commit ba861e0c30adc65bf6b45695071e3c34a8243c0d Merge: 4c3be7c 99239ed Date: Sat Jul 16 11:45:59 2016 -0500 Merge pull request #1465 from RosettaCommons/amelie-stein/ddG_with_ligands On behalf of Amelie, merge in some fixes to the ddg_monomer applicaition to allow it to work with non-amino acid residues. commit 4c3be7cd05e33361cdbdd1f7bfbb666530440f85 Merge: a49b29d 0588286 Date: Thu Jul 14 18:33:24 2016 -0700 Merge pull request #1458 from RosettaCommons/vmullig/ncaa_betanov Fix loading of NCAA rotamer libraries when using beta_nov15 The problem turned out to be that beta_nov15 turns on the Shapovalov rotamer libraries, which have a slightly different file format (an extra column in the middle of the file, which is irritating). When an NCAA library is loaded, it is therefore misinterpreted: Rosetta assumes that the extra column is there when it is not. The solution is to count the columns in the first line and to determine whether a file is a Shapovalov-format file or not. Tasks: - Fix the bug. - Merge the latest master into branch. - Fix the fix so that it doesn't break the loading of gzipped rotamer libraries. - Beauty. commit a49b29d96564db596b09f5a6e72239dc797b8ba1 Merge: 98ae263 e319077 Date: Thu Jul 14 15:44:29 2016 -0700 Merge pull request #1455 from RosettaCommons/tlinsky/constraint_generator_nonglobal Remove global data from ConstraintsManager commit 98ae2632f27254659d148005391190df046f57e2 Merge: 4069494 fb3b467 Date: Thu Jul 14 08:32:00 2016 -0700 Merge pull request #1459 from RosettaCommons/tlinsky/tlinsky/ss_filter_selector Add residue selector support to SecondaryStructureFilter commit 40694948a6960c135c0cf53d381f5bee569690f2 Merge: 196fc44 fc9d964 Date: Wed Jul 13 21:36:31 2016 -0400 Merge pull request #1453 from RosettaCommons/lqtza/prepack_centroid_fix Docking Prepack Outputs Full-Atom Poses Only commit 196fc442ba8b95d82325bf539612ff458ddc9254 Date: Wed Jul 13 20:51:00 2016 -0400 Fixing PyRosetta build on Ubuntu 16.04 commit 2ed6b8e4427473c98bd7a4ca47ad9fc92439ae84 Merge: 892c812 baf8c2e Date: Mon Jul 11 14:32:32 2016 -0700 Merge pull request #1446 from RosettaCommons/bfrenz/denovo_density_point_selection Bfrenz/denovo density point selection commit 892c8123fdeea22b6119abecf2ea6de9edda8e5d Merge: 0f120c1 b81112d Date: Mon Jul 11 13:32:53 2016 -0700 Merge pull request #1448 from RosettaCommons/xingjiepan/LoopBuilder_bug_fix Remove the idealize_loop() function in LoopBuilder::do_apply() commit 0f120c1d363716d95e0ab07af64388db5c3998db Merge: 6f2c615 5b2c6c5 Date: Mon Jul 11 15:43:01 2016 -0400 Merge pull request #1452 from RosettaCommons/Cyrus/mergetarget Cyrus/mergetarget Included in this PR: PR Cyrus 35: add comment clarifying pilot_apps.src.settings.release (there was some list traffic here) PR Cyrus 31: global replace old UNC address with gmail address in doxygen tags (smlewi@unc->gmail) PR Cyrus 33: Tweaks SSPredictionFilter (actually PsiPredInterface) to automatically allow for a second type of name mangling from a different version of runpsipred PR Cyrus 32: Smlewis cyrus/beta nov15 score catcher: Catches the problem where you pass a beta weights file without the accompanying required flag to activate the params overrides. (exit from ScoreFunctionFactory in the (in)appropriate circumstance). Also PR Cyrus 29, which got caught in a time vortex, and was merge -X theirs overwritten because Rhiju was forced to duplicate the code itself instead of taking it from its original crossfork PR. commit 6f2c615bc0ae0effe0c8dcc30fc5cf9bb182fd6e Merge: 6e1fba8 ea775dc Date: Sun Jul 10 17:54:27 2016 -0700 Merge pull request #1449 from RosettaCommons/vmullig/small_genkic_tweak Adding option to the GeneralizedKIC