commit f1b7bfe7a847394873e11f6e1ebbd669d61f43c9 Merge: 0849c77 db5fd4a Date: Thu Jun 29 11:28:53 2017 -0700 Merge pull request #2364 from RosettaCommons/dimaio/ref15_compatability_fixes Dimaio/ref15 compatability fixes commit 0849c77b223d56c657c807003e341a191bf61701 Merge: e5c4b96 9caeb4f Date: Thu Jun 29 00:56:26 2017 -0700 Merge pull request #2334 from RosettaCommons/vmullig/fix_genkic_sugars Fix bug in GenKIC that was preventing its use for sugar chains I was rebuilding connection-dependent atoms foolishly in GenKIC, resulting in an inadvertent distortion to the C2 atoms in sugars. I'm pretty sure that the place where I was doing this is a place where this doesn't need to be done at all. This might cause very minor integration test changes to anything that uses GenKIC. A number of GenKIC-related integration test changes are expected. commit e5c4b96bda7a8f3810dc22686ec56df052c44d8a Merge: d8d8fcd 0cd3cbb Date: Wed Jun 28 22:22:26 2017 -0400 Merge pull request #2360 from RosettaCommons/aleaverfay/threadsafe_rts This PR lays down some thread safety for an eventual JD3 MultiThreadedJobDistributor. Here, I am working to ensure thread safety for the just-in-time ResidueType loading system as implemented by @rhiju and maintained by @roccomoretti and @everyday847. The idea is this: The ResidueTypeSet (RTS) will create read locks on its ResidueTypeSetCache (RTSC) before each time it is read from. If it determines that an operation it requries will modify the RTSC, then it releases the read lock and then tries to obtain a write lock. (Briefly, the "ReadWriteMutex" allows several threads to say "I'm reading" by incrementing a mutex-controlled counter when they start reading, and decrementing that counter when they are done. If a thread decides it needs write permission, then it prevents any more readers from coming along and gaining read permission, while waiting for all the existing threads to complete their work. Once they've completed, then the write lock is granted and the thread may write. One complexity of working with read/write locks is that a thread may deadlock itself if it does something such as obtain a read lock, and then later try to obtain a write lock. Since the read lock is never released, the write lock will never be obtained and the thread will sit there and do nothing. Indeed, if the locks are obtained in the opposite order (first the write lock, then the read lock), the system will also deadlock. Systems involving read/write locks need to build into themselves rules about which functions are off limits at which times.) The RTS's public interface will handle all the locking required -- the complexity of who is allowed to do what is managed internally by the RTS and its derived classes. The RTS base class provides several template methods that derived classes will supply implementations for (i.e. the GlobalResidueTypeSet and the PoseResidueTypeSet) where these methods will come with lock-based promises and requirements (e.g. generate_residue_type_write_locked is only invoked by the base class after a write lock has been obtained therefor all interactions inside this function with the RTSC are safe -- but the function should not call any of the methods of the RTS that themselves try and obtain read or write locks). This system is significantly less brittle than the one I had begun working on, and which @roccomoretti helped talk me out of, where the ResidueTypeFinder would be obtaining read and write locks on the RTSC -- that system might have slight performance advantages, however, as it allows the thread to obtain a single read lock or a single write lock and then to complete all of its operations. The PR where I began working on that, PR #2353, has been shelved. Perhaps if this current system proves too slow, we can reconsider its approach commit d8d8fcd8263ffcab42df16edcaeb4e89a57c7387 Merge: b4b752a 62537d0 Date: Wed Jun 28 11:03:43 2017 -0500 Merge pull request #2361 from RosettaCommons/roccomoretti/mpi_cycpep_logfix Attempt to fix stochastic interleaving of logs in mpi_simple_cycpep_predict We're getting some spurious logfile changes on the test server due to interleaving logs. Use -mpi_tracer_to_file to address this. commit b4b752a1c875ed65deebafb61d37ff295d56de02 Merge: 7836ccf 1628162 Date: Wed Jun 28 11:01:07 2017 -0500 Merge pull request #2362 from RosettaCommons/roccomoretti/rosettacm_template_length Fix bad error message with RosettaCM length mismatch. If you have a mismatch between the length of the template and the length of the input in RosettaCM (Specifically if your templates are accidentally longer than your input.) You can get really non-informative errors. (e.g. memory corruption due to writing off the end of a vector in release mode.) Check for this condition, and pop up an intelligible error message if it occurs. commit 7836ccfb62ede827b0309fe0c0f2e5d2870ebb03 Merge: fedf822 1366358 Date: Tue Jun 27 15:07:05 2017 -0400 Merge pull request #2300 from RosettaCommons/lqtza/SlideIntoContact_with_delta DockingSlideIntoContact updates. commit fedf8229362294bb5c9d5551dc388418b7cad650 Merge: 6ff0bf7 e40755b Date: Tue Jun 27 11:47:28 2017 -0700 Merge pull request #2294 from RosettaCommons/bfrenz/enumerative_sampling_integrationfix Fixed my integration test. commit 6ff0bf7f2c5331d2bf59e8a313efa8aa72e7108c Merge: 11b529c 18014b4 Date: Tue Jun 27 09:53:41 2017 -0500 Merge pull request #2356 from RosettaCommons/roccomoretti/gcc7.1_fixes Fixes for GCC 7.1 There's a number of issues (both warning-as-errors as well as actual compiler-quits errors) that pop up when compiling Rosetta with GCC 7.1. This PR should fix those. The main changes are in places where switch/case statements can "fall through" (breaks/returns added) and a change in how we handle multi-level templated class resolution in SingelResidueDunbrackLibrary (as GCC 7.1 has issues with the way we were doing it before.) Surprisingly, no test changes are expected, aside from the ones that are failing in master. commit 11b529c546921ef3fac507f44414d4da673f7e30 Date: Mon Jun 26 15:51:47 2017 -0700 Switching all simple_cycpep_predict integration tests to use ref2015 (more commonly known as "Scorey McScoreface") instead of talaris2014. All future simple_cycpep_predict development will be for the new Park/DiMaio energy functions. commit b3906d1f49ca4ed1528e24baedd16fefcd5006c4 Merge: ee40d93 f07db3b Date: Sun Jun 25 15:26:11 2017 -0600 Merge pull request #2350 from RosettaCommons/sergey/f Adding workaround for setuptools include argument commit ee40d93a3045250fe0ab5bae9d17bd3a03552dca Merge: c2597b2 5200bfe Date: Sun Jun 25 00:17:08 2017 -0700 