commit 44710f97b20e0d4310140acc1e62dc36a249f03f Date: Fri May 11 20:26:06 2018 -0400 removing merge conflict markers that was accidentally committed into `master` commit b4f0cb7ce0243040cee89955746dea9a232f22c1 Merge: 91f2754 bf1660d Date: Fri May 11 16:04:37 2018 -0700 Merge pull request #3203 from RosettaCommons/vmullig/fix_tailless_lariats Fix peptide structure prediction with tailless lariats Problem identified by @stephen-rettie and @deiblerk. Tasks: - [x] Diagnose the problem --> I'm mistakenly trying to randomize backbones of terminal residues. - [x] Integration test the problem. - [x] Fix the problem. - [x] Beauty. Also: - [x] This pull request is branched from #3202, and must be merged after that one. commit 91f27543620293b2ff0995b562390026b99bb26e Merge: 52cd055 19977d7 Date: Fri May 11 15:53:42 2018 -0700 Merge pull request #3202 from RosettaCommons/vmullig/fix_lariat_issue Fix an issue affecting correct placement of O and V1 atoms in isopeptide lariats There were a couple of spurious lines in a function that's intended to return connection atom IDs, and this was creating problems with the SidechainConjugation patch. (Come to think of it, this might have worked if we changed the order of patches, but I wanted a less fragile solution.) There was an additional function that I needed to write, too, to preserve backwards compatibility with the old ASX/GLX patches. This also updates a feature in GenKIC. Old behaviour: - You have a residue with two polymeric connections (1, 2) and a sidechain connection (3). - You apply a patch that removes polymeric connection 2. - Sidechain connection 3 is now connection 2. - Atoms whose internal coordinates depended on sidechain connection 3 still depend on sidechain connection 3. - The Residue::inter_residue_connection_partner() function would correct for this by checking whether a residue was an upper terminus or lower terminus type, and subtracting 1 from the connection ID if it was. This was fragile (especially since someone might query the ICOOR records from anywhere, not just from this function). New behaviour: - You have a residue with two polymeric connections (1, 2) and a sidechain connection (3). - You apply a patch that removes polymeric connection 2. - Sidechain connection 3 is now connection 2. - When the patch is applied, we iterate through all atoms and update all ICOORs that depended on connection IDs greater than 2, so that they depend on the N-1 connection ID now. - The ICOOR records for each atom are always correct, now, and the Residue::inter_residue_connection_partner() function doesn't do any silly -1 logic, now. commit 52cd055b1faeeb3fb59b3081bc1cb5d2ecd5d7a5 Merge: cfdc4de 18ff53a Date: Fri May 11 15:52:38 2018 -0700 Merge pull request #3204 from RosettaCommons/vmullig/fix_app_exception_handling Fix the app_exception_handling integration test. Ensuring that make_motif_tables exits with error status when an exception is thrown. commit cfdc4de80e863ab019244d2739ddb97a23647208 Merge: 5a1f5c5 5e992a1 Date: Fri May 11 16:27:22 2018 -0500 Merge pull request #3179 from RosettaCommons/jadolfbr/simple_metrics Fix SM features integration test + various bug fixes Also fix: - The cdr length metric output for RAbD - A bug in GlycanTreeRelax when using multiple apply calls, round=1, or when window=1. - AnchoredGraftMover XSD - AnchoredGraftMover copy constructor from changes to the way rosetta numbering was parsed. - Fix rare FoldTree crash for grafting by using `set_reasonable_foldtree`, which is generally reliable. - Add integration test for RS-interface of CCDEndsGraftMover, which calls the AnchoredGraftMover XSD commit 5a1f5c51c69eb4a16abfff567b228bcdc50a3196 Merge: