as git submodule commit ecf20c70f6174219fae37c75918976b6a30ac2e2 Merge: 9b89e01 f0df223 Date: Thu Aug 2 16:48:36 2018 -0500 Merge pull request #3350 from RosettaCommons/roccomoretti/fix_san_tests Fixes for some of the ubsan/addsan/valgrind errors. commit 9b89e019cde3bf78f829037644bc82daec0a79d7 Merge: 005f50a 04322d5 Date: Thu Aug 2 13:03:43 2018 -0600 Merge pull request #3317 from RosettaCommons/sergey/f2 Adding workaround for serialization test. Disabling serialization to `JSON` and `XML` archives commit 005f50a5bc3c92c4449a771e50d75af2d31affcc Merge: 469d6ff ca9d399 Date: Thu Aug 2 10:37:52 2018 -0400 Merge pull request #3348 from RosettaCommons/aleaverfay/jd3_fix_score_file_in_jobdef jd3 fix score file in jobdef I discovered that a few things concerning how score file output is controlled in the job definition file for JD3 were not working correctly. 1. If a (non default) filename were provided inside the ScoreFile tag, it was not getting used. 2. If multiple ScoreFiles were listed in a single SecondaryOutput tag for a job (say you want to record the job's scores in two locations), then the schema validator would throw an error. 3. (related to 2.) The StandardJobQueen didn't really support the idea of allowing multiple SecondaryOutputters, so even when you fix the schema definition bug, there are other things lying in wait. I've fixed these issues. Now you can say for job 1 that the outputs will go to directory1/ and for job 2 that the outputs will go to directory2/. commit 469d6ff9cb2c10bb359440529f4e83ca53599968 Merge: 7c22c7d 235b64e Date: Wed Aug 1 19:55:08 2018 -0400 Merge pull request #3355 from RosettaCommons/JackMaguire/FastDesignScriptsInDatabase Creating Database Directory For RelaxScripts Currently, the only way to run FastRelax/FastDesign is to either provide your own relax script or use one of the defaults hard-coded in the c++. This PR creates the directory main/database/sampling/relax_scripts where anyone can add scripts that are non-default but general enough to be used by other people. Now, FastRelax parses the optional relaxscript tag and looks for the script in database/sampling/relax_scripts if it otherwise does not exist (i.e., if the file is not local to the working directory). For example, you might develop a relaxscript that works well for carbohydrates and write database/sampling/relax_scripts/carbohydrates.txt. Anyone could use it by adding the tag . I think it's worth noting that I have not changed any of the previously defined behavior; nobody's rosetta_scripts will behave differently if this PR is accepted. All I have done is added a set of additional cases for the relaxscript option and rearranged how some information is stored. commit 7c22c7d14f04598a377c09f1773c531398f5006c Merge: 64f6cb6 29cc28c Date: Wed Aug 1 11:32:10 2018 -0400 Merge pull request #3364 from RosettaCommons/vmullig/fix_carbohydrate_issue Fixing the PyRosetta build commit 64f6cb6d360bc29b58ce232460ce876666d8ff6c Merge: 2a24446 befd8d0 Date: Wed Aug 1 11:02:50 2018 -0400 Merge pull request #3359 from RosettaCommons/MelanieAprahamian/per_residue_solvent_exposure pilot app to calculate per residue solvent exposure in a variety of ways commit 2a2444608b94891ff2d8f371919c894f0bf4ab09 Merge: 1001831 e0c92bd Date: Wed Aug 1 00:20:42 2018 -0400 Merge pull request #3360 from RosettaCommons/everyday847/hotfix_stochastic_failures Set UPPER to NONE in 3prime_deoxy commit 10018315bd8b443eafcb2a9b5ac3f3783019afaa Merge: 99888c0 1d62571 Date: Tue Jul 31 19:04:01 2018 -0600 Merge pull request #3342 from RosettaCommons/bcov/BuriedUnsatsDAlphaBall Adding dalphaball_sasa option to BuriedUnsatsFilter