mover ("dont_fail_if_no_solution_found=true") to NOT set mover status to failure if no solution is found. (The default is false, which means that the mover WILL exit with failure status if no solution is found, aborting a trajectory. There are some cases in which one might not want this, though.) Tasks: - Add option, setter function, and parsing in parse_my_tag(). - Have it control mover status. - Update documentation. - Beauty. commit 6e1fba8ddaff1dd266a9d2886f5755dda4a4f037 Merge: 7575a41 579bbba Date: Sun Jul 10 14:53:45 2016 -0700 Merge pull request #1433 from RosettaCommons/everyday847/n3_adenine_prot Adenosine protonation variants commit 7575a419bd978497b411db00240c2622d5d9480d Merge: 679718a 6608372 Date: Sun Jul 10 10:22:11 2016 -0500 Merge pull request #1447 from RosettaCommons/bazzoli/ignore_waters_by_default Ignore waters by default. commit 679718a25282a2bc8c5f2601a57af3f706afb541 Merge: 4fa8a7c 3a0b68a Date: Sat Jul 9 22:16:36 2016 -0600 Merge pull request #1450 from RosettaCommons/sergey/binder Adding bindings for ObjexxFCL commit 4fa8a7c2566212456f87ba925d74c89d37390a03 Merge: d6e5143 ebe9685 Date: Fri Jul 8 18:45:21 2016 -0700 Merge pull request #1441 from RosettaCommons/tlinsky/symmetry Add simple unit test and doxygen for core::pose::symmetry::symmetrize_fold_tree commit d6e5143553a5ce5eaa3f4dc02231fb89eae59f02 Merge: b0fa12d fe66630 Date: Sat Jul 9 02:40:56 2016 +0800 Merge pull request #1443 from RosettaCommons/dimaio/multichain_hybrid_bugfixes A bug in my previous checkin with multichain hybridize commit b0fa12d5047586049e2ed40a42094f117eae2c8d Merge: e0e867a e1d6361 Date: Thu Jul 7 21:15:40 2016 -0700 Merge pull request #1431 from RosettaCommons/tlinsky/helix_pair_filter Update and clean up HelixPairingFilter, add unit test commit e0e867ae858c66ff32f9754069ad631b9cbfe2a7 Merge: c384a55 416785f Date: Thu Jul 7 20:16:22 2016 -0400 Removing unneeded include to fix release’s commit c384a555794a9577971b5b0503f5a0fe9a99514f Merge: da19bd8 1152fe7 Date: Thu Jul 7 08:39:48 2016 -0700 Merge pull request #1439 from RosettaCommons/tlinsky/delete_region_pdb Make DeleteRegion parse_my_tag congruent with documentation commit da19bd82721e0d78c06fb3888483bdfaa3a13769 Merge: 02cecca 37c4103 Date: Thu Jul 7 11:10:12 2016 -0400 Merge pull request #1442 from RosettaCommons/rhiju/rna_denovo_setup + hotfix to FARNA integration test that includes VRT residue + also removing some unnecessary verbiage from rna_denovo_setup + restoring rna_puzzl5_P15P3P8... test which used virtual residue & rigid body docking of all segments. + tests look OK commit 02ceccaa92244b8c096a4e2a38b59e4ca5b90907 Merge: 5f0a431 60919f2 Date: Thu Jul 7 08:29:50 2016 +0800 Merge pull request #1436 from RosettaCommons/dimaio/multichain_hybrid_bugfixes Fix a few bugs in hybridize with multichain poses. - Run a bit faster when DetailedControls are enabled by skipping unnecessary calcs. - Move some output to Trace level. hybridize/mr_protocols integration test changes expected. commit 5f0a4310ff9d47a33afca4c7a8eca7d867f4881f Merge: 5cdaa7a ada631c Date: Wed Jul 6 13:42:28 2016 -0400 Merge pull request #1437 from RosettaCommons/rhiju/rna_denovo_setup fix getcwd() compile bug in ubuntu. standard tests look OK (except profile, not yet complete), and separately ran ubuntu builds commit 5cdaa7aefea25017eb4ba68f34c6e4c9deec17b7 Date: Tue Jul 5 19:00:35 2016 -0400 PyRosetta, decreasing runtime of Workshop5test.py test commit bc361c50ee2051250ea236870f25e5a88258ffcd Merge: 5209f47 2251974 Date: Tue Jul 5 06:14:59 2016 -0700 Merge pull request #1434 from RosettaCommons/rhiju/rna_denovo_setup Rhiju/rna denovo setup Some small updates to input & help in