a81712b 8ff98c2 Date: Fri May 11 13:43:42 2018 -0400 Merge pull request #3199 from CyrusBiotechnology/forcommons/3195-refactor_pdb_diagnostic Refactor pdb diagnostic - resolves #3195 for the scientific tests drive Cosmetic itest changes expected in pdb_diagnostic and some of the jd2 mmCIF tests commit a81712b5a61d64b0bd4453e5f5c1887dcab076d2 Merge: c172315 fcdabc5 Date: Fri May 11 12:04:29 2018 -0400 Merge pull request #3200 from RosettaCommons/everyday847/fix_5prime Better five-prime capping for mRNA simulations commit c172315f697c794472e34dd20eebe1fff622af0a Merge: 1122679 b6fef1e Date: Thu May 10 11:30:02 2018 -0400 Merge pull request #3035 from RosettaCommons/ssrb19/ensembledock_separate RosettaDock with adaptive conformer selection and motif dock score commit 1122679cd61d946c25c5303223cd845fa14e6ed9 Date: Wed May 9 20:26:32 2018 -0400 beautifying commit daf5f34620ba54a4a38afc4d7009c41446c8e91d Merge: f763bc4 6ba9124 Date: Wed May 9 10:18:13 2018 -0400 Merge pull request #3192 from RosettaCommons/guffysl/revert_sewing Reverting sewing merge to diagnose testing failures commit f763bc447fcec212db4d5a1c597f9caa7607d821 Merge: e78b4ea 3d42d73 Date: Tue May 8 16:50:20 2018 -0700 Merge pull request #3189 from RosettaCommons/bfrenz/rosettaESrunscript_fix Fix to ES script to stop it from continuing to run after relaxing the… commit e78b4ea9b162481139b824c1eae251496bc1b9c9 Merge: 493e3de 2aa0de7 Date: Tue May 8 16:49:25 2018 -0700 Merge pull request #3188 from RosettaCommons/bfrenz/glycan_xmls Bfrenz/glycan xmls commit 493e3de7b3808d008efdeb61b26d1d8caa1dddcb Merge: c67b814 bda0b8b Date: Tue May 8 15:14:37 2018 -0400 Merge pull request #2923 from RosettaCommons/frankdt/frankdt/smart_sewing This pull request introduces the new SEWING refactor and its associated applications. This new refactor introduces a number of changes and new features into SEWING, including but not limited to: · SEWING can now be run without generating an edge file (formerly known as a score file). This “unhashed” mode is default and is recommended for most helical proteins. It also avoids the onerous memory requirements of generating an edge file. · Legacy SEWING only stored one possible overlap for each pair of matching helices, limiting the number of possible designs. SEWING is now able to sample all alignments that pass a user-specified minimum overlap residue cutoff, which greatly increases the sampling space. · Legacy SEWING input files contained large amounts of data which could not be held in memory simultaneously; therefore, SEWING had to read from disk periodically throughout the protocol, which led to significant slowdowns. SEWING now reads the entire file from disk at the start. · SEWING now recovers and outputs the lowest-scoring structure encountered during the assembly process. Legacy SEWING did not store and recover the lowest-scoring assembly during a Monte Carlo protocol, instead outputting whichever structure was present at the end of the run. Users can return to this old behavior by setting the new recover_lowest Boolean option to false. · SEWING now performs temperature ramping between user-specified minimum and maximum temperature values. · Users can choose not to include binding partners in their output structures via the output_partner Boolean option. · SEWING now reads all input information at the beginning of a run. · SEWING score terms and their weights can now be customized by users in their RosettaScript XML files using the AssemblyScorers subtag. Previously, all scorers and their weights were hard-coded. · SEWING is now compatible with ligands. Users can specify which residue in their starting structure is the ligand and can