commit 2c8402493efd5aee13c46a7984193b2b26242435 Merge: b7e897d c3a4b3c Date: Sun Apr 17 10:53:06 2016 -0500 Merge pull request #1270 from RosettaCommons/roccomoretti/appexcepthandling_speedup Attempt to speed up the app_exception_handling itegration test. commit b7e897de86c9e849f2a7dbc9192497a84b734260 Merge: 9546568 3b95517 Date: Fri Apr 15 18:54:36 2016 -0400 Merge pull request #1245 from RosettaCommons/JWLabonte/sugars/general PyRosetta/Carbohydrates: Adding sample files/tests for sugars to ship with PyRosetta This merge adds a new directory to PyRosetta and a new unit test for carbohydrate functionality within PyRosetta. It also includes a miscellany of other sugar- and/or PyRosetta-specific tweaks/improvements/corrections. This merge also fixes a bug in the Windows build, because apparently "rad2" is a keyword for Windows! Thanks to @lyskov All unit tests pass. carbohydrates test changes expected. commit 9546568d2a2517e7da6361967089c186b09bbd74 Merge: 954c876 43b9ac4 Date: Thu Apr 14 16:48:05 2016 -0700 Merge pull request #1220 from RosettaCommons/yhsia/MutateSelf Added option "mutate_self" to MutateResidue mover. commit 954c876de631d23c7f16e7a0f28c80966bc8c80f Merge: 93d738b a7fafc7 Date: Thu Apr 14 11:02:20 2016 -0700 Merge pull request #1252 from RosettaCommons/jadolfbr/sugars/glycan_clash_check Adding a pilot app specifically for glycan clashes which quantifies clashes between specified glycan branches and other chains and glycan branch - glycan branch clashes. Does not count clashes for intra glycan branch. Does not echo input files, adds info to output scorefile to allow for MPI runs. Also adding description of Rosetta LJ in AtomType from a description by @aleaverfay in a dev list discussion some years ago (sigma1 vs sigma2) to help future travelers. Clash Definition ============ Atom is clashing if it clashes with ANY other atom Count up clashes (hard and soft) per-residue - Hard: - distance <= LJ1 + LJ2 - Soft: - distance <= (LJ1 + LJ2) * (1 - S). S is between 0 and 1. Here, we use .33 as default. -> Intuitive definition, easily conceptualized, still quantitative Relevant Options: ====== -glycan_branches - Required. Vector of glycan branches. Rosetta Residue numbering or PDB like RosettaScripts -chech_chains - Required. A list of chains to compute chain-based clashes. If not given, will only compute glycan-glycan clashes! -ignore_hydrogens - Should we calculate only heavy-heavy atom clashes? -soft_clash - When we calculate atom-atom distances using LJ distances, clash if distance < (atomI_LJ + atomJ_LJ)*(1 - soft_clash) commit 93d738b90e0bc37fa96c706a6c31b7f159d2a5c7 Merge: b1a514c c8cc153 Date: Thu Apr 14 11:43:40 2016 -0400 Merge pull request #1274 from RosettaCommons/JWLabonte/sugars/CAPRI_redux Carbohydrates: CAPRI Redux Part II missing file; unit tests pass; carbohydrates test changes expected commit b1a514c449e4beda6622112ec539bddcbec28c48 Merge: b69eccb c5bc2a5 Date: Thu Apr 14 10:48:26 2016 +0300 Merge pull request #1248 from RosettaCommons/fixRestrictToAlignedSegments Added name attribute in RestrictToAlignedSegments TO to fit new XML s… commit b69eccb0e535caccb9ce4452b49c399d1f94f242 Merge: 710c6ac c7f9783 Date: Wed Apr 13 15:14:25 2016 -0700 Merge pull request #1224 from RosettaCommons/vmullig/binselector Add a ResidueSelector to select residues based on their torsion bin (e.g. ABEGO bin) This should be useful for peptide design, as well as for canonical design in which one might want to design positions in the A bin with helix-favouring residues and positions in the B bin with strand-favouring residues, etc. Tasks: - Create ResidueSelector with Jared's nifty scripts. - Add BinSelectorCreator to ResidueSelectorCreators.hh. - Add ResidueSelector to core.3.src.settings. - Loading of bin definitions. - Write apply() function. - Write parse_my_tag() function. - Unit tests. - Selector XSD. - Integration test. - Add bin_params files for selecting residues in L- or D-proline bins. - Test for this, too. - Option to only select alpha-amino acids. - Documentation. - Beauty. Also: X Fix PhiSelector bug identified by Parisa --> put off to a future pull request. - Fix a little bug in the RESET command in ResidueLevelTask_ (unnecessary debug_asserts that tripped things up in debug mode). - Integration test for PhiSelector, too. commit 710c6acaf5b543ab1dfd0143190e7af491d80bfc Merge: f7017b0 22509d2 Date: Wed Apr 13 14:34:30 2016 -0500 Merge pull request #1268 from RosettaCommons/roccomoretti/icc_pseudofix Change RotamericSingleResidueDunbrackLibrary to avoid unnecessary intermediate data structure. This should fix the current issue with fa_dun score differences between GCC and ICC. This