Merge pull request #2272 from RosettaCommons/vmullig/ui/bundle_gui Add a GUI pilot app that permits interactive, realtime parametric design MOTIVATION AND DESCRIPTION This is primarily intended to be a fun demonstration of the power of a graphical user interface for Rosetta design. There are many tasks that we currently do in a very time-consuming and painful manner. One such task is the selection of parameter ranges for parametric design. Typically, a helical bundle designer must arbitrarily pick some parameter values, write a RosettaScripts XML file that calls the MakeBundle mover or the BundleGridSampler mover to generate geometry from those values, write the geometry out to disk as a PDB file, read the PDB file into a program like PyMOL, examine the output, and make decisions about how to vary the parameter values. One iteration might take a minute or so, a few milliseconds of which are spent actually computing the geometry. Wouldn't it be better if we could make that an interactive process? This application does just that, making it easy to select parameter values that one might then sample around in a large-scale, non-interactive sampling session. I've also added some extra bells and whistles that let you call the packer and the minimizer (to get a crude idea of the packed geometry possible with a given backbone), or to import additional non-parametric geometry (e.g. for small-molecule binder design) that you can drag and rotate independently from the parametric geometry. INTERNALS This pull request adds: - The app (which internally is calling the MakeBundle mover, PerturbBundle mover, PackRotamersMover, and MinMover). - New UI directories (note that these are not currently separate libraries, but could be made into separate libraries should the need arise) for: - Code that only links up to Rosetta's utility library. - Code that only links up to Rosetta's core.5 library. - Code that links up to Rosetta's protocols.7 library. - A new base class for a basic OpenGL pose-drawing widget. This is NOT meant to replace the work being done by @jadolfbr to create pose-drawing widgets. This is just a temporary standin. Its current features include: - Van der Waals sphere representations of a pose (but no sticks, ribbons, or anything else that's fancy). - Colouring by selection or by per-residue score. - Dragging to rotate, and right-dragging to zoom. - Tens of millisecond refresh on moderately-sized poses (i.e. realtime interactivity). - A derived OpenGL pose-drawing widget class specific for this app, which adds the ability to drag the nonparametric geometry separately from the parametric. I think that we can handle a lot of the specialization of the visualization widget by subclassing, and this demonstrates that idea. - Some specialized widgets built for Crick parameter manipulation. ADDITIONAL STUFF (done now): - Figure out what copyright text needs to go at the top of Rosetta ui files. It oughtn't be identical to the Rosetta copyright, I think, since this isn't strictly part of the Rosetta software suite. It should convey that it's covered by the same type of licence and all that, though. --> Update: Dennis at CoMotion has confirmed that we can just use the regular Rosetta copyright text, so I shall do that. - Figure out how to cover this with unit tests. --> Put off to a future pull request. - Fix bug when helix 1 is deleted and other helices copy from it. commit c2597b2e5432f089377cfcc291aebeff77bc456f Merge: 7e56941 51f9fe9 Date: Sat Jun 24 17:28:07 2017 -0500 Merge pull request #2348 from RosettaCommons/jadolfbr/rs_jd3 RosettaScripts - JD3 Port and PyRosetta Support Overview ====== This PR brings RosettaScripts into the modern era of JD3 and PyRosetta. The implementation is version 1 - with support for different protocols and script_vars being passed to the job_definition file. This should enable fairly robust benchmarking of protocols through RosettaScripts. Thanks to @aleaverfay for his guidance, debugging, and code added to the branch! PyRosetta support is here through a slew of new functions in RosettaScriptsParser to easily take an XML/Pose and return a ParsedProtocol. @basantab ``` ///@brief /// Main, Basic XML to Mover Function. /// ParsedProtocolOP generate_mover_and_apply_to_pose(core::pose::Pose & pose, std::string const & xml_fname); ``` This PR also removes the JD2 integrated code in the RosettaScriptsParser and removes the 'Parser' class as it was unused. An example JD3 job_definition file for RosettaScripts: ``` ``` Command to run this: ``` rosetta_scripts_jd3.macosclangrelease -include_sugars -write_pdb_link_records -in:file:job_definition_file jd3_rs_definition.xml ``` Other Changes ========== - Add Overwrite support to JD3 (Thanks @aleaverfay ) - Fix a few JD3 bugs ( @aleaverfay ) - Add support for prefix/suffix - Move ```protocols/jd2/parser``` to ```protocols/parser``` - Add Integration test - @vmullig Port -info and -output_schema options to the JD3 implementation, moved functions to rosetta_scripts/util.hh Integration tests: =========== All changes are cosmetic and have been gone over manually. commit 7e56941afcd8dcb07adc2535cadfacce5f5ad7fb Merge: 8815dd0 db255b3 Date: Fri Jun 23 18:20:22 2017 -0500 Merge pull request #2306 from RosettaCommons/roccomoretti/add_residuetype_reporting Better reporting of double-addition of ResidueTypes to an RTS Change a runtime_assert to an if + tracer output + utility_exit. commit 8815dd06750daf5486f0095866792aab434225fb Merge: ff14aaf 6e18834 Date: Fri Jun 23 18:18:26 2017 -0500 Merge pull request #2311 from RosettaCommons/roccomoretti/fix_atom_alias_delete Fix issue with delete_atom and atom_aliases. If you had a patch which deleted an atom which has an atom alias, there's a good possibility that it wouldn't work, as it would crash when you're attempting to delete the alias and the stripped alias name. commit ff14aaffffa1c49b1b9dd47bb12036c1f820ab4e Merge: dc0b9cf ce44227 Date: Thu Jun 22 10:31:41 2017 -0400 Merge pull request #2205 from RosettaCommons/guffysl/setup_metals_mover Added SetupMetalsMover, which provides auto_setup_metals functionality in mover form. In addition to the normal command line options for auto_setup_metals (which default to the command line values), this mover takes as attributes an optional selector or resnum list to specify which metal(s) should be set up and an option to only add constraints and not chemical bonds/patches (useful for reapplying constraints if they are removed during a protocol). commit dc0b9cf5e6fc1125aec34ef713af9cb8667ef6b1 Merge: f537f8e 479e002 Date: Wed Jun 21 14:16:43 2017 -0500 Merge pull request #2351 