either specify its protein contacts manually or, in the case of metals and covalently bound ligands, those contacts can be detected automatically. All ligand contacts and the ligand itself will be preserved as vital residues during the SEWING run. · The new LigandBindingAssemblyMover allows users to introduce new contacts to existing ligands during the assembly process using user-provided specifications of the ligand’s binding geometry. · Both vital residues and ligands can now be specified using residue selectors. · Vital residue information can now be written into the output PDB file; whichever residues so identified in the starting structure will be listed, renumbered, in the output structure as "VITAL" and can be extracted with a ResiduePDBInfoHasLabel ResidueSelector. · Several new score terms and requirements have been introduced, including terms that allow users to more closely control their assembly’s interactions with binding partners as well as scorers and requirements that provide compatibility with ligand molecules. · In AppendAssemblyMover, users can either allow SEWING to automatically detect the boundaries of segments by DSSP (a new feature) or can specify the segments and their secondary structures manually. Manual setting of pose segment starts and ends now occurs in the mover tag rather than via command-line options. · AppendAssemblyMover can now be set to simply extend the starting helix without adding more helices via the extend_mode Boolean option. Note that the new SEWING refactor does not currently support discontinuous SEWING. For those cases, users will still need to use Legacy SEWING. Integration test change to simple_metric_features expected due to old changes in ModelFeatures (associated with LegacySEWING). commit c67b814768067e700fa6300e5f3b5911c0fd9994 Merge: a2b1f5b e46c081 Date: Tue May 8 13:52:09 2018 -0400 Merge pull request #3178 from CyrusBiotechnology/forcommons/213_62chains Simple test to ensure that Rosetta is cool with all 62 officially legal chain characters [a-zA-z0-9]. Changes to unit tests only. commit a2b1f5b29c9910ebcad9302c8cb84f651324e7af Merge: a5357fe 34385dc Date: Mon May 7 18:41:35 2018 -0500 Merge pull request #3186 from RosettaCommons/roccomoretti/fix_make_centroid Fix silly issue with make_centroid When checking if an atom has been deleted from a residue, it helps to check the residue for which you've deleted the atom. Checking the original that still has the atom doesn't work as well. commit a5357fe588bb65c3c88b60c99edf36d51ab03ee3 Merge: cfda974 818888c Date: Mon May 7 15:45:04 2018 -0700 Merge pull request #3187 from RosettaCommons/dimaio/fix_galigdock_integration_tests Fix broken ga ligand dock integration tests commit cfda97409aa5539ffcc20e18cf0053e2e38dd6d6 Merge: 8dca687 157619e Date: Mon May 7 16:35:18 2018 -0600 Merge pull request #3184 from RosettaCommons/sergey/binder PyRosetta update. Updating LLVM build procedure so it track compiler family and gcc-install-prefix as dependency for Binder deployment. commit 8dca6870a4144647d86b12b402baef16a737014d Merge: 25a6ce5 50f4a87 Date: Mon May 7 11:46:38 2018 -0500 Merge pull request #3185 from RosettaCommons/roccomoretti/fixClangSAparsing Fix breakage in ClangSA test parsing. Python3.6 requires that a file be opened in binary mode (where Python2.7 was fine with text mode). Update this so the clang_analysis test no longer fails. Also, add additional checks such that such parsing errors show up in the log. commit 25a6ce563ed91d7d3f9122eb57b986f4bb7cbed2 Merge: ca7ee24 863f95a Date: Mon May 7 10:12:28 2018 -0500 Merge pull request #3180 from RosettaCommons/roccomoretti/fix_pymol_cif (Partially) Fix from-Pymol CIF