commit 033713c32c8afae6f21d595098926ec14e073cf5 Merge: f9601f2 54c76a8 Date: Sun Mar 15 21:33:11 2015 -0700 Merge pull request #374 from RosettaCommons/tlinsky/multiplepose_keepmover MultipleOutputWrapper now has "keep_mover_state" option which re-used th... commit f9601f28026878dc5a4f6fb138eca2a7ffce7aea Merge: d896591 7fa3ff3 Date: Fri Mar 13 15:46:00 2015 -0700 Merge pull request #384 from RosettaCommons/rpache/KIC_outer_cycles_bugfix Loop modeling outer cycles refactoring This commit makes perturb_outer_cycles and refine_outer_cycles the flags to control the number of outer cycle iterations in the centroid and fullatom stages, respectively, for all loop modeling protocols. The default values for those two options are now being read directly from the Rosetta options system instead of using hard-coded values. The old loops:outer_cycles flag is now deprecated. Cosmetic splice and antibody loop modeling integration test changes. commit d896591508c0005654ee85dbb89901052c57c663 Merge: 267fcbf c7f9ff3 Date: Thu Mar 12 11:21:20 2015 -0500 Merge pull request #380 from RosettaCommons/roccomoretti/fixhbonds Fix uninitialized variable issue in HBEvalType table. Add a hbe_UNKNOWN as an uninitialized variable sentinel commit 267fcbf9fef90a1aa61356ee273a723ab08225c3 Merge: 38f1f6e d2e6546 Date: Thu Mar 12 11:19:59 2015 -0500 Merge pull request #377 from RosettaCommons/roccomoretti/fixscoreman Fix uninitialized variable issue with the ScoringManager and the ProQ potential. commit 38f1f6e3c48b1e928044cc2689ea434cae5e840c Merge: 751ac26 9a26a9d Date: Wed Mar 11 20:17:30 2015 -0700 Merge pull request #363 from RosettaCommons/tlinsky/rescountfix Remove runtime_assert from ResidueCountFilter's parse_my_tag that requir... commit 751ac262ac911b3deceecedf88485c7a14cfcfdc Merge: b702d89 7f7ffd7 Date: Wed Mar 11 21:40:39 2015 -0400 Merging master into branch aleaverfay/map_to_etables_from_etable_options This commit changes the behavior of the ScoringManager so that now fewer Etables get created. The ScoringManager stores only a single data structure for holding etables: a map from the EtableOptions object to EtableOPs. This change means fewer etables get constructed -- this is a very good thing, since Etables (especially the pre-analytic ones) occupy a good chunk of memory. It does however produce copious cosmetic integration test changes, as the integration tests now report fewer etable constructions. commit b702d89bf3a3a8d9d67a707c26cd918bb0c50eff Date: Wed Mar 11 21:34:15 2015 -0400 Restoring the previous etable-retrieval-by-string interface to the ScoringManager to fix the broken PyRosetta unit tests, but changing the functionality so that instead of returning an Etable cached by string, it constructs a default EtableOptions object (reading from the command line), changes the etable_type string in that EtableOptions object, and then queries the central map of EtableOptions-->Etables that the ScoringManager holds. commit aed0564a142e50fa8f0de26f477d75ef5cf0382e Date: Tue Mar 10 14:34:12 2015 -0400 Removing a debugging statement commit 371cf11cdb1d2142e55dd1874f515b5b2353870f Date: Tue Mar 10 11:17:39 2015 -0400 Changing the logic in the ScoringManager to map to etables by the EtableOptions object; moving data into the EtableOptions object from the EnergyMethodOptions object that's specific to Etable construction. commit 94950d075eb9da6150f5abeae6be17d7748e4299 Merge: 522e2e6 2d93f64 Date: Tue Mar 10 04:24:55 2015 -0700 Merge pull request #378 from RosettaCommons/vmullig/fix_omega Vmullig/fix omega Fixes behaviour of omega score term for beta-amino acids. (Thanks to Andy for pointing out the problem, and for ultimately coming up with the solution.) No integration test changes expected; all unit tests pass (including newly-added one). Tasks: Switches the test for beta-amino acids to the