from RosettaCommons/roccomoretti/erraser_fix Add missing dot to ERRASER linuxgccrelease test Make it look like the other platform settings. Should address an issue mentioned on the forums: https://www.rosettacommons.org/node/9955 commit f537f8e1738c39f418c9f4552d020da32fcc7248 Merge: 9a41be8 942ea37 Date: Tue Jun 20 23:02:40 2017 -0400 Merge pull request #2347 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Adding a few more sugars to the database for the GlycanRelax benchmark All tests pass (except the broken ones). commit 9a41be8934ae5e2e68702498ed6d22047a844c7f Merge: 1dacdae 96212f1 Date: Tue Jun 20 15:45:29 2017 -0500 Merge pull request #2265 from RosettaCommons/roccomoretti/grid_global_fix Fix global state usage in ScoringGrids The protocols::qsar::scoring_grids::GridManager was a strange mix of a global cache and modifiable global state. That wasn't great because the implementation resulted in a lot of cross-dependencies between grid usage. This pull request should hopefully decouple the global grid caching (still held by GridManager) from the modifiable state (now held in local variables as a GridSet object). An upshot of this change is now you can have multiple GridSet objects in a single RosettaScripts run. Previously, all grids you were working with were . The multiple-grid approach is being done in a backwards-compatible way, so existing XMLs should be able to work as-is. commit 1dacdae363e1a1234e51409c978790a8210473bd Merge: fb2dbcb 7552734 Date: Tue Jun 20 14:28:07 2017 -0500 Merge pull request #2332 from RosettaCommons/jadolfbr/jd3_template Add JD3 Code Template - Note that this will change the app from generate_app_templates_jd2 to generate_app_templates and you will need to specify the --type option to either jd2 or jd3_standard. commit fb2dbcb366a55929776102b626f2e006d3d39ab2 Date: Tue Jun 20 12:54:38 2017 +0200 Revert "Update pyrosetta distro to bootstrap minimum setuptools." This reverts commit 7b4b4e0db91e111c9c5898287c02368820f7fad3. commit 7b4b4e0db91e111c9c5898287c02368820f7fad3 Date: Tue Jun 20 12:52:22 2017 +0200 Update pyrosetta distro to bootstrap minimum setuptools. Update pyrosetta distribution to include ez_setup.py and bootstrap a minimum setuptools version if setuptools is not present in the install environment. Specify a minimum setuptools version needed to support setup.py. commit 6bfef9b6fd654c0380feeaee2362e394db0b1511 Date: Tue Jun 20 12:48:45 2017 +0200 Remove miscommited version.py. commit 61343ef9c1fa9c7a6789699ed6b98a1898b99dda Date: Tue Jun 20 12:46:12 2017 +0200 Revert "Removing unneeded include key-arg from find_packages" This reverts commit c8aa271dc6a4f10ec7ae13fcc11ee12f368f177a. commit c8aa271dc6a4f10ec7ae13fcc11ee12f368f177a Date: Mon Jun 19 18:39:52 2017 -0400 Removing unneeded include key-arg from find_packages commit 5da0f9b5af42bac475595d6ab8040f987567308b Merge: 8ef775e fe93cc7 Date: Mon Jun 19 13:13:25 2017 -0600 Merge pull request #2342 from RosettaCommons/sergey/f Merging parts of #2285 related to adding new JSON library to add json.hpp into external lib files commit 8ef775e15b6050f5abf85f4225e1824cb161fa2b Date: Fri Jun 16 18:24:43 2017 -0700 Beautifying unbeautified file in master. commit 672906cd37d76ee4a0b431a1ff01dd004100a867 Merge: 5287df8 283b79d Date: Fri Jun 16 17:00:49 2017 -0700 Merge pull request #2337 from RosettaCommons/bcov/fixes/NeighborhoodDontIncludeFocus NeighborhoodResidueSelector include_focus_in_subset=false fixes commit 5287df8acaa90b4cc59bfafb0dad801d4b9adab5 Merge: a5ed37f 46165ef Date: Fri Jun 16 14:32:25 2017 -0700 Merge pull request #2336 from RosettaCommons/dimaio/cartsymmmin_fix Bugfix for cartesian symmetric minimization with new min scheme commit a5ed37f352856a54a8715fc6c9905efbe1034726 Date: Thu Jun 15 15:56:02 2017 -0700 Modify Ca params file for centroid to be consitent with fullatom (enabling CA sites to be modelled in RosettaCM) commit d2339c8ec61f528fd7a7e3560085069014c782ee Date: Thu Jun 15 15:48:10 2017 -0700 Clean up debug output format in make_symmdef_file commit 1d20429ae76bc6314aab230ee40837409f82e8f8 Merge: 3657069 0b7e637 Date: Wed Jun 14 11:03:45 2017 -0500 Merge pull request #2331 from RosettaCommons/jadolfbr/template_fixes Jadolfbr/template fixes A few small fixes for app templates as found by @smlewis (Also adds print function from future as Python3 rocks) This addresses #2327 commit 36570699c26d01edcb92c4bf7302cefbefeef4eb Merge: 7880b6f 94a82f8 Date: Wed Jun 14 01:08:58 2017 -0400 Merge pull request #2197 from RosettaCommons/everyday847/sidechain_rebuild_hotfix Avoid weird mainchain condition commit 7880b6f57ecb65d69e9c8faf3321246e7e625de2 Date: Tue Jun 13 14:19:00 2017 -0700 Removed assumed connections between non-polymers and glycans. There was a problem when a non-polymeric HETATM (metals e.t.c.) appears before a protein-bound glycan in the pdb file. There was a check whether something is NOT a lower terminus, but also the previous residue is not a polymer. If that is true, Rosetta makes that residue a terminus, because a bond non-polymer -> polymer doesn't make sense. I added another condition, which checks if residue i has a lower_connect to another polymer to get around that. commit 88bbe75510a117f164304d77ff363f55831bb206 Merge: 556e443 79480ba Date: Mon Jun 12 15:04:59 2017 -0400 Merge pull request #2324 from RosettaCommons/everyday847/goto_slayer remove protocols gotos commit 556e443c5bb51729852721f167eecac2b3520d13 Merge: bb4834f 6bbe2f8 Date: Mon Jun 12 10:03:10 2017 -0400 pulling remote commit bb4834faad6195f623b9512b0893adcf3e6f8e1b Date: Mon Jun 12 09:56:52 2017 -0400 Accept utracers AGAIN commit 6376c6cd85b238c8b9364e16a96230c40e323fe3 Date: Mon Jun 12 01:00:21 2017 -0400 Reaccept utracers with good distances on disulfides commit 9744aac90f9c5ffecfa6dcc85bb60499a123df3a Date: Mon Jun 12 00:08:50 2017 -0400 beautified commit 75015e7bb6f865dc97613d74e0307244257cb20b Date: Mon Jun 12 00:08:35 2017 -0400 OK, now we work. commit de1cd2409717c94849ec988b763c78ab96373cc9 Date: Sun Jun 11 22:12:56 2017 -0400 Accept utracers commit 6ec2c7cab5a8cbe5deabf498476caa31e6ed5dd7 Date: Sun Jun 11 17:39:14 2017 -0400 Turn on commit c4528b378eeb40eb2f13d939c5d932ba7e5effc7 Date: Sun Jun 11 17:07:00 2017 -0400 Removing deprecated files commit 1890fbfa458430c39a6a36bf5fd2cfeaa968ee90 Date: Sun Jun 11 00:38:30 2017 -0400 Re-adding Binder submodule that was accidentally deleted by @orlypolo commit cfdba7b24f42d4d1ae7a94bad3e1118d27828de8 Merge: 2d5adb7 47adafe Date: Sun Jun 11 00:34:29 2017 -0400 Updating PyRosetta build script so it now check if Binder submodule is present commit 2d5adb720fcbaa8e16f0b60bdb062a4eea0f102c