reading Pymol's mmCIF output is apparently less extensive than from-RCSB ones, and this is causing the Rosetta CIF reader to choke. Note that Pymol CIF input still has an issue - apparently CIFPARSE-OBJ (the external library from the RCSB which we use to parse CIF files) completely ignores the last table in the CIF file. For from-Pymol output this is the atom_site table, which means that you lose all the coordinate data, resulting in an empty pose. The way to fix it is for you to add a dummy line to the end of the CIF file. As I'm not keen on debugging the external library, I've added a warning message to highlight how to get around the issue. commit ca7ee2437234a2090529774aa7b35141a4f97e36 Merge: c89ef43 b122d7e Date: Sat May 5 19:12:44 2018 -0700 Merge pull request #3169 from RosettaCommons/everyday847/pathfinding Update erraser_util.py for better pathfinding commit c89ef43f3e7a7bcea01a3f7f71ed81944b74f359 Merge: e045b6a d406d30 Date: Sat May 5 19:12:36 2018 -0700 Merge pull request #3166 from RosettaCommons/everyday847/GTP_CCC_loadin Load in GTP and CCC as polymeric residues commit e045b6af5d162ef00c65d5fefd9454dd9233b713 Merge: f836162 b908916 Date: Sat May 5 14:00:05 2018 -0700 Merge pull request #3058 from RosettaCommons/dimaio/genpot_to_merge This PR adds several tools aimed with making the Rosetta scorefunction reasonably behaved for arbitrary ligands. Three specific improvements have been added: A new ligand atom typing scheme has been added. An alternate param file generation app, scripts/python/public/generic_potential/mol2genparams.py has been added to handle parameter generation with the new atom typing. NOTE that this new typing is completely separate from protein atom typing. A generic torsional potential, 'gen_bonded' has been added using these new types. This potential is undefined (returning 0) for non-ligand residues currently. LK and LJ parameters have been fit for these new atom types using a combination of small molecule crystal data and ligand-bound protein structures. A new ligand docking protocol has been added in 'protocols/ligand_docking/GALigandDock'. It combines fast scoring on a precomputed grid with a genetic algorithm to allow very accurate ligand docking in 3-10 CPU minutes total per target (fixed sidechain) or 10-30 CPU minutes total (flexible sidechain). It is exposed as an XML-parsible mover, GALigandDock. To use: generate ligand parameter files using the new app mol2genparams.py add the flag -gen_potential (or -beta) to the command line (both load exact same corrections ... note -beta will always load the latest-and-greatest energy function variant) if using RosettaScripts, be sure the term 'gen_bonded' is turned on (recommended weight = 1) More detailed information at https://www.rosettacommons.org/docs/wiki/rosetta_basics/scoring/Overview-of-Seattle-Group-energy-function-optimization-project commit f8361627cf790aa8edf2b979e38863930c68dc17 Merge: 1629f99 fc2407d Date: Thu May 3 09:31:36 2018 -0600 Merge pull request #3171 from RosettaCommons/sergey/binder Fixing PyRosetta GCC build commit 1629f99a95b87e0685c1b74bad26a5bb1998eb2d Merge: 7f35f73 8a8c626 Date: Thu May 3 09:26:21 2018 +0200 Merge pull request #3170 from RosettaCommons/secstruc_strucfrags secstruc strucfrags commit 7f35f735c8bb90e3b54dd06af985a2e79233578b Merge: ab81993 f6cb9ba Date: Wed May 2 09:50:33 2018 -0500 Merge pull request #3158 from RosettaCommons/revert-3157-revert-3145-roccomoretti/centroid_autosetupmetal Revert "Revert "Make auto_setup_metals work with centroid mode."" Enable the relevant metapatches in centroid mode, as well as enabling the automatic centroid-mode residue type generation to work with connected