is_beta_aa() function in ResidueType (instead of my earlier kludge of looking for a "CM" atom). Fixes the behaviour for beta-amino acids. Moves all of the code for figuring out which mainchain torsion is omega to one place. Adds a unit test for beta-amino acids. Alters the derivative calculation WRT phi and psi in the special case of beta-amino acids to use mainchain torsions 2 and 3 instead of 1 and 2. commit 522e2e63dab17879883c7eac5fa82b327fe2e5e5 Merge: bec8e81 1a8c17a Date: Mon Mar 9 20:31:45 2015 -0700 Merge pull request #370 from RosettaCommons/vmullig/genkic_sampling Fixing an issue with GenKIC Since GenKIC now respects the exit status of the pre-selection mover, it is possible for there to be no valid solutions after applying the pre-selection mover despite having a number of candidtates beforehand. This was causing GenKIC to fail, but should be handled gracefully, now. No test changes expected. commit bec8e81ee01e79fe5c4b733b5425b0d871639d13 Date: Mon Mar 9 18:47:31 2015 -0500 Fix missing variables in ligand Motif constructors Should fix a Valgrind issue commit eb7b423d6f30a75cf3e622ebe04f2abdc38820d9 Merge: 62f7e55 e355977 Date: Mon Mar 9 12:29:56 2015 -0700 Merge pull request #357 from RosettaCommons/tlinsky/selectbylayerfix Fix crash in SelectResiduesByLayer when sidechain_neighbors is used with... commit 62f7e552dcd1be9c97b8ce3a1849ac398d9ecc7f Merge: 12e7bb9 462f2b4 Date: Mon Mar 9 12:29:01 2015 -0700 Merge pull request #356 from RosettaCommons/tlinsky/psipredfix Bugfixes to devel::denovo_design::filters::PsiPredInterface commit 12e7bb9a3ff2191d96718b6789faffff86825d29 Merge: b00349e b386e81 Date: Mon Mar 9 12:28:29 2015 -0700 Merge pull request #354 from RosettaCommons/tlinsky/hotfix Fixed bug where OperateOnResidueSubset could not be used to make customi... commit b00349ed6906a6ee3acf72cec996d87befd8d3c7 Merge: 9109f17 27f743d Date: Sun Mar 8 19:54:27 2015 -0400 Updating PyRosetta release script. This should fix libboost issues. commit 9109f1768fad455465906632ebe93537f678768e Merge: b9e35b5 fde111e Date: Sun Mar 8 15:28:38 2015 -0700 Merge pull request #366 from RosettaCommons/vmullig/genkic_sampling Vmullig/genkic sampling Updating the ABBA.bin_params database file with new stats generated by Gaurav. Thanks, Gaurav! This should cause integration test changes in all tests that use mainchain torsion bin transition probabilities. This includes bin_initialization, bin_perturbation, genkic_bin_perturbing, genkic_bin_sampling, and genkic_bin_setting. commit b9e35b58a84c6aa0ca3da52dd25dc2a77284652a Merge: 9d1deb3 129128a Date: Sun Mar 8 20:39:05 2015 +0200 Merge pull request #367 from RosettaCommons/kwikwag/peptiderive-talaris Fixing some issues in PeptiDerive: - fixed flags mix up between dump_cyclic_poses and dump_peptide_pose (PeptideDeriverPoseOutputter) - fixed markdown report listing cyclic peptides as linear peptides - remove redundant separators after tables in markdown - fixed not choosing best cyclizable peptide correctly commit 9d1deb3dcc02dca1178d0c0d370814d8fe734113 Date: Sat Mar 7 16:42:52 2015 -0500 Changing benchmark_scale to 5 Rather than chasing individual tests, I think we have to simply average more than 3 trials per test. commit 6404c17a3693dc3437e2fca64cf103591b8833ea Merge: b975692 bea3472 Date: Sat Mar 7 14:21:45 2015 -0700 Merge pull request #365 from RosettaCommons/benchmark Adding valgrind_detailed tests commit b975692fb7ff72e11aadf74987d43b3b2bd1de91 Date: Sat Mar 7 12:20:55 2015 -0500 Additional scoring benchmarks needed more reps. Vaguely attempting to get everything in the 1-2 seconds range if it is below. commit 2fa5847707ad835a1daeb41ee7a2a1a20cb9a207 Merge: 4644b67 c40ffac Date: Fri Mar 6 23:05:41 2015 -0800 Merge pull request #359 from RosettaCommons/calebgeniesse/rna_bulge fixing SWM rna_bulge calculation SWA/SWM integration test changes