Date: Sat Jun 10 17:15:33 2017 -0400 OK, this is the final hotfix commit ec2510419481ed952c3c1288cb2239973489aaa3 Date: Sat Jun 10 17:06:54 2017 -0400 whoops commit 792b5a54c3fb83b78ee382552a56037ead0a8bed Date: Sat Jun 10 17:03:25 2017 -0400 OK... this might work out. It turns out we NEED not to flip NEUTRAL_PHI. We just also had to support other conditions! commit ca452e5f526902113805afd6cb36625bad4dbbbf Date: Sat Jun 10 14:03:08 2017 -0400 OK, this should rescue things commit 8c17d54b35224ad7cc71a5dae3c160af44e2a569 Date: Sat Jun 10 13:36:33 2017 -0400 OK, now a better condition for Dunbrack2002Test -- for real; found a typo (lower for upper!) commit b549c90efe44688fd1f283bd46e1cbbe935fc5f4 Date: Sat Jun 10 13:29:44 2017 -0400 OK, now a better condition for Dunbrack2002Test commit ea9a570304df0cc4b5d0dc719735ccab9b2aae1f Date: Sat Jun 10 13:27:58 2017 -0400 remove entirely commit 20798a0a7e183582e2e7204940e7d89db5cdd9fd Date: Sat Jun 10 13:26:57 2017 -0400 Just change d_multiplier within get_bbs to be 1. that makes cyclic_geometry pas. commit ff49fec1947b0b2e14a7bdbda681f0d27f3eaab3 Date: Sat Jun 10 13:08:13 2017 -0400 ok, step 1 is revert to master before I screwed things up. Now cyclic geometry should pass and my new unit test should fail. commit 4086ca62a9b57d4ad7ad1e36c6b6df97eca61a51 Merge: 5f7ed58 698afca Date: Sat Jun 10 12:03:36 2017 -0400 Merge pull request #2314 from RosettaCommons/everyday847/fix_LD_fadun_equivalence L/D equivalence for fa_dun when upper and lower are ill-defined commit 5f7ed586cb326cc7a249df91ae1d080929075c0d Merge: 62b5907 f65c802 Date: Sat Jun 10 14:30:01 2017 +0300 Merge pull request #2230 from RosettaCommons/orlypolo/peptiderive-head-to-tail-cyc reformatting handling of candidate cyclic peptide information to allow… commit 62b59070f357d30e25ee3dde59b6cb5f14fbd52a Merge: 99aef3c ab91d72 Date: Fri Jun 9 19:16:42 2017 -0700 Merge pull request #2313 from RosettaCommons/dimaio/cartbonded_ncaa Remove an unnecessary check for canonic amino acids in cart_bonded commit 99aef3cc4b629877df4e830d8db72aa9b184cf79 Merge: 9b824a4 d452eba Date: Thu Jun 8 23:09:56 2017 -0600 Merge pull request #2310 from RosettaCommons/sergey/binder Fixing Linux PyRosetta build commit 9b824a43a1eb31ab0345e4ae9871a2ab01805334 Merge: c33afff be850af Date: Wed Jun 7 12:35:36 2017 -0500 Merge pull request #2293 from RosettaCommons/jadolfbr/glycan_data_updates Jadolfbr/glycan data updates This PR updates the default glycan conformer sampling table with new data derived from the PDB using Adaptive Kernal Density estimates (same methods as the 2010 rotamer library) and a Von Misses Kernal to derive dihedral bins for each glycan linkage type seen in the data. Raw Data was provided by Thomas Lutteke of Glycosciences.de and the densities were generated by Maxim Shapovolov and Roland Dunbrack. This PR also updates a few default parameters to Glycan Relax and adds a few options for benchmarking. Integration test changes expected to tests that use Glycan Relax. Density estimates were used to generate cubic spline(s) in matlab in order to identify torsion bins and assign conformers to each linkage data point using the inflection points of the spline to define single-dihedral conformer bins. For example, the Chi1/Omega2 of an ASN a-D-GlcpNAc has three bins, as identified by the maxima of the density and boundaries at the minima on either side of each maxima. commit c33afffc5a88f5d9af785c0f517d42458885727f Merge: ada22a1 db287d1 Date: Tue Jun 6 15:54:51 2017 -0700 Merge pull request #2299 from RosettaCommons/vmullig/add_trimesic_acid Re-activiate commented-out TMA unit test The added unit test produces weird NaN behaviour ONLY in the Mac/clang build. I think that this is illustrating an underlying bug in the way that the Mac/clang build is doing math in `core::kinematics`, and this might be related to the existing unit test failure for that build (where different numbers are appearing than what we're getting for the other builds). It's easiest to debug the problem if the master branch is highlighting it. We might get to this at the noncanonicals meeting this week. commit ada22a12553952d3d4ca4fd7a2e9b487c16a8438 Merge: ea52e90 3485199 Date: Tue Jun 6 15:05:30 2017 -0700 Merge pull request #2107 from RosettaCommons/raemisch/glycan_pdb_io Raemisch/glycan pdb io commit ea52e9050b931fbccf90a3123a8624866477360f Merge: fd18fbc 80edb0c Date: Tue Jun 6 12:51:53 2017 -0600 Merge pull request #2301 from RosettaCommons/sergey/binder Updating PyRosetta build script to use LLVM-4.0 when building Binder commit fd18fbc0756bf6432a09942009f1d5360ae05028 Merge: 4d211ff 9e0e742 Date: Mon Jun 5 21:10:59 2017 -0700 Merge pull request #2303 from RosettaCommons/vmullig/fix_score12_test Fixing currently-failing unit tests on test server The beta_nov15-as-default merge broke the ScoreTests:test_Score12 unit test. The changes seem to be purely cosmetic changes to output formatting. I'm updating the UTracer for the test to fix the test. Note that no score values change. commit 4d211ffc93308c3b27be75d8e327d0d84976b856 Merge: 455b057 07bc1b3 Date: Mon Jun 5 17:26:33 2017 -0700 Merge pull request #2302 from RosettaCommons/hahnbeom/support_to_centroid_min adding interface on weights file for calling CENTROID_MIN etable commit 455b05767daf5398f822622cb63be44b8ea8d169 Date: Mon Jun 5 15:21:40 2017 -0400 Fixing PyRosetta documentation index generation, thanks to @jadolfbr for reporting this! commit 282e2a07a1b6853810782f45b2d9f5c478bc169f Date: Sun Jun 4 20:52:49 2017 -0700 Forgot to re-beautify my unit test after commenting out some stuff. Sorry! commit 5973c1323d81ed129c0c248a113cd7a6314aa9b7 Merge: b6257e0 e9bd761 Date: Fri Jun 2 21:47:26 2017 -0700 Merge pull request #2216 from RosettaCommons/rhiju/swm_checkpoint_fixes Merging this fix to stepwise checkpointing -- I think it's substantially more important for this to be working at the two basic levels (i.e., good checkpoints for last and low) rather than ensuring that it gets trajectory stats right too. commit b6257e06bab52021abbaa952604ef47cb0371e45 Merge: 769df8c a679cc7 Date: Fri Jun 2 21:42:02 2017 -0700 Merge pull request #2298 from RosettaCommons/everyday847/more_farfar_unification A couple minor improvements for FARFAR CSA commit 769df8c0a7939a8b69119005c07eb37749d919b6 Merge: a5916d5 a7c67a5 Date: Fri Jun 2 19:10:22 2017 -0700 Merge pull request #2075 from RosettaCommons/vmullig/add_trimesic_acid Add trimesic acid (crosslinker) This adds trimesic acid, a three-way crosslinker that can be used in peptide synthesis. Tasks: - [x] Add params file (note that crosslinkers are off by default in residue_types.txt). - [x] Set up virtual atoms. - [x] Set up connections. - [x] Ensure overall neutral charge. - [x] Ensure symmetry. - [x] MM atom types. - [x] Chi definitions and rotamers (using PROTON_CHI lines in params file). Note that trimesic acid prefers +/- 30 or +/-150 degrees for chi1, chi2, and chi3. - [x] Add symmetric version of params file. - [x] Add DAP, if it doesn't already exist --> It exists; params file updated. (Called DPP in PDB; renamed to DPP in database, too.) - [x] Add DAB, if it doesn't already exist. --> It exists; params file updated. - [x] Update ornithine params file. - [x] Add sidechain conjugation patch for LYS, ORN, DAB and DAP, if it doesn't already exist. - [x] Unit test for this. - ~~Deprecate LYX? (Will have to update integration tests that use it.)