commit 99888c02b8a299eb0d1113f31e2b67b05b03ec73 Merge: 70e699e b1ce044 Date: Tue Jul 31 15:06:48 2018 -0400 Merge pull request #3354 from RosettaCommons/JWLabonte/sugars/output GlycanTree: Adding a method to output the IUPAC sequence for an individual glycan This merge will add a function `Pose::glycan_tree_sequence` that will output a string representation of a glycan in IUPAC format. Currently, `Pose::chain_sequence` will output the IUPAC sequence for a polysaccharide chain, but this is simply a linear sequence. The new function will give the branches and their connectivity using the standard IUPAC bracket notation. In the process of writing this code, I made a few modifications to `CarbohydrateInfo` in regards to nomenclature: * Reducing-end residues now include their anomeric form as part of their name. (They usually don't in the literature, but that's because of ignorance because of their instability. In a modeling case, we absolutely know which anomer we have.) * A bug is fixed regarding sugar-modification abbreviations as suffixes in short-form names. Reducing-end GlcpNAc, for example, no longer outputs as GlcpN. I have also corrected input files for use with the 'glycosylate_pose()` functions, reordering their branches so that Rosetta no longer gets confused. CCD_loop_closure and carbohydrate integration test changes expected, because of the bulleted changed noted above. All unit tests pass. commit 70e699e95c32d9a6af9e63a5b2901a3bf6d27b33 Merge: 3606cd4 6cbe151 Date: Mon Jul 30 13:54:01 2018 -0700 Merge pull request #3357 from RosettaCommons/asford/conda_packaging Fixup fixup of buildkite post-checkout hook. commit 3606cd4dc5fad8455c4cb328566b5266434aedab Merge: 405d569 c8bbaf0 Date: Sun Jul 29 19:17:56 2018 -0700 Merge pull request #3356 from RosettaCommons/asford/conda_packaging Fixup handling of remote HEAD in buildkite branch update hook. commit 405d56973c5921700a385e1ca0eb7982c966e12c Merge: 839c46d 0abaabe Date: Sun Jul 29 14:28:18 2018 -0600 Merge pull request #3329 from RosettaCommons/sergey/ui UI update commit 839c46dfa78c34e537afeb0d345643e09242f9b5 Merge: 12a0db6 c5742b2 Date: Sat Jul 28 13:54:01 2018 -0700 Merge pull request #3339 from RosettaCommons/asford/conda_packaging Add conda build configuration and recipes. commit 12a0db6d5c5fb60f2233552765ab3a376449f535 Merge: 103307d 583cb9e Date: Fri Jul 27 11:25:24 2018 -0400 Merge pull request #3351 from RosettaCommons/guffysl/add_sewing_protocol_data Add SEWING data files to additional_protocol_data submodule commit 103307d6597138b935ac6053d719ef36b61116b7 Merge: e127da7 89dea05 Date: Thu Jul 26 14:22:19 2018 -0400 Merge pull request #3328 from RosettaCommons/lqtza/make_snugdock_integration_stable_again SnugDock updates to fix strange EllipsoidalRandomizationMover behavior. commit e127da7468121f1f92883e3e73e76b6a2952f8de Merge: a340a56 04f9ffd Date: Thu Jul 26 11:53:49 2018 -0600 Merge pull request #3349 from RosettaCommons/sergey/binder PyRosetta: fixing GCC build, adding support for Python-3.7 platform commit a340a569ba62df4dedb39e83057275227579ada7 Merge: e2d8b42 92fc631 Date: Wed Jul 25 16:24:33 2018 -0400 Merge pull request #3337 from RosettaCommons/everyday847/more_readin_fixes More PDB read-in fixes commit e2d8b421d8a6ed88a64c079c3eb340874ab30bf0 Merge: 87d408e 13af767 Date: Wed Jul 25 04:08:44 2018 -0700 Merge pull request #3319 from RosettaCommons/vmullig/parametric_rna_fix Fix for parametrically-generated RNA helices. The parametric code wrongly assumed that the first N atoms of a polymer type are always the mainchain atoms. Correcting this assumption with explicit lookups from ResidueType::mainchain_atom(). commit 