are expected commit 4644b67df9a7d946819c2c08dd6fa85f2b38e7a0 Date: Fri Mar 6 23:57:56 2015 -0500 More fixes re: tests that still vary occasionally! commit afbe193531b71e6ba1c6c2f45e4fc429ef529c0b Merge: 3383555 7534fec Date: Fri Mar 6 16:56:44 2015 -0800 Merge pull request #364 from RosettaCommons/vmullig/valgrind_issue Vmullig/valgrind issue I think I've fixed the major issue causing many of my unit and integration tests to fail the Valgrind tests on the test server. It was an issue with order of initialization of variables in the Conformation assignment operator and copy constructor (I think). In the middle of the copy constructor, I was calling a function to which I was passing the new, partially-initialized Conformation object, which was problematic. This has been cleaned up. Testing now. (This does fix all of the unit and integration tests of mine that were being flagged by Valgrind. No unit or integration test changes.) commit 3383555833e7f7960906a0ba53988ac79de7f9e0 Date: Fri Mar 6 19:11:41 2015 -0500 Update ScoreEach.bench.hh Reduced tests of intra scoreterms by 10x was too much! commit 455658240c1ae36cf4c0a4f02ff257d71db6910c Date: Fri Mar 6 19:10:01 2015 -0500 Update ScoreAnalyticEtable.bench.hh Reversed reduction in number of trials--we were actually encountering a significant figure issue with these. I didn't know because before these always had at least one outlier! commit 45564faa506b7763723eaf8210c6551d3f97bbca Date: Fri Mar 6 15:13:36 2015 -0600 Fixed Valgrind errors in pocket_suggest_targets commit 97bddae7c321d8bd898dd7ce067d0ea67802a192 Merge: 193948e 7ce1620 Date: Fri Mar 6 11:32:27 2015 -0500 Merge pull request #361 from RosettaCommons/everyday847/performance_tests Outlier detection for the performance tests commit 193948e35d26b87a63026fd4e743bcb81405bc67 Merge: 61abadc 305ba00 Date: Thu Mar 5 16:19:42 2015 -0800 Merge pull request #355 from RosettaCommons/vmullig/genkic_binfilter Adds a new GeneralizedKICfilter based on whether pivot residues are in desired mainchain torsion bins This creates a new GeneralizedKICfilter called "backbone_bin". It rejects solutions in which a particular residue (presumably a pivot residue) is in an undesired mainchain torsion bin. Tasks completed: -- Clean up GenKIC clone and copy functionality a bit. -- Create the backbone_bin GeneralizedKICfilter. -- Add an apply() function for the filter. -- Add suitable hooks in the BinTransitionCalculator object for the check that we want to do. -- Add RosettaScripts parsing for the unique filter options. -- Add integration test. -- Documentation. Expected test changes: -- set_backbone_bin integration test should change considerably, since it now tests this filter in addition to the set_backbone_bin perturber. (This filter is intended to be used with this perturber, so it makes sense for the integration test to test both.) commit 61abadc6d21b4b33ff6eff4b7af6378ee390834f Merge: 9a3e7d4 affe19a Date: Thu Mar 5 13:20:10 2015 -0600 Merge pull request #294 from RosettaCommons/justinrporter/env_devel Environment Disulfide Bug -- environment now actively detects sulfides after broking. commit 9a3e7d4b8388c3769d75152e3ec7c2369d27306e Merge: aa8a827 968f987 Date: Thu Mar 5 02:09:19 2015 -0800 Merge pull request #351 from RosettaCommons/vmullig/genkic_sampling Adding some new features to GenKIC Tasks: -- Add a set_backbone_bin GeneralizedKICPerturber. -- Add integration test for set_backbone_bin GeneralizedKICPerturber. -- Have GenKIC use and respect mover status. -- Update documentation. Cosmetic integration test changes expected for the genkic_bin_perturbing integration test. Failure expected for the new genkic_bin_setting integration test, since it is new. commit aa8a8272bec1854644aaad0e6a2dff636c2467e7 Merge: c44c565 ef0a9bf Date: Wed Mar 4 18:01:27 2015 -0600 Merge pull request #290 from