~~ --> maybe in the future. - [x] Add support for TMA to CrosslinkerMover: - [x] Cherry-pick in change of name from ThreefoldLinkerMover to CrosslinkerMover (from pull request #1839). - [x] Add setup logic for TMA in the asymmetric case. - [x] Add setup logic for TMA in the symmetric case. - [x] Allow LYS, ORN, DAB, or DAP side-chains to present TMA. - [x] Unit test for functional form of constraints. - [x] Integration test -- asymmetric case. - [x] Integration test -- symmetric case. - [x] Documentation. - [x] Add support to simple_cycpep_predict for TMA. - [x] Integration test. - [x] Documentation. - [x] Add weight option to GaussianFunc (needed for the construction of a suitable torsional potential for TMA). - [x] Document changes to GaussianFunc. - [x] Calculate correct values for torsion potential to ensure +/- 30 degree minima (calculus -- yay). - [x] Add potential offset to give minimum value of 0 (more calculus). - [x] Update PatchOperations to report their own names for errors / debugging. - [x] Beauty. - [x] Document change of name of ThreefoldLinkerMover --> CrosslinkerMover. @gbhardwaj commit a5916d5a8963ee1df1f5fe32dcee55a9c3c93a9a Merge: 1451d9a 62f473f Date: Fri Jun 2 12:11:06 2017 -0600 Merge pull request #2296 from RosettaCommons/sergey/binder Removing Binder sources and re-adding them as Git sub-module commit 1451d9aa4d4d9dc3b278802698ff4b501008fc84 Merge: b7f55a0 c3ce983 Date: Thu Jun 1 19:21:40 2017 -0700 Merge pull request #2295 from RosettaCommons/everyday847/native_screen_design Enable design in RMSD-screening stepwise runs commit b7f55a05be40f1016c0eeaa36c17cf8a3e2354fc Merge: fcb89ac 1f010ed Date: Tue May 30 22:55:07 2017 -0700 Merge pull request #2145 from RosettaCommons/vmullig/correct_xsd_info Correct some XSD information I've seen a few instances of incorrect descriptions in XSD stuff. This pull request corrects some of that. commit fcb89ac9ab30f44734c048812737754fd6b53e81 Date: Tue May 30 14:46:50 2017 -0400 Updating Context::sort_binders so it print clear error message and exit instead of throwing the exception. commit fd612f6c2470919a2f73606984a54d5ea6a30613 Merge: c9cb347 74afc52 Date: Mon May 29 22:02:20 2017 -0700 Merge pull request #2166 from RosettaCommons/everyday847/true_CSA First draft of a new CSA that anneals the RMSD commit c9cb3477555aebaf888776b72c090e294648e31b Date: Mon May 29 21:25:26 2017 -0700 Adding "restore_talaris_behavior" to threefold_symm_peptide_design integration test. commit 66693447c9472371fd450355ffc5021b384aeef7 Date: Mon May 29 21:13:57 2017 -0700 Fixing the simple_cycpep_predict_terminal_disulfide integration tests. Note that the enumerative_sampling tests also have the same problem (beta_nov15 in the flags), but they have additional problems, too -- bad paths in the run script. I'm not fixing those. commit b4c9cf5965c7660d5c69f593566450887643c446 Merge: 694ecf5 d79bc83 Date: Fri May 26 12:44:40 2017 -0600 Merge pull request #2290 from RosettaCommons/sergey/binder PyRosetta, adding name simplification for std:: container classes This should make Python names for set, map, vector, list, deque, forward_list, unordered_set, unordered_map, multiset, multimap, unordered_multiset and unordered_multimap classes considerably more readable. commit 694ecf5fd1864a52ccd8d7cf1ce49294622f349d Merge: dd4853f 7274cc2 Date: Fri May 26 11:23:44 2017 -0700 Merge pull request #2278 from RosettaCommons/rhiju/rna_denovo2017_stage2 more RNA denovo/stepwise updates. Tests look fine, with minor changes in integration that are expected from changes in flag names, except very latest test run where the `beta_nov15` merge has broken some tests. commit dd4853f1327d3b765a23cf170f99e18ae0d88739 Merge: 9da7a3d 01afc9b Date: Thu May 25 20:06:30 2017 -0700 Merge pull request #2283 from RosettaCommons/everyday847/stepwise_submovers_rs Allow the sub-movers of StepWiseMonteCarlo to be accessed through RosettaScripts commit 9da7a3d81aca90cbbf2a0be31f709aeaacb7f672 Merge: 816aebf d30825e Date: Thu May 25 17:54:42 2017 -0700 Merge pull request #2012 from RosettaCommons/hahnbeom/beta_nov15_as_default Merging beta_nov15 as default energy function into master commit 816aebf79eac0fd4f103e61e017905d8d234fa4d Merge: c96d96d b1974fb Date: Thu May 25 17:37:18 2017 -0700 Merge pull request #2284 from RosettaCommons/fordas/feature/vim_ymc_ninja_support Update ninja_build.py path support and YouCompleteMe compilation db support. commit c96d96d14e94457ed5ec9c32665cf8f6ebb450e7 Merge: 39fc860 0116274 Date: Thu May 25 16:37:56 2017 -0700 Merge pull request #2274 from RosettaCommons/fordas/py_build_refactor Update pyrosetta to support dynamic library links and wheel distribution. commit 39fc86063b5706ac5e187484c1247d6a8eef02c5 Date: Thu May 25 17:52:27 2017 -0500 Fix on-error printing of tests for failed test/run.py test selection. Needs to be Unicode-robust. commit ea8af99eb179dbe8ab583ee1e1560c77d51effe9 Merge: ba0f510 987b8998 Date: Wed May 24 15:39:14 2017 -0600 Merge pull request #2282 from RosettaCommons/sergey/f Updating PyMOLMover so UDP address and port could be set from XML scripts commit ba0f510132c092e0f33ce6922016ed415d0877b6 Merge: 040a8e7 4d5a201 Date: Wed May 24 12:58:05 2017 -0700 Merge pull request #2250 from RosettaCommons/vmullig/tweak_perturb_bundle Add options to PerturbBundle mover to allow parameter values to be set directly. This allows the PerturbBundle mover to set the absolute value of a parameter if the user so wishes, instead of perturbing a parameter value. Tasks: - [x] Add the options. - [x] Update `parse_my_tag()`. - [x] Update `provide_xml_schema()`. - [x] Update `apply()`. - [x] Integration test. - [x] Beauty. - [x] Documentation. Also: - [x] Fix current problems with `provide_xml_schema()` function. Note that the new integration test is set to use the current default scorefunction, be