residues. (Like sidechain-bound metalbinding residues.) The established covalent connections and constraints from fullatom mode should transfer to centroid mode. For connections/constraints to sidechain atoms, a special all heavyatom-present residue will be created. While this allows maintaining and round-tripping the constraints/connections through centroid mode, there's limitations on scoring/sampling in centroid mode. For scoring,the lack of a CEN atom results in differences in how the residue is scored versus a non-sidechain-metalbinding residue. For sampling, the lack of sidechain flexibility in centroid mode protocols may result in rejection of otherwise-acceptable conformations, due to the presence of the inflexible metalbinding sidechain. (Both of these should be minimal if you're not sampling directly in the vicinity of the metalbinding atom.) commit ab819933844e0ed13e59fce789cf06bd09350875 Merge: d0b8db7 9f9660b Date: Tue May 1 17:32:17 2018 -0700 Merge pull request #3156 from RosettaCommons/vmullig/buried_unsat_score_incremental_merge_7 Incremental merge 7: Trying for some additional speed improvements with the buried_unsatisfied_penalty scoreterm Unfortunately, the speedup is pretty small. This does simplify the code a little bit, though. Tasks: - [x] Pull request #3155 must be merged before this one. - [x] Reduce the amount of node-swapping needed. - [x] Track down and fix the decrement errors. - [x] Beauty. commit d0b8db714f763694fea402b8065c0b81bfbb67db Merge: 5aef58e f38a48d Date: Tue May 1 15:55:12 2018 -0700 Merge pull request #3155 from RosettaCommons/vmullig/buried_unsat_penalty_incremental_merge_6 Incremental merge 6: Fix some spiky memory use in the buried_unsatisfied_penalty scoreterm Tasks: - [x] Add cleanup after packing. - [x] Benchmark -- does this help with overall memory consumption? - Yes, it does. It eliminates the spikiness, though usage is still somewhat high. - [x] Also, caught a really stupid `runtime_assert` error that was needlessly aborting trajectories. Fixed. - [x] Beauty. commit 5aef58e6a92d4526d4c628342d0e9304e407d079 Merge: 8d46f45 5780a0c Date: Tue May 1 13:44:52 2018 -0700 Merge pull request #3142 from RosettaCommons/everyday847/remove_cached_data_from_suite_potential Remove cached data from suite potential commit 8d46f45c1202286be5fd62fbad91a556baf12cbc Merge: b70d814 815b857 Date: Tue May 1 15:55:14 2018 -0400 Merge pull request #3164 from RosettaCommons/JackMaguire/MCHBNetCorrection Very Small Multistage Rosetta Scripts Update Multistage Rosetta Scripts currently can not use some filters because they get added to the CalculatorFactory singleton in RosettaScriptsParser (which MRS did not use). This PR adds a call to this RosettaScriptsParser function from the MRS Job Queen. Thanks to Vikram for approving! commit b70d814769c0b2a80d16adb32f1f69f5448b2c4a Date: Tue May 1 14:56:54 2018 -0400 beautifying commit ca3b994c3b7df5022bbbde9daec6ad54e8b93126 Date: Tue May 1 14:49:19 2018 -0400 updating beautify test so it now update options, residue types and version before attempting to beautify code commit ab2bc2578b900e8a90c340070b5d21b99707f171 Merge: b30a93b 3f7cf31 Date: Tue May 1 11:40:54 2018 -0500 Merge pull request #3099 from RosettaCommons/roccomoretti/parallelize_symmetry Symmetry: Remove additional dependencies on the option system. This PR removes most of the inappropriate uses of `-symmetry::symmetry_definition` in determining if we're operating under symmetry, preferring instead to use `core::pose::is_symmetric( pose )` to determine if we need symmetry. Additionally, SymMinMover, SymPackRotamersMover, and SymRotamerTrialsMover have been stubbed out, moving any symmetry-specific code into the non-Sym versions. This means that the non-Sym-labled versions can be used for both symmetric and asymmetric poses, and will do the right thing in each case. The Sym versions are deprecated, and are kept around only for backward compatibility with existing XML and PyRosetta scripts. *Note that TaskAwareSymMinMover apparently has slightly different default behavior than the non-Sym version, so I left both as-is for now.