doesn't, however, necessarily address the underlying issue of why ICC was breaking the code when optimizing. I've (separately) put together a test case to pass along to Intel as a possible bug report. commit f7017b003254f119f4a24e536d979156b19363fa Merge: 96317f6 0aa3011 Date: Wed Apr 13 11:41:32 2016 -0700 Merge pull request #1269 from RosettaCommons/jadolfbr/antibodies/skip_cis_trans_cluster_matching Jadolfbr/antibodies/skip cis trans cluster matching Adds an option to Rosetta Antibody for North/Dunbrack Clusters: -allow_omega_mismatches_for_north_clusters - Skip first grouping by cis and trans designation for clusters in which a cis/trans designation currently does not exist. This is due to the North clusters being first grouped by the omega cis/trans for each residue, and then clusters within that (for example TTTTTTTCTT ). This directly relates to the sequence profiles used for design. We may eventually make this option default on, but for now it stays off. If a cluster for a CDR cannot be found because of this mismatch, we give a nice warning to users in Red and let them know of this new option. Also add an integration test for identify_cdr_clusters. Thanks to @lyskov for helping with the tracer colors. I added some info to the Tracer header that gives examples on how to do it for most common purposes. commit 96317f60b41d20b20f48fc1440b6b1737fb7e3b7 Merge: 90f9d2e dc03c74 Date: Wed Apr 13 00:54:05 2016 -0400 Merge pull request #1259 from RosettaCommons/JWLabonte/sugars/branching Post-ChemicalXRW: removing the -read_pdb_link_records option LINK records are now read always. All unit tests pass. Integration test changes expected where options have been changed. Note that the C-terminal_conjugation patch causes a bug in some unit tests, so it has been commented out of patches.txt until the bug has been squashed. In the meantime, it can be included by the option system. commit 90f9d2e4a7b91dc847901fc7f8aea9f0506bd1e7 Merge: d586c96 989cccd Date: Tue Apr 12 22:34:26 2016 -0500 Merge pull request #1266 from RosettaCommons/havranek/multipole_sasa Bugfix to VDWTinker, adding analytical, differentiable SASA term. commit d586c96c037e0457f841b0fe1ca0599e4701c8c4 Merge: 0bed02c e815d27 Date: Mon Apr 11 22:40:43 2016 -0400 Merge pull request #1265 from RosettaCommons/xiaotongzuo/carbohydrate Carbohydrates: Adding new sugar params and patch files commit 0bed02c846ef09fad4846a1cc441a7167f0962d6 Merge: 697d468 174e8a1 Date: Mon Apr 11 16:23:33 2016 -0700 Merge pull request #1262 from RosettaCommons/jadolfbr/antibodies/de_loop_design Antibody DE Loop Design Description ======== This PR finally enables Proto CDR4, also known as the DE loop, to sequence design within RosettaAntibodyDesign. L4 and H4 are specified the same way as others within the cdr instruction file. L4 and H4 can also be specified as neighbor CDRs. 'DE' can used as in 'ALL' keyword in the instructions file to set options for both loops. Proto CDR4 is not designed by default. Testing ===== Unit tests have been updated to include and test this new functionality, and an integration test has been added. The current antibody_designer integration test has also been shorted by changing the min type. commit 697d468bc6d6f8eb0ba1073f922e8b6aa19e4493 Merge: 3e859bf 168cb73 Date: Mon Apr 11 12:17:41 2016 -0700 Merge pull request #1264 from RosettaCommons/jadolfbr/sugars/glycan_relax_random_start Glycan Relax updates Description ========= This PR makes the default number of Glycan Relax rounds to 50 and adds two ways to start the modeling off, either by randomly sampling every glycan torsion first from the move map, or by randomly sampling each torsion using the sugarBB probabilities for those with which we have sugarBB data. @raemisch Has run preliminary tests on 50k models per experiment and found that if you do not have a real starting glycan conformation, that 50 or 75 rounds and random start both produces greater sampling diversity in the final models (with a lower number of decoys needed) and enriches for low-energy models. Still much benchmarking to do, but this is a start. Options ====== cmd-line: - -glycan_relax_random_start - -glycan_relax_sugar_bb_start RS: - random_start - sugar_bb_start commit 3e859bfd62e9fd3ba9ca39efd69bd3a8f6597091 Merge: 25879bc b16b7fc Date: Sun Apr 10 18:05:57 2016 -0700 Merge pull request #1263 from RosettaCommons/tlinsky/disulfidize_mutate_to_ala Disulfidize no longer mutates disulfides outside of specified subsets to ALA commit 25879bcba067c46f9da9f0d3d0f19dd924865fdc Merge: ce02443 d777606 Date: Sat Apr 9 22:20:32 2016 -0600 Merge pull request #1261 from RosettaCommons/sergey/binder Fixing some PyRosetta compilation and linking errors