that talaris2014 or ref2015. This test shouldn't change significantly (except for the score line in the output PDB file) with the switch to ref2015, and I want it to continue to use whatever the current default Rosetta scorefunction is in the future. commit 040a8e7742b89265b64c75439db3609be0444145 Date: Wed May 24 12:51:32 2017 -0700 Fixing a code template. This addresses issue #2288. commit 7a7b283b6a63dab9aa9035847dc91572c6b5477c Merge: e2b232d 2fcb9da Date: Wed May 24 13:50:07 2017 -0400 Merge pull request #2253 from RosettaCommons/Cyrus/mergetarget From Indigo King at Cyrus: RandomResidueSelector: option to select random residue clusters RandomResidueSelector currently has an option to select >1 residue at a time. This PR adds new option to ensure that, when multiple residues are selected, they are all close to each other (within N angstroms, where N is also an option) commit e2b232dc9055dc8ca4b6b9c533016d1f0c87b321 Merge: e418c4e d216706 Date: Wed May 24 10:33:52 2017 -0400 Merge pull request #2280 from RosettaCommons/dougrenfrew/fix_eusec The change to the MPIWorkPoolJD job index a while ago caused an issue for the the explicit unfolded state energy calculator JD which derives from it. commit e418c4e800002eb53931a85f0beba6a9438df646 Merge: 28c9e44 64b58ea Date: Wed May 24 08:30:57 2017 -0400 Merge pull request #2279 from RosettaCommons/lqtza/enable-vhh-antibody-cc Enable heavy-chain only antibody homology modeling commit 28c9e44d71d43a1bbfaa703287419626870702a2 Merge: 6a9831f 9476607 Date: Tue May 23 18:36:17 2017 -0700 Merge pull request #2245 from RosettaCommons/imv-uw/abego_score Imv uw/abego score This adds a new score term based on ABEGO bin occupancy. commit 6a9831feb1745f669fa45d471f208685eb8e44b3 Date: Tue May 23 02:21:07 2017 -0700 Beautifying unbeautified files in current master. commit 4d28b436d476a17f53bc75514cd9691902c7806f Date: Sat May 20 22:07:50 2017 -0700 A poor way to avoid some issues in nbors commit 7cb6d3dbe754c7a9454f63546f6c90b82a2010bf Date: Sat May 20 18:55:29 2017 -0700 ignore_list update commit 30f57657596eade0a0a807bf5aef90204693a165 Merge: c4e6a4f 76ca094 Date: Sat May 20 16:12:29 2017 -0700 Merge pull request #2273 from RosettaCommons/everyday847/fix_polymeric Fix read_polymeric_components integration test. commit c4e6a4fc3bcf96d2157acea86379c08ef75d44eb Merge: f981a37 3a3113c Date: Fri May 19 13:07:56 2017 -0700 Merge pull request #2009 from RosettaCommons/everyday847/calibur_stuff Make calibur better accord with the coding conventions commit f981a37d7495dadcb62692c7d201b176537c9688 Date: Thu May 18 16:22:43 2017 -0700 Hotfix to linuxgccrelease builds commit 0597eed9b9f45da6a6fa713120dcca4b071d098d Merge: 45a9216 8ca68f4 Date: Thu May 18 11:03:15 2017 -0700 Merge pull request #2266 from RosettaCommons/yhsia/align_com_option Adds option to AlignChainMover to align to center of mass instead of a 2nd pose. commit 45a921660cd58732a8998b91d832938dff163a78 Merge: 2e6ce7c 9e40fcf Date: Thu May 18 09:21:15 2017 -0500 Merge pull request #2127 from RosettaCommons/justinrporter/broker-devel Broker Fragments Initialization commit 2e6ce7cc99818542f1ca13a1d1be525b2c4570d8 Merge: c6bd3fe cd5abf4 Date: Wed May 17 19:51:30 2017 -0700 Merge pull request #2267 from RosettaCommons/everyday847/polymeric_ccd_nucleic_acids Polymeric nucleic acid residues from the CCD commit c6bd3fef7da4e19d6c799c8518050ebb48d920e0 Merge: d678d01 7661f40 Date: Tue May 16 22:26:34 2017 -0700 Merge pull request #2254 from RosettaCommons/bfrenz/RosettaES_script added integration test for ES, changed default parameters, and includ… commit d678d01d10ee5417a4e8dc92069ba5072393b0b2 Merge: a134f67 9d6ee4c Date: Tue May 16 17:57:19 2017 -0700 Merge pull request #2182 from RosettaCommons/vmullig/support_disulf_cyclization Add support for simple_cycpep_predict structure prediction for disulfide-cyclized peptides Although the "simple" in simple_cycpep_predict was initially meant to refer to backbone-cyclized single-loop peptides, the application can already predict structures of backbone-cyclized peptides with any number of internal disulfides, or with three-way TBMB linkages. There's no reason that the application should be limited to N-to-C amide bond-linked cyclization. This pull request will add support for cyclization with a terminal disulfide _in lieu_ of a terminal amide bond, and will leave open the option of adding support for cyclization through a crosslinker. @csykang @gbhardwaj @hssnzdh2 @twcraven @atom-moyer @stephen-rettie TODO: - [x] Add option for alternative cyclization schemes. - [x] Add enum for alternative cyclization schemes. - [x] Set from options system in non-MPI mode. - ~~Set by master node in MPI mode.~~ --> Not actually necessary. Will be set by options system when slave node SimpleCycpepPredictApplication instances are initialized. Can be overridden if ever I need to. - [x] Update GenKIC setup in SimpleCycpepPredictApplication.cc to allow amide bond or disulfide cyclization. - [x] Closebond statement for S-S bond. - [x] Set up suitable GenKIC perturbers for cysteine side-chains. - [x] Modify GenKIC perturbers for cysteine backbone at cyclization point. - [x] Remove rama randomization for these residues. - [x] Ensure that full chain is pre-randomized before calling GenKIC. - [x] Make terminal amide bond constraints contingent on the N-to-C amide bond cyclization mode. - [x] Make terminal amide bond contingent on N-to-C amide bond cyclization mode. - [x] Make S-S bond contingent on terminal disulfide cyclization mode. - [x] Correct calls to function to form terminal covalent bond. - [x] Disable cyclic permutation in disulfide case. - [x] Update logic for selecting middle pivot. - [x] Update logic for selecting anchor residue. - [x] Update minimum peptide length. Add checks for adjacent disulfide-forming residues. - [x] Handle tail residues, if present. - [x] Check GenKIC filters. - [x] Don't do rama check on cysteine residues involved in disulfide. **Put off to a future pull request:** - Add non-GenKIC filter for rama check of cysteine residues involved in disulfide. - Filter by disulfide energy (non-GenKIC filter). - Filter by fa_dun (non-GenKIC filter). - [x] Exclude terminal cysteines (or loop-forming cysteines) from disulfide permutation testing. - [x] Prohibit quasi-symmetric sampling with disulfide cyclization. - [x] Prohibit linking all cysteine with TBMB with disulfide cyclization. - ~~Option to specify which cysteines form loop.