* commit b30a93b32e6284fc233c15ebc22e6ee850eb5304 Merge: 08dfca8 ae78d41 Date: Tue May 1 11:29:10 2018 -0500 Merge pull request #3154 from RosettaCommons/roccomoretti/octothorpe_component HydroxylTorsionPotential was trying to parse comment lines. This resulted in warning messages from the PDB components loading machinery. Add a check to avoid trying to parse comment lines. commit 08dfca8c4439603d4f465fdd5638ac08955b817d Merge: 6077d40 0c57ca2 Date: Tue May 1 00:09:31 2018 -0600 Merge pull request #3151 from RosettaCommons/sergey/ui Updating JSON library to 3.1.2 commit 6077d4053e9975b402e20d63b489925b2ecd2113 Merge: a16c809 8acfacd Date: Mon Apr 30 18:47:27 2018 -0700 Merge pull request #3162 from RosettaCommons/vmullig/fix_prepend_issue Fix an issue affecting the GenKIC tutorials. Fix suggested by @rpavlovicz. commit a16c809f2545972e63b17c5b306b7ea4eb2e34e2 Date: Fri Apr 27 15:36:05 2018 -0400 Fixing PyRosetta build: looks like Binder submodule head was accidentally downgraded in #3128 commit a2f12e07d533cda15228c1fce0ff36378b4e54e7 Merge: 9d9411f 52c61cf Date: Fri Apr 27 12:08:43 2018 -0700 Merge pull request #3139 from RosettaCommons/danpf/disulfide_ft_fix Fix disulfide ft in set_reasonable_foldtree commit 9d9411fca2da09ad8814603ef68c5980ab4f183c Merge: a20bfbc c7f84db Date: Fri Apr 27 10:44:06 2018 -0700 Merge pull request #3153 from RosettaCommons/everyday847/fix_phenix_erraser Fix Phenix-ERRASER integrations commit a20bfbcd96db81640526a522c497a88a8fe71853 Merge: d5b1db1 aa3b8db Date: Fri Apr 27 10:03:04 2018 -0500 Merge pull request #3157 from RosettaCommons/revert-3145-roccomoretti/centroid_autosetupmetal Revert "Make auto_setup_metals work with centroid mode." Reverting commit until I can figure out what I broke and why. commit d5b1db1c5797ac4f913a0b1dad1011f561281582 Merge: 7b5a45e ef69c5c Date: Fri Apr 27 00:52:41 2018 -0700 Merge pull request #3128 from RosettaCommons/everyday847/add_TNA Rudimentary support for TNA (threose nucleic acids) commit 7b5a45ef2f62fa12e9bf09f0bcd7048b473d73f3 Merge: ffc403b 7f22dc1 Date: Thu Apr 26 18:01:34 2018 -0700 Merge pull request #3149 from RosettaCommons/vmullig/buried_unsat_score_incremental_merge_5 Incremental merge 5: Another couple of small improvements to buried_unsatisfied_penalty efficiency Reducing the amount of unnecessary copying of data during the packer run. Also, when packer trajectories alter multiple residues (_e.g._ when jumping back to a low-energy state), node substitutions are now automatically accepted to minimize the number of nodes that have to be updated with each packer step. Tasks: - [x] Eliminate direct storage of data in edges, and add an edge data class (pointers to which can be swapped out). - [x] Benchmark. - Packaging edge data in a special object and only swapping out the const smart pointer to the object results in about a 21% speedup. Not bad, but still not the dominant inefficiency. - The speedup from updating nodes more efficiently is inconsistent from benchmark replicate to replicate, and probably negligible. So still not the dominant inefficiency. - Final cost of `buried_unsatisfied_penalty`: 4.36x increase in packing time, for much better results, with these optimizations. Scaling is linear with pose