rna_denovo • iccbuild is failing due to license issue on test server • in integration tests, new test `rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation` is having a problem -- will fix in a separate pull request. • `hybridization` test was broken previously. commit 5209f47ba636688f3470733c4c5bc878d2f022ab Merge: 55ba4c3 2da458d Date: Mon Jul 4 12:09:28 2016 -0700 Merge pull request #1432 from RosettaCommons/rhiju/rna_denovo_setup Rhiju/rna denovo setup + integration tests for `rna_denovo` give cosmetic changes -- all confirmed/checked locally. + some new integration tests `rna_puzzle_*`. + other integration tests that change only do so in linux.release_debug or mac.clang but not both, suggesting uninitialized variables or other stochastic choices depending on system state. + icc build broken on Hojo3, but error message is about license problem, so i don't think that's this pull request. + profile may have changed in 1-2 tests, but getting timeout on test server. 1-2 profile test changes in previous build appear within bounds of variability of these tests. commit 55ba4c3a290fdf4e54ccc02a6b0a9e628c881614 Date: Sun Jul 3 18:40:05 2016 -0400 Increasing run time for PyRosetta4 test. Increasing profile tests tolerance. commit 680b8217792076090e9199f7946de6ec3a5bbd3f Date: Sat Jul 2 19:58:35 2016 -0400 Adding PyRosetta4 release tests commit 8439cb3a2493c8f243d6178797c1d060c138ed9f Merge: ff77e15 d3818bb Date: Sat Jul 2 17:52:04 2016 -0400 Merge remote-tracking branch 'origin/master' into sergey/binder commit ff77e156480078151619850a066217ceb148ff96 Date: Sat Jul 2 17:51:33 2016 -0400 Updating PyRosetta4 package to include demo and tests commit 8e0a129e628ed0ac0f308b3c71df0fb0d9b6c49f Date: Fri Jul 1 20:04:18 2016 -0400 Adding PyRosetta4 release tests commit 2e6f3507baba16db564a0507209450964e1224c4 Date: Sat Jun 25 19:37:16 2016 -0400 Refactoring PyRosetta generation procedure to make results more reproducible on different os/compiler/filesystems commit 442254b23335349ada054fe847d4561628a117aa Date: Sat Jun 25 12:47:59 2016 -0400 disabling deprecated code commit 97869caeaf0dd23a1484f88020a62967b5401331 Merge: d8d0ecd 0142294 Date: Fri Jun 24 21:31:17 2016 -0700 Merge pull request #1419 from RosettaCommons/vmullig/better_errors Add some more informative error messages commit d8d0ecd7982d60b7494207740747fcc33c2a569d Merge: afeafd3 ccb5ba9 Date: Fri Jun 24 18:11:03 2016 -0600 Merge pull request #1416 from RosettaCommons/sergey/binder fixing PyRosetta SubClassing* tests commit afeafd30570a2eb1d0b353527e1edb7a009f6772 Merge: fa97b18 dbe4249 Date: Fri Jun 24 11:33:54 2016 -0400 Merge pull request #1413 from RosettaCommons/Cyrus/mergetarget Cyrus/mergetarget Four changes here: README.md: a minor informational change, originally meant to test these cross-fork PRs source/src/apps/pilot/smlewis/LoopAnalyzer.cc: bitrot repair in a disabled pilot app source/src/protocols/constraints_additional/BindingSiteConstraint.cc: adding comments gleaned from a deep SVN archaeology dive source/src/protocols/constraints_additional/BindingSiteConstraint.hh source/src/protocols/loops/loop_mover/perturb/LoopMover_KIC.cc: fixing a bug introduced by 543ed88 (a two year old refactoring) source/src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc No test changes expected. The only compiled code change prevents a crash, so this code path was perforce untested before. commit fa97b18fe8f8daca1444cd6600061db516c5e146 Merge: 3a6815b 29345d3 Date: Thu Jun 23 00:53:17 2016 +0200 Just updated my old pilot app and merged with master commit 3a6815b8ab0333ba6a457c4d2f39ef8777616450 Date: Wed Jun 22 14:34:46 2016 +0200 a small fix to my pilot app