~~ --> Put off to future pull request. - [x] Tests: - [x] Basic integration test. - [x] Tail residue integration test. - [x] MPI-mode integration test. - [x] Check compatibility with option to try disulfide permutations. - [x] Beauty. - [x] Documentation. Also: - This pull request fixes a really stupid simple_cycpep_predict symmetry bug that was hindering the efficiency of symmetric sampling. commit a134f678065736f8cde1424443e68d8cec0aac2d Merge: ffc74a6 a71f0a1 Date: Tue May 16 15:49:27 2017 -0700 Merge pull request #2258 from RosettaCommons/vmullig/fix_min_flavour_typo Fix typo in minimization flavours in the RosettaScripts XSD Fixing typo: it should be "strong_wolfe", not "stronge_wolfe". This is actually a kind of disturbing bug, since it means that there are absolutely no RosettaScripts integration tests that use this minimization flavour. commit ffc74a6dd6ebaa43bfac29cabaf0f04df0bd184e Merge: 9608ce8 6f58df7 Date: Tue May 16 14:54:08 2017 -0700 Merge pull request #2261 from RosettaCommons/yhsia/SSCountFilter_edits Adds a few options to SecondaryStructureCountFilter. adds residue_selector option to only count the SS elements from a subset of residues. Defaults to "all residues" as of the original behavior. add option to actually return a value to the score file. Defaults to 0 (original behavior). add option to specify how many residues (of the selected subset) are on each SS element before a SS element is counted. Defaults to 1. commit 9608ce8d1469f2d4e69400ae81bc9ba094fb1ab7 Merge: 11d0afc 3729110 Date: Tue May 16 13:28:51 2017 -0500 Merge pull request #2263 from RosettaCommons/roccomoretti/tracer_threaded_init_fiasco Attempt to fix static initialization order fiasco in threaded basic::Tracer Seth Cooper pointed out on the FoldIt mailing list that there's a potential static initialization order fiasco issue with tracer_static_data_mutex -- It's used by the constructors of static objects (Tracers) in different translation units, and it isn't well defined by the C++ standard if the mutex will be valid when the Tracer constructor runs. It's a simple enough fix to convert this to a construct-on-first-use style access, which should solve the fiasco in a threadsafe manner for C++11. commit 11d0afcb3bce411e11b8ff2ee0688ff4d03a3eec Date: Mon May 15 14:50:45 2017 -0400 Updating 'beautify' test logic so it ignore master branch commit 8c3e313dcc65baa8a2e265b72170d88a751785d7 Merge: ddc87c2 40a1a01 Date: Mon May 15 10:06:12 2017 -0700 Merge pull request #2255 from RosettaCommons/dimaio/disulf_symm_fix Small symm disulf bugfix commit ddc87c2f0380b6a94c82aad977ef949d44e4b42c Merge: 76c5b2d 7aed686 Date: Sun May 14 10:24:21 2017 -0500 Merge pull request #609 from RosettaCommons/roccomoretti/cartbonded_auto_torsion Cart_bonded: automatically add torsion parameters if missing The cart_bonded term can automatically pull bond lengths and angles from the ResidueType if there isn't values listed in the database. It didn't, however, do anything about constrained improper torsions (e.g. for planar systems). These changes take the existing improper torsion parameter generation code from molfile_to_params.py that @yfsong added and puts it into Rosetta to allow autogeneration of torsional restraints for planar systems (aromatic bonds, double bonds to carbon) for ResidueTypes which don't already have any data listed in the database. -- It doesn't change anything for other sorts of impropers (e.g. aniline protons) that might also have a constrained geometry, though those should be easy enough to add later, if someone figures out what needs to be added. Potential User Facing Change: While the autogeneration of parameters should be turned off if you feed manual parameters for the residue to -score::extra_improper_file, the behavior of the residue identifier for that file (and for the Rosetta database files) has changed. For non-protein, non-nucleic acid residue types, the residue identifier is the full name, rather than the name3. In most cases this shouldn't be an issue (as normally for ligands and the like name3 == full name), but it might catch someone out on edge cases. commit 76c5b2d906af280ec77fe937a4e5b939146f463b Merge: c66e78d 2e310f4 Date: Sun May 14 10:07:47 2017 -0500 Merge pull request #2260 from RosettaCommons/roccomoretti/fix_ligand_database_io Attempt to fix ligand_database_io test I think I've tracked the instability in this test to the use of a std::set< ConstraintOP > in ResidueTorsionRestraints. This was used in removing/re-adding constraints, such that the order of the constraint addition was different run-to-run, as the address layout is different. Different constraint orders means that there are slight differences in energy summing (due to machine precision rounding), which snowball during minimization. Changing the set to a vector1 appears to fix the instability issue. Integration test changes in ligand docking tests expected, as they settle down to their (hopefully) stable trajectories. commit c66e78da477d251aa249002b7b42deb288700e62 Date: Sun May 14 10:00:16 2017 -0500 Clean up and beautify files in master commit 229c8f84cb6394f06eadf4de2114b29faafdc1f0 Merge: 98b4e41 bc736a8 Date: Sat May 13 08:20:22 2017 -0500 Merge pull request #2244 from RosettaCommons/havranek/memfix_sasa Havranek/memfix sasa commit 98b4e41183c5a05f9db208000eb7199b13caae45 Merge: dadbb40 de52710 Date: Fri May 12 15:15:23 2017 -0500 Merge pull request #2098 from RosettaCommons/roccomoretti/Transform_reporting_additions Fixes to ligand scoring grid caching While docking large ligands with multiple starting locations, I realized the ligand docking scoring grid caching wasn't working appropriately. * Only the conformation and not the grid center was being hashed, which means for multiple starting locations you could get a grid from the cache that wasn't over any of your ligand. * Const-correctness was not a thing in the scoring grid hierarchy, which meant that even if you get the correct caching key, the cached grid might not be what you want, as it might have been modified in the meantime. -- I attempted to impose const-correctness and proper copy-before-modifying semantics on the scoring grid. While I was at it, I added more reporting functionality to the Transform mover, to recognize when the grid size is inadequate, and to recommend a grid size that's hopefully better. (Grid size recommendation are still somewhat "beta".) commit dadbb40b38ec2d4232fe9aa72241646019c4a758 Merge: 94998f0 ec6cfb3 Date: Thu May 11 16:24:03 2017 -0700 Merge pull request #2206 from RosettaCommons/csykang/retro_inverso Adding a pilot app: This pilot app will take a pose and generate a retroinverso version of it. commit 94998f0e5b038b6d8083995a664cb96641cb844b Date: Thu May 11 15:10:16 2017 -0500 Back out ligand_database_io