size (with or without `buried_unsatisfied_penalty`, but intercept is negative (in both cases) -- so for small poses, the relationship is different and the cost might be more negligible. - [x] Beauty. commit ffc403b9b5447e03edcc37406da86c80317f9a78 Merge: a3cc9b6 b9b4297 Date: Thu Apr 26 15:32:20 2018 -0500 Merge pull request #3145 from RosettaCommons/roccomoretti/centroid_autosetupmetal Make auto_setup_metals work with centroid mode. Enable the relevant metapatches in centroid mode, as well as enabling the automatic centroid-mode residue type generation to work with connected residues. (Like sidechain-bound metalbinding residues.) The established covalent connections and constraints from fullatom mode should transfer to centroid mode. For connections/constraints to sidechain atoms, a special all heavyatom-present residue will be created. While this allows maintaining and round-tripping the constraints/connections through centroid mode, there's limitations on scoring/sampling in centroid mode. For scoring,the lack of a CEN atom results in differences in how the residue is scored versus a non-sidechain-metalbinding residue. For sampling, the lack of sidechain flexibility in centroid mode protocols may result in rejection of otherwise-acceptable conformations, due to the presence of the inflexible metalbinding sidechain. (Both of these should be minimal if you're not sampling directly in the vicinity of the metalbinding atom.) commit a3cc9b6514d71a901e906619bd412e463ef7fa5b Merge: a276d2c ca54555 Date: Thu Apr 26 15:21:14 2018 -0400 Merge pull request #3007 from RosettaCommons/aleex-adal/mpupdate2 Add parse_my_tag() functions + unit tests for RosettaMP movers commit a276d2cce3fc5d9b4d19fd7e1ff131947e707b02 Merge: 9732d04 f876530 Date: Thu Apr 26 11:00:31 2018 -0700 Merge pull request #3146 from RosettaCommons/ckrivacic/loop_modeler_ramp_constraints Ckrivacic/loop modeler ramp constraints commit 9732d041f190dc2dc1e23d69c6b8697440ad5c45 Merge: 9426fbf 0e61ca4 Date: Thu Apr 26 08:53:35 2018 -0700 Merge pull request #3150 from RosettaCommons/everyday847/gcc_8_fixes Get building with GCC 8 commit 9426fbfb9a940a188d9e643f4ecf6087e8568526 Merge: c8fec8f 84c21e9 Date: Wed Apr 25 17:43:05 2018 -0700 Merge pull request #3148 from RosettaCommons/vmullig/selection_counter Add a SimpleMetric that counts the number of residues in a pose or selection Requested by @srgerb. Tasks: - [x] Add the SimpleMetric. - [x] Unit tests. - [x] Documentation. - [x] Move to core. - [x] Integration test. - [x] Change name to SelectedResidueCountMetric. - [x] Documentation, too. - [x] Beauty. commit c8fec8f048d977f018ebff4556558b91e118c675 Merge: 71619a3 899a68d Date: Wed Apr 25 14:57:49 2018 -0600 Merge pull request #3141 from RosettaCommons/sergey/binder Adding Python-3 compatible PyMOL-RosettaServer script commit 71619a37ebfa03a0723eb7203aa423313fa811c5 Merge: ef334a5 fe55ddd Date: Wed Apr 25 06:49:35 2018 -0700 Merge pull request #2354 from RosettaCommons/raemisch/FindGlycanSeqonsMover Raemisch/find glycan seqons mover commit ef334a50fe5ae4a5e98a59a981d86a888f211f9b Merge: 7714f56 1c4dd3a Date: Tue Apr 24 15:33:45 2018 -0700 Merge pull request #3144 from RosettaCommons/vmullig/buried_unsat_score_incremental_merge_4 Incremental merge 4: Efficiency improvements for the buried_unsatisfied_penalty scoreterm OK, now that it works, let's make it fast. This should significantly speed up the calculation, especially for large poses or large rotamer sets. Tasks: - [x] Add logic to update only relevant nodes during packer run. - [x] Beauty. - [x] Benchmark speedup -- how much does this help? - Ugh -- without optimizations, it was resulting in a 67-fold slowdown