87d408ef856ed73bf44ed76795e1ff4875ea013a Merge: 2a2dfd7 3aebd4b Date: Tue Jul 24 10:46:52 2018 -0400 Merge pull request #3322 from RosettaCommons/BYachnin/EnzFilter_tests Adding EnzScore filter unit and integration tests commit 2a2dfd79a124a93543b34b060e8ef7f7dd1701f8 Merge: 9d51cf9 8c41643 Date: Mon Jul 23 16:20:46 2018 -0700 Merge pull request #3210 from RosettaCommons/bfrenz/glycan_xmls added cryoem glycan refinement xml and merged with master commit 9d51cf9021e9c22093e62b099d9f3299a859decb Merge: 9df4200 550c2d5 Date: Mon Jul 23 13:51:29 2018 -0700 Merge pull request #3338 from RosettaCommons/asford/pyrosetta_env_compilers Update pyrosetta build process for isolated environments. commit 9df4200b7a21562fe1be243bff7f4960cce092d7 Merge: 3dca8cc 43a1a6b Date: Sun Jul 22 23:09:54 2018 -0700 Merge pull request #3331 from RosettaCommons/kkappel1/drrafter_print_help very minor changes to DRRAFTER.py commit 3dca8cc65a3a02b8f75dc76c9ae1ac38aae65f62 Date: Sat Jul 21 12:15:38 2018 -0400 beautifying commit 8511e093542348b7f71193aeebbe8af8559dfc21 Merge: 0428f6e e594131 Date: Fri Jul 20 15:33:04 2018 -0400 Merge pull request #3330 from RosettaCommons/JackMaguire/DebugMSRS David Thieker found a bug where multistage rosetta scripts does not produce any output if too many trajectories fail their filters. The fix is pretty simple: now I update the number of results a stage expects to produce when the previous stage under-performs. commit 0428f6e9bbec51b0190497771319ca5b38b77d16 Merge: 569315a 856aa60 Date: Thu Jul 19 21:24:29 2018 -0700 Merge pull request #2760 from RosettaCommons/fordas/pyrosetta_distributed Basic support for pyrosetta & rosettascripts via python distributed libraries. commit 569315af274482580554c7e14b5b9bd5129b93a1 Merge: 87a46d3 2e6c61a Date: Thu Jul 19 22:21:12 2018 -0400 Merge pull request #3313 from RosettaCommons/lqtza/fix-bug-in-make-lattice-mover-when-ligand-is-present Fix bug in MakeLatticeMover.cc commit 87a46d31199163a62d09eafb2b869267e58ec6b3 Merge: 1e5c718 72e4686 Date: Thu Jul 19 18:15:55 2018 -0700 Merge pull request #3318 from RosettaCommons/bcov/FixBunsProbe Fixed BuriedUnsatFilter probe_radius="X" commit 1e5c718b533ff30b165432580aafb477b2970e56 Merge: 36b0bfb 15ebb92 Date: Wed Jul 18 17:53:55 2018 -0500 Merge pull request #3311 from RosettaCommons/jadolfbr/new_per_residue_metrics Add a few PerResidueRealMetrics and put native pose into the data map as resource New PerResidueRealMetrics ==================== This PR adds 4 new `PerResidueRealMetrics`, and refactors other SimpleMetrics to use them as their base code: - `PerResidueEnergyMetric` - calculate per-residue total_energy or any given score type. Uses delta if input is given - `PerResidueSasaMetric` - calculate per-residue sasa - `PerResidueRMSDMetric` - calculates per-residue RMSD in same vein as the RMSDMetric - `PerResidueDensityFitMetric` - calculates the density fit for each residue. This is now used by the `DensityFitResidueSelector` Add Integration test for all of these. Their core code is unit tested by others as sums. Fix up code templates, ref_pose functionality has been moved to core. All metrics that were previously tied to loading the native pose have been moved to core to increase their utility. Note: ==== This also adds any set `-in:file:native` as a resource in the DataMap. This reduces code duplication and allows the native to be loaded once and accessed as a resource in any RS class without global data. This also works with JD3 - as it uses a local `OptionsCollection`, and is MUCH easier to use than the `SavePoseMover` commit 36b0bfbbccc50b344ef3e579e7ddfcba1e320454 Merge: 956f2fb b28961a