debugging changes. commit 1f2fd2a44a2f110e8503dffb56711d9933b899bf Merge: 23790bf 398b4c8 Date: Thu May 11 09:22:29 2017 -0500 Merge pull request #2247 from RosettaCommons/roccomoretti/asst_test_fixes Two quick test fixes * ResidueType::delete_atom() was using atom data after deleting, which the unit.addsan tests was tripping over. * There was an uninitialized member variable in NPDHBondInteractionGraph that unit.ubsan was tripping over. commit 23790bf4900cd4b3e934b6de3ac9c69ddfa62c76 Merge: 5b7bf92 881a9e3 Date: Wed May 10 17:07:20 2017 -0700 Merge pull request #2251 from RosettaCommons/vmullig/fix_select_by_layer_bug Caught a bug in SelectResiduesByLayer DSSP was being called even when explicitly disabled. commit 5b7bf922647cd3295ae00d831403ab8ed6e10524 Date: Wed May 10 16:19:18 2017 -0700 Beautifying unbeautified files in master. commit 74763ccf397f9ca3589df879ecca14ed3e70bcab Date: Tue May 9 14:12:07 2017 -0500 More annotation of ligand_database_io integration test. I can't replicate the test server changes locally, so hopefully more loging output will help track down the instability. commit 3dbeb922166a5e97a9fdef3ce35d6130fae41226 Merge: e639896 4e9cdc5 Date: Tue May 9 13:09:44 2017 -0600 Merge pull request #2248 from RosettaCommons/sergey/f Adding bindings for xyzMatrix .xy properties commit e6398966e7d219b717f61fb02b1847723450e0ab Merge: 2bda40f 198d948 Date: Tue May 9 12:02:45 2017 -0700 Merge pull request #2246 from RosettaCommons/everyday847/stepwise_NCNTs Somehow, my last PR stopped being updated with commits in this branch... commit 2bda40f8d7d1138372f8d20f110c418a33ab90de Merge: fb7757b ae88261 Date: Tue May 9 09:20:15 2017 -0400 Merge pull request #2239 from RosettaCommons/aleaverfay/faster_lkball_rpe LK_Ball performance improvements Two speedups for lk_ball in anticipation of it becoming part of the default score function. First: Avoid construction/destruction of a count_pair object in the LK_BallEnergy evaluation by using the "invoker" scheme where a stack-allocated object with the virtual function "invoke" is handed a stack-allocated count-pair object by the CountPairFactory. This avoids a call to new and delete. Stack allocation is much much faster than heap allocation. (The same thing could be done with the FA_ElecEnergy.) This speeds up the off-rotamer packer by 1.18x when using lk_ball. Second: Speed up lk-ball when using the linear-memory interaction graph by splitting RPE calculations for LK_BallEnergy into bb/bb, bb/sc, sc/bb, and sc/sc interactions. This drops LK-ball evaluation from being the largest single expense in the packer's deltaE calculation, to being the smallest of the atom-wise energy calculations. This is surely the result of the tighter bounding sphere pruning that allows the calculation to skip interaction calculations that it can prove are out of range. commit fb7757bba4706249c71128a9318e45dc5e1dfd0f Merge: e057771 80d5d21 Date: Mon May 8 13:24:51 2017 -0700 Merge pull request #2249 from RosettaCommons/everyday847/RT_count Update ignore_list to ignore RT # change commit e057771426ce584c0476473a6d70c96e27606170 Merge: 0ebf4b5 49d270a Date: Mon May 8 09:42:00 2017 -0500 Merge pull request #2100 from RosettaCommons/roccomoretti/RosettaScripts_empty_sfxn A few small, unrelated administrative changes. * Tell git to ignore the DAlphaBall executable if it's built (in main/source/external/DAlpahBall/) * Update the naive/default runtimes for integration tests. This was originally going to add "empty" to the list of pre-defined scorefunctions in RosettaScripts -- I dropped that plan, as it conflicts with the manual definition of "empty" within the XML, which a number of scripts are using. commit 0ebf4b56da6b623a6f2862905a1944e8a74b9908 Merge: 12b7b0f 46c25ba Date: Mon May 8 08:55:08 2017 -0400 Merge pull request #2211 from RosettaCommons/aleaverfay/bugfix_chain_endings_in_pdb_reading Bugfix in Pose construction logic Fixing another chain-endings bug that is tripped when the Cterm of onechain (residue i) is missing some backbone atoms, AND the Nterm of the next chain is also missing some backbone atoms, so that Rosetta won't put a Cterm at residue i-1 nor an Nterm at i+2. As a result, a two chain PDB will get read in as a single chain. Super simple fix for this. commit 12b7b0fc73ebe53479dfe8cf291a1f9748d44f28 Merge: 5ed9d14 4bafcb4 Date: Sun May 7 14:55:35 2017 -0700 Merge pull request #2243 from RosettaCommons/everyday847/misc_pedantry A few loop refactors, and use of fixedsizearray1 for some suites commit 5ed9d146a9ac3577559e38900efb033bafd10065 Date: Sun May 7 16:48:03 2017 -0500 Better annotation of ligand_database_io integration test. I can't replicate the test server changes locally, so hopefully more loging output will help track down the instability. commit 26d01defc0ed29bff3e58e38cd205dc6e9a8065b Merge: 6c5f433 b0ae373 Date: Sat May 6 23:11:32 2017 -0700 Merge pull request #2224 from RosettaCommons/vmullig/fix_pdbinfo_on_helix_append Fix issue with PDBInfo and appending helices to an existing pose with MakeBundle/BundleGridSampler commit 6c5f43317387c3bbea573736e265a30c7e067052 Merge: a472443 6143c18 Date: Sat May 6 15:36:38 2017 -0600 Merge pull request #2188 from RosettaCommons/atom-moyer/unfriend-function Unfriend xyzMatrix operators so they appear in PyRosetta commit a472443b479e3ad080291c38920a548183fab9d6 Merge: 8e64845 2feb8d5 Date: Sat May 6 08:02:46 2017 -0700 Merge pull request #2242 from RosettaCommons/everyday847/analogue_na_scoring A couple places to generalize torsion scoring based on analogue_na() commit 8e64845ff2858d26fba17b2293543db7d31c5324 Merge: d8a0897 a44b2a1 Date: Fri May 5 17:09:57 2017 -0700 Merge pull request #2237 from RosettaCommons/bfrenz/ES_bugfixes added removal of terminal truncation types to safely append/prepend r… commit d8a0897781ab9362f8330722907699ae6ba1caea Merge: 740e051 dd5aac6 Date: Fri May 5 14:44:06 2017 -0600 Merge pull request #2238 from RosettaCommons/sergey/binder Add-on to PyRosetta serialization support - Adding binding for std::stream classes. - Adding mapping-to-standard-name for std::stream classes. - Adding extra bytes method for std::*stringstream classes so they could be used in Python3. - Adding PyRosetta serialization test. commit 740e0518dc72b64f35fe791658527f051a4a4dfc Merge: 0b2fc78 e5accfa Date: Fri May 5 12:46:32 2017 -0700 Merge pull request #2234 from RosettaCommons/everyday847/cAMPtown_races Cyclic mononucleotides commit 0b2fc781f0ee1f0d126a41b16966cfc81c5c72a0 Merge: f30827e 85e404c Date: Thu May 4 17:53:26 2017 -0700 Merge pull request #2204 from RosettaCommons/tlinsky/tomponents Fix BuildDeNovoBackboneMover