on a naïve PackRotamers run with all canonicals. (The scaling seems quadratic -- this is why I wasn't seeing much slowdown on my small test cases). - With optimizations, it's a 6-fold slowdown. This scales linearly with pose size (_i.e._ it remains a 6-fold slowdown even for a large pose). - There may be additional optimizations possible. - [x] Double-check unit tests. - [x] Double-check integration tests. - [x] This pull request must be merged after #3143. commit 7714f56f60222543163b1b40f23454bf594f02f9 Merge: 3de476d fe90e380 Date: Tue Apr 24 11:43:06 2018 -0500 Merge pull request #3137 from RosettaCommons/roccomoretti/seq_in_poseinfo Add sequence information to PoseInfoFilter output report. commit 3de476d50c2d9de1c3a6dadc0c0c03c36b54919d Merge: 3a8a0c1 af315ea Date: Tue Apr 24 03:36:14 2018 -0700 Merge pull request #3143 from RosettaCommons/vmullig/buried_unsat_score_incremental_merge_3 Incremental merge 3: Add a visualizer for buried polar groups (for use with buried_unsatisfied_penalty) Tasks: - [x] Add the visualizer (a SimpleMetric). - [x] Integration test. - [x] For symmetry, too. - [x] Debug integration test. - [x] Beauty. - [x] Make changes suggested by Jared. - [x] Check tests on test server. - [x] Documentation. - [x] Pull request #3140 must be merged before this one. commit 3a8a0c120ce6f497631c1b80b48cc98327712bec Merge: 701220c 1272013 Date: Mon Apr 23 22:39:04 2018 -0700 Merge pull request #3140 from RosettaCommons/vmullig/buried_unsat_score_incremental_merge_2 Incremental merge 2: Add symmetry support to the buried_unsatisfied_penalty scoreterm This pull request must be merged after pull request #3135. This adds symmetry support to the buried_unsatisfied_penalty scoreterm, plus unit and integration tests. Tasks: - [x] Symmetry support. - [x] Remove error if used on a symmetric pose. - [x] Documentation. - [x] Beauty. - [x] Unit tests. - [x] Integration test. @sboyken @JackMaguire @asford @bcov77 commit 701220c2c58daf73371a76a2ab02e83addcd43ae Merge: 83cbd28 c9cf08f Date: Mon Apr 23 11:19:18 2018 -0500 Merge pull request #3133 from RosettaCommons/jadolfbr/simple_metrics Bug fixes: SequenceMetric and sequence motif split - Fix major bug in SequenceMetric where the unit test was also wrong. - Fix minor bug in splitting of sequence motif that made the CreateSequenceMotifMover/SequenceMotifTaskOp to incorrectly design motifs which had no inner brackets. So this - `N-T` would fail, but `N[-]T` would be designed correctly. Expand unit tests for this specific motif type. - Fix `simple_metric_features` integration test through dumping the db. Thanks @roccomoretti ! - Condense splitting sequence motif function into a single function. - Add cluster and distance info to scorefile for antibody design as a stop gap until we have a full SimpleMetric. commit 83cbd28d003c13365cdf0e6d48421adf0203f744 Merge: 6dc40c1 a3b540a Date: Sun Apr 22 22:09:34 2018 -0700 Merge pull request #3135 from RosettaCommons/vmullig/buried_unsat_score_incremental_merge_1 Incremental merge of buried unsatisfied penalty scoreterm. (This currently lacks symmetry support.) This is an incremental merge of pull request #2597. This pull request adds basic support for asymmetric poses, but no support yet for symmetric poses. This scoreterm guides the packer to solutions with no buried unsatisfied hydrogen bond donors or acceptors. It is intended for use with the rest of the scorefunction, and possibly for use with the `voids_penalty`, `aa_composition`, and `hbnet` scoreterms. Tasks: - [x] Basic support for asymmetric poses. - [x] (Temporary) error if used on a symmetric pose. - [x] Unit tests. - [x] Integration tests. - [x] Documentation. - [x] Beauty.