Date: Wed Jul 18 06:55:39 2018 -0700 Merge pull request #3316 from RosettaCommons/everyday847/additional_element_support More element support for pose visualization commit 956f2fb9b428af833153142a223ba14108d16cca Merge: 51cfd44 95655b8 Date: Tue Jul 17 14:22:11 2018 -0700 Merge pull request #3254 from RosettaCommons/vmullig/bluegene_firstime_issue Attempting fix to Blue Gene/Q first-time execution. First-time rotamer binary generation fails on the Blue Gene/Q infrastructure. This is another fconfig issue. commit 51cfd44147445970bfc22489ecdb98924ef8edca Merge: 1ce334d 57eb803 Date: Tue Jul 17 13:06:47 2018 -0700 Merge pull request #3297 from CyrusBiotechnology/indigo/argobody Code from @indigogo at Cyrus: Antibody grafting, option to define CDRs with an input JSON in exact same format as the preexisting output JSON (from Indigo:) Additions to antibody grafting public app. This adds a non-default option to define CDR loop begin/end positions with an input JSON configuration file. If this file is defined on cmdline input, then the RegEx-based CDR prediction is skipped and the CDR begin/end points are defined by the information in the input JSON. This PR adds the following: a new class to set the CDR sequence position information in AntibodySequence.sequence.cdr.* based on input json numbers. the input json is parsed using the json parsing tools in utility/json_utitlties.hh. JSON format is checked every time and exit with informative message is called if input JSON is misformatted. control logic in apps/public/antibody.cc to check if -json flag is defined on input, and if it is, skip the RegEx step and do the JSON reading step instead. I am not touching anything else in the antibody.cc code. The point of all this is to add functionality for connecting any CDR detection tool's output with antibody grafting protocol input. commit 1ce334d44e78eec9b440086935f0e0b0bf4d76e8 Merge: 9820fea 8a7b022 Date: Mon Jul 16 12:30:42 2018 -0400 Merge pull request #3291 from RosettaCommons/lqtza/add-ca-check-in-ellipsoidal-randomization Fix bug in EllipsoidalRandomizationMover commit 9820feaaaad8dc00d2cc304bd830a7db51f7f64a Merge: f74982f 5b93556 Date: Thu Jul 12 15:38:50 2018 -0600 Merge pull request #3312 from RosettaCommons/sergey/ui Updating pose_viewer and hal apps commit f74982ffc50fd53ef8daf00a67deb96700f44195 Merge: 599543f 8996b6b Date: Wed Jul 11 13:21:25 2018 -0600 Merge pull request #3309 from RosettaCommons/sergey/binder PyRosetta: adding `--no-zmq` build option commit 599543fbb4e83538c46a20c46e179fbfb4378237 Merge: f45d9f2 91f0082 Date: Tue Jul 10 12:28:27 2018 -0500 Merge pull request #3020 from RosettaCommons/jadolfbr/glycan_symmetry Fix GlycanRelax compatibility with Symmetry Make sure ResidueSelector subset and MoveMap are only for the main asymmetric unit in GlycanRelaxMover. commit f45d9f2240d03f1ae820e8eb359e79c512e4c03f Merge: c996496 8dbca3c Date: Tue Jul 10 10:40:20 2018 -0500 Merge pull request #3299 from RosettaCommons/jadolfbr/per_residue_metrics Add support for Per-Residue SimpleMetrics This PR adds two new types of `SimpleMetrics` and associated Code Templates: - `PerResidueRealMetric` - `PerResidueStringMetric` These metrics return values for each residue that is masked by a `ResidueSelector` (which is specified in the base classes for a more consistent interface across all PerResidue metrics). During their apply, they write a value for each residue using Rosetta (default) or PDB identification, as well as the SUM over all of the residues specified. These have also been incorporated into the `SimpleMetricFilter` and `SimpleMetricFeaturesReporter` systems. For the filter, these