RosettaCommons/justinrporter/env_release ParsedProtocol MoverStatus handling. Merge a bugfix for MoverStatus handling by EnvMover. A few scattered integration test differences on the test server, but I don't think they're real. Will revert if they persist. commit c44c56519c94b3132cd1aab9594cb93c04053243 Merge: b0dd2d1 3135658 Date: Tue Mar 3 19:55:34 2015 -0800 Merge pull request #350 from RosettaCommons/vmullig/ssshapecomp_threshold Add min_sc option to SSShapeComplementarityFilter Updating SSShapeComplementarityFilter with a threshold option ("min_sc" in RosettaScripts), so that it may be used to filter designs. Also, updating the tracer for the ShapeComplementarityFilter to properly reflect its namespace. (This also fixes a trivial typo in LayerDesign). Tasks completed: - Write code. - Write documentation. commit b0dd2d1282b0dcad333262bce682494caaab40ca Date: Tue Mar 3 19:41:47 2015 -0500 Bugfix: B3P.params Beta-3-proline had a problem! It only listed two chi angles and didn't have a virtual nitrogen shadowing its nitrogen, so it wouldn't work with cart-bonded either commit 62ad7fdef1bdac05bfd739c6ba5a7d62757ac2fa Date: Tue Mar 3 11:18:45 2015 -0800 adding an option "-rscc_wdw" to control the residue window size while calculating RSCC. By default, it's set at 3 (the original behavior). commit 23ae729db16b48cfcad7e1f05ba94798b6c028e2 Merge: 2601c04 389dd92 Date: Tue Mar 3 09:30:47 2015 -0800 Merge pull request #339 from RosettaCommons/tjbrunette/repeatExtract Tjbrunette/repeat extract mostly updates apps. But in the main code there was a fix to the linkRes command. For some reason a residue needed to be linked to itself or the code seg-faults commit 2601c04c461a122ec0f03b1877ac82d5fc7b376a Merge: 3ddd651 4edd2f1 Date: Tue Mar 3 11:11:34 2015 -0500 Merge pull request #341 from RosettaCommons/jkleman/mp_updates Jkleman/mp updates: small updates for membrane proteins: = changed the scorefunction names to match the one in the supplement for the paper (also changed that in demos) = changed default thickness for both membrane viewers from 12.5 to 15A (in options file) integration test changes: expected commit 3ddd6514932960475043abe1068112ee06e683f5 Merge: 39a2542 bcf06b1 Date: Tue Mar 3 12:32:43 2015 +0200 Merge pull request #279 from RosettaCommons/RMSDAlignedThread Rmsd aligned thread commit 39a25422b8b906139192594bfb70082daa436f03 Merge: fcd38e7 da52578 Date: Mon Mar 2 20:41:47 2015 -0800 Merge pull request #349 from RosettaCommons/vmullig/fix_unfolded_e_calc_instability Trying to fix instability that I introduced in the unfolded state energy calculator integration test I think this is due to a couple of uninitialized variables in some of the constructors for the MutateResidue mover. Fixed now. Integration test changes are possible in the msd_mover, unfolded_state_energy_calc, and remodel_disulfides_rosettascripts integration tests, all of which were potentially affected by this uninitialized variable. commit fcd38e727e099d09824d29bd5600b12578661966 Merge: fd49958 50f5aa5 Date: Mon Mar 2 11:00:04 2015 -0800 Merge pull request #325 from RosettaCommons/rhiju/stepwiseJD_fix_uninitialized_var initializing uninitialized variable. commit fd499585c2bd7aac73ed4d39e06ceb01fb928026 Merge: 2e72350 a0b756d Date: Mon Mar 2 10:47:14 2015 -0800 Merge pull request #344 from RosettaCommons/hahnbeom/patchs Hahnbeom/patchs commit 2e7235013ebcb45c5fdb87e9eaebeb695a6f7101 Merge: 04a11dd 8ef14d0 Date: Mon Mar 2 10:04:24 2015 -0800 Merge pull request #332 from RosettaCommons/raywangyr/autorefinement Raywangyr/autorefinement commit 04a11dd6c3a226d1d64b63556dcaabeaa2a7f08b Merge: fd6d7e7 7e0fa9d Date: Sun Mar 1 08:15:30 2015 -0800 Merge pull request #342 from RosettaCommons/kalekundert/loop_modeling Remove floating point equality comparisons from the LoopModeler unit tests. commit