can act as a `CompositeMetric`, or a user can filter on the Sum, acting as a normal SimpleMetric. For the Reporter, the data goes into their own per-residue table, with `resNum` as a foreign Key to aid in robust analysis. Unit tests have been updated to test this new functionality. Existing SimpleMetrics such as the `SASAMetric`, `RMSDMetric`, and `EnergyMetric` will be converted to have their primary code as a `PerResidueRealMetric`. commit c996496ae10598500d83e74891d755269c481ad4 Merge: 769b677 97aa017 Date: Tue Jul 10 07:44:07 2018 -0700 Merge pull request #3304 from RosettaCommons/rhiju/fix_derivs_lknonpolar_stackelec Rhiju/fix derivs lknonpolar stackelec commit 769b67772635db94d499d2b55ab48b5c59154718 Merge: c869d56 5af3505 Date: Tue Jul 10 10:29:31 2018 +0300 Merge pull request #3300 from RosettaCommons/another_SpliceOut_filter_fix In SpliceOut removed a line that I previously introduced that called … commit c869d56abb713ec2f8552048670acca3247a5423 Merge: 23b3051 fe216c2 Date: Mon Jul 9 18:12:08 2018 -0400 Merge pull request #3260 from RosettaCommons/JWLabonte/sugars/sampling Carbohydrates: Adding RingPlaneFlipMover This merge will introduce a new pyranose-specific Mover that will flip an appropriate ring 180 degrees about its anomeric bond with a counter move (similar to how shear moves work) at an equatorial bond at the opposite position on the ring. This move can thus only occur for 4-linked aldopyranose or 5-linked ketopyranose residues, but most natural sugars are aldopyranoses, and the 4-linkage is common. It is expected that this Mover will help sample in cases where a oligo- or poly-saccharide is "stuck" with its ring plane in the wrong orientation, with substituents trapped on the wrong side of the ring. All tests pass. commit 23b3051a1a53e1fa568ff972ef90a3f86e8caaec Merge: d7b42a1 a578b80 Date: Mon Jul 9 12:55:13 2018 -0400 Merge pull request #3292 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Database additions and .pdb input (and output) bug fixes This merge attempts to increase the percentage of sugar-containing .pdb files that can be read in to Rosetta without modification. I have a current benchmark of 104 .pdb files containing (free) glycan ligands. Before these changes, 78/104 files could load. Files that do not load have 5 separate problems, 3 of which I address with this merge. After this merge 92/104 files should load. As an extra bonus, this merge expands on @BrandonFrenz's work and completes the database such that all sugars can be output with the PDB 3-letter codes, if that is what is desired, not only the limited subset. It also integrates (effectively) the bug fix made in PR #3289 and negates the need for PR #3175. All unit tests pass. c-term_conjugation test is simply the centroid ResidueTypeSet reporting on its larger size. carbohydrates integration test expanded. glycan_anomers test is currently unstable and it is hoped that this merge corrects that. Note that master was already broken when I made this merge. commit d7b42a161a8db16595be962bfc92432db9902788 Merge: 42c75e6 a134ebf Date: Sun Jul 8 21:42:52 2018 +0200 Merge pull request #3305 from RosettaCommons/jaumebonet/fflchem allow FFL to work with chemical binders commit 42c75e693d8509d478c697f4950122d263c8f2f6 Merge: c7c6c8f fc85e0b Date: Thu Jul 5 13:41:41 2018 -0400 Merge pull request #3303 from RosettaCommons/everyday847/revive_cif_io Hotfix 2: unit tests are ok now commit c7c6c8f24db60230dc83e0b84400564fe5501600 Merge: 2803f85 c8f3251 Date: Wed Jul 4 17:18:34 2018 -0600 Merge pull request #3301 from RosettaCommons/sergey/binder PyRosetta, updating Binder submodule and putting `Pybind11` into system includes commit 2803f85183030e4abb7e7c665f4500bbaf90d104 Merge: 06c897a ab0bd7b Date: Wed Jul 4 17:58:34 2018 -0400 Merge pull request #3302 from RosettaCommons/everyday847/revive_cif_io Master unit test hotfix -- adding new centroid-rot params that I didn't commit earlier. commit 06c897a0cb6c70a06f144fc74b937e30d9ae433f Merge: 7deda35 9fb62d5 Date: Wed Jul 4 15:49:16 2018 -0400 Merge pull request #2845 from RosettaCommons/everyday847/revive_cif_io Revive CIF I/O and fix some big bug classes At final tally, this branch fixes about 8K new PDBs (~1/2 of broken PDBs) and 1K cifs (and thousands of others it moves to a more 'chemically realistic' bug class'). Massive bugfix to `metalloprotein_abrelax` which had been loading in the CCD type `pdb_CYZ` for its centroid_rot phase, and to various enumerative_sampling and related tests that had been loading in `pdb_VRT`. A couple trajectory changes are observed due to floating point issues. Some logfiles change due to spacing alterations in atom names. (Use stripped names in more places -- the RT will always have them in addition to the with-spaces alias, while the CCD residue will ONLY have the stripped version.) Also prevented `PartitionContactScreener` from wiping out protein trajectories -- residues often won't make adjacent-residue contacts in typical (say) cyclic peptides. commit 7deda350387909882721e82407e30054a16def51 Merge: c003446 e96b0ce Date: Tue Jul 3 14:29:33 2018 -0700 Merge pull request #2984 from RosettaCommons/kalekundert/cbrss Improvements to CoupledMoves and ClashBasedRepackShell commit c00344612c629eddb993ad58d2fd6ce11244a1b2 Date: Tue Jul 3 17:29:05 2018 -0400 beautifying commit 226627e8a7932024ae51084e7bd070076cd8db45 Merge: 32653e1 1077e88 Date: Tue Jul 3 13:12:32 2018 -0600 Merge pull request #3298 from RosettaCommons/sergey/f2 Fixing an inclusion-order related problem and removing `/usr/include` and `/usr/local/include` from our default include paths commit 32653e1e37cacf5573b6f6e243cea48df188bc83 Merge: d1b9f3e a7fc6e7 Date: Tue Jul 3 11:45:55 2018 -0500 Merge pull request #3177 from RosettaCommons/darwinyfu/ProtEnsemble Adding of protein ensembles to small molecule docking. Can now pass in multiple receptor files to dock ligands against when using the Transform and TransformEnsemble movers. Expected integration test changes: hash signature of ligand docking applications. hts_io will change since it runs Transform with repeat option and transform conformation update has been moved outside of the repeat loop so it only updates the final pose once. commit d1b9f3ec57e693983213b0bf94345f9add42f6cd Merge: d8516a2 2fd1416 Date: Mon Jul 2 13:43:48 2018 -0700 Merge pull request #3213 from RosettaCommons/hssnzdh2/unsatsel2 Updating UnsatSel to be better commit d8516a28f439cb488a1d882d98a23a668be723f4 Merge: c0e3112 692ec3c Date: Mon Jul 2 10:53:06 2018 -0500 Merge pull request #3286 from RosettaCommons/roccomoretti/scientific_test_update Update the PDB diagnostic scientific test reference results, in light of the recent fixes. In addition, I've added a few extra failure categories, which will further separate out the unknown category into manageable chunks to fix. commit c0e311245b9b1bfbf962826952765fb4b8f50499 Merge: 590c1cf d9ef58a Date: Sat Jun 30 21:11:30 2018 +0300 Merge pull request #3293 from RosettaCommons/fix_SpliceOut_bug In SpliceOut, Splice_filter() did not use the scorefunction defined i… commit 590c1cf1124c8d2aeb009a65883f1934a9f69034 Merge: 3dfd733 ba129b6 Date: Fri Jun 29 12:55:57 2018 -0500 Merge pull request #3294 from RosettaCommons/jadolfbr/iam_ft Make InterfaceAnalyzerMover FT independant This PR makes