fd6d7e79b229a907366cc4686f9325fd06facbc3 Merge: 83aed01 a7d1315 Date: Sat Feb 28 20:08:02 2015 -0800 Merge pull request #346 from RosettaCommons/vmullig/mutate_bug vmullig/mutate_bug Trying to fix an irritating bug in the MutateResidue mover and elsewhere. When a residue is mutated to another type, the default behaviour was for any atoms with matching names to have their positions preserved, and for any missing atoms to be rebuilt from ideal coordinates. This was fine for Y->F or F->Y mutations, but created serious problems when dissimilar residues had similar atom names. The new default behaviour will be to copy mainchain heavyatom positions only, with everything else built from ideal coordinates; chi values will then be copied from the old residue to the new. The old behaviour can be restored with a RosettaScripts tag when setting up the MutateResidues mover. Tasks completed / TODO: Overloaded copy_residue_coordinates_and_rebuild_missing_atoms() to have a version that takes a bool. False yields old behaviour, true yields new. Set up new behaviour (rebuilding all but mainchain heavyatoms, copying chi values). Created unit test for new behaviour. Modified MutateResidue mover so that its settings can be set without invoking parse_my_tag() by functions called from parse_my_tag(). Updated MutateResidue mover and added flag to restore old behaviour. Updated Remodel mover (really, the form_disulfide() function in core/conformation/util.cc). Updated MutateResidue documentation. Expected integration test changes due to this merge: --remodel_disulfides_rosettascripts: Expected and desired change. The added disulfides now have beta-carbon protons in the right places. --unfolded_state_energy_calc: Looking at the code, this calls the MutateResidue mover, so this is also expected. (The change is small.) --msd_mover: The FindConsensusSequence mover that this test's script calls uses the MutateResidue mover, so this is also an expected change. (The change is very small.) commit 83aed01c90cefb7a7986093ef93c2f43dbba29d7 Merge: e65b831 45d6606 Date: Sat Feb 28 17:51:22 2015 -0800 Merge pull request #345 from RosettaCommons/nollikai/coupled_moves_output_structures Added flag to coupled_moves protocol to save structures for all designs commit e65b8312598418dac01e11369317b2db8b6105b3 Merge: 66cab58 0ca1b8d Date: Sat Feb 28 14:03:14 2015 -0800 Merge pull request #321 from RosettaCommons/centroid_rotamer Update Centroid Rotamer Model all unittest passed integration test change expected (new score term info only): abinitio fold_cst_new hybridization metalloprotein_abrelax mr_protocols 1. Add "sin" correction for dunbrack lib (internal coordinates to cartesian coordinates) 2. Optimize score weights (pair, env, ss) using Mike's 80 decoysets discrimination score (lower the better): -- score12: -0.11 -- centroid: 0.0 -- cenrot: -0.09 3. Identify rotamers using density based clustering method, optimize score weights (vdw, dun) using Dunbrack's 379 set rotamer recovery rate (within 40 degree) -- bfactor< 30: 84.46% -- bfactor< 30 and nbr > 16: 86.94% 4. Optimize reference energy using HQi54 set with optE sequence recovery rate: 25.5% commit 66cab58850a96b31e2b23ef2ef2d31df03d73a6c Date: Sat Feb 28 09:53:43 2015 -0600 Add more dunbrack binary generation lines to the integration test ignore list. commit 20c61c57d62032e783db203b14aea24009b9bf35 Merge: 586d7a6 de27d8b Date: Fri Feb 27 18:43:56 2015 -0800 Merge pull request #347 from RosettaCommons/vmullig/bgs_parallel Silly off-by-one error in BundleGridSampler.cc -- fixed. Apparently I can't count. Bundle grid sampler nstruct mode integration test change is the only expected test change. I'm going to merge this without testing. commit 586d7a6bd8cd78b8d5599772553dfd2dc8e73b64 Merge: bd611dd d5def5a Date: Fri Feb 27 13:03:34 2015 -0500 PyRosetta: adding bindings for vector1