the explicit constructors independent of the FoldTree (those other than the Jump Number specification). It does this through moving chains in cartesian space instead of dihedral space for ignored chains and interface chains to create the separated pose needed. This makes IAM crash a lot less on general structures and enables its broad use for ligands (of different chains). Consequently, `InterfaceMonteCarlo`, which is used in `RosettaAntibodyDesign`, is much more robust. Thanks to Joel Karpiak from GSK for identifying this issue and testing. A new integration test is added that would segfault fail before this PR. commit 3dfd733776c8ea369efbfe912b8f93357f4099b4 Merge: ff95a51 2ca9f82 Date: Fri Jun 29 09:53:03 2018 -0500 Merge pull request #2850 from RosettaCommons/roccomoretti/clang_SA_fixes Knock out most of the Clang Static Analysis issues There's still about 12 files with issues. As I've knocked out all of the "easy" ones, all of these are pointing to potential bugs (perhaps). It will take expert eyes to figure out what should be going on here. See https://github.com/RosettaCommons/main/pull/2850 for a list of remaining issues. commit ff95a51558f1a4a97f622c609a049ce20613ac76 Merge: 9a384a3 7a52c47 Date: Thu Jun 28 20:14:02 2018 -0400 Merge pull request #3288 from CyrusBiotechnology/196_BASE_cm_ligand_mode resolves #3275, #3276. CoupledMovesProtocol now exits with more interpretable errors when misconfigured (ligands present but not flagged as on) instead of segfaulting. It also takes ligand-related settings via getter/setter instead of command line flag. commit 9a384a30b573e8717c77864667311ef0db417ae9 Date: Thu Jun 28 19:16:57 2018 -0400 beautifying commit 397a159f16d674c5b01edcca6105fb435e249920 Merge: c6c5f7c a52911c Date: Thu Jun 28 10:37:28 2018 -0600 Merge pull request #3290 from RosettaCommons/benchmark Benchmark scripts: updating unicode handling to Python-3 commit c6c5f7c4db49f24d14a0b64f8a930c68eadec10b Merge: 6f59745 c689086 Date: Thu Jun 28 10:36:06 2018 -0600 Merge pull request #3287 from RosettaCommons/sergey/scientific adding scientific.protein_data_bank_diagnostic.cif test commit 6f59745c598e398fae372463f1334c8770969d7c Merge: c4ca64e 1699668 Date: Thu Jun 28 11:05:12 2018 -0500 Merge pull request #3165 from RosettaCommons/raemisch/DensityScoreResidueSelector DensityFitResidueSelector This ResidueSelector aims to select residues that have good fit (default) /bad fit (invert) into electron density. Uses either a Zscore made up of density, nbr_density, rama/sugar_bb (for glycans), and cartesian geometry OR the correlation to density that is used internally to determine the density score. The Zscore has been adapted and refactored from `FragmentBiasAssigner`, which is used to determine poor density in hybridize. Thanks to @fdimaio for his help in this! Numbers and cutoffs match well with Coot's density fit analysis tool. Additional options are present to give a residue selector as a mask, which either acts as a subset for `match_res` OR (by default) acts to only calculate the Zscore among those residues (which CAN be turned off). This is VERY important for glycans or other poorly-resolved residues, or the zscore will be inherently bad for all of them due to the protein bias. commit c4ca64e68b90938d036923eb5320d72bf2d907c9 Merge: 757388b 603c7be Date: Wed Jun 27 17:43:46 2018 -0700 Merge pull request #3257 from RosettaCommons/yhsia/TaskAwareSymMinMover_memory Changed default minimization type in constructor to dfpmin_armijo_nonmonotone to match the rest of the code. @vmullig made some changes to AACompositionEnergy for efficiency, doesn't quite fix the exact issue though.