commit 2e17b38dff4f4e1c50c23299f02380fbfdab10a5 Merge: 3bbe46d 003ddae Date: Thu Mar 17 10:55:32 2016 -0700 Merge pull request #1202 from RosettaCommons/tlinsky/constraint_generator Rename NtoC_RCG and RemoveCsts movers to better names commit 3bbe46d476e83d2aeb1321a3b5ad8f05150058b8 Merge: 2574e15 a8fcc87 Date: Thu Mar 17 10:07:22 2016 -0400 Merge pull request #1077 from RosettaCommons/rfalford12/transmembrane_selections Residue Selector for Transmembrane Spanning Regions This pull request includes residue selectors specific for transmembrane proteins. To use them, the pose must be membrane-aware (i.e. `AddMembraneMover` has already been applied to your pose). The following residue selectors are included here: New Residue Selectors in `src/core/select/residue_selector` * **TMSpanSelector**: Select all or a subset of transmembrane spans in the pose * **MembraneResidueSelector**: Select only the membrane residue (the special virtual that stores the membrane coordinate) * **ByMembraneDepth**: Select all residues located at a certain depth in the membrane Each residue selector includes a corresponding unit test in `test/core/select/residue_selector` commit 2574e150990b65d081476cea83a664a22e7588ad Merge: 19da22e 704b052 Date: Mon Mar 14 18:29:26 2016 -0400 Merge pull request #1197 from RosettaCommons/JWLabonte/sugars/input Carbohydrates: Allowing glycans with sialic acids to be created by sequence This merge will fix a bug preventing sialic acids from being read into Rosetta by IUPAC sequence. This was caused by the fact that the handedness designation is inherent to the 3-letter code for some codes, such as Neu. commit 19da22e6a3e4648e93ae8b405affa26f1144e3f4 Date: Mon Mar 14 11:02:17 2016 -0700 moved my inactive pilot apps superficial changes to "ls src/apps/pilot/will" expected commit 8593296b7113e18d4a0a390c1f25d6df38b7925d Merge: 82596e4 9bb00c2 Date: Mon Mar 14 12:52:12 2016 -0500 Merge pull request #1194 from RosettaCommons/roccomoretti/public_template_features Promote the template_features application to public. This application has been used in a published protocol, and external users are hoping to use it. A new template_features integration test has been added, and will "fail" the first time. commit 82596e4ff0fd945267f56316027be2c21c4e128a Merge: 6f819a7 874264b Date: Mon Mar 14 13:29:37 2016 -0400 Merge pull request #1193 from RosettaCommons/mlnance/glycam_codes Expanding list of GLYCAM 3-letter codes. This merge will introduce a list of all the 3-letter GLYCAM codes and their corresponding Rosetta name. commit 6f819a74eba9a779a30334d3f8563a1639648538 Merge: e50e360 eb00234 Date: Sun Mar 13 20:47:34 2016 -0700 Merge pull request #1181 from RosettaCommons/tlinsky/constraint_generator Clean up AddConstraintsToCurrentConformation::parse_my_tag() commit e50e3604470110738bcc1548b73d063645153cee Merge: afbea8b 195c461 Date: Sun Mar 13 17:42:27 2016 -0700 Merge pull request #1191 from RosettaCommons/revert-1190-revert-1176-vmullig/genkic_tweaks2 Re-merge "Add a low-memory mode option to GenKIC" This reverts RosettaCommons/main#1190 (reverting the reversion, bringing back the original merge). This adds a low-memory option to GenKIC (minus the bug that I had inadvertently created the first time I tried to merge this). Tasks: - [x] Debug integration tests that fail to run. - [x] Fix vector element erasure issue that was causing the problem. - [x] Re-beautify. commit afbea8b332443711bf8f80f74a6166474e457c2a Merge: 8b2b03e 8e90eab Date: Sun Mar 13 15:59:37 2016 -0700 Merge pull request #1192 from RosettaCommons/dimaio/fix_centroid_symm_silent Small bugfix for reading symmetric centroid silent files inadvertantly introduced in mirrorsymm checkin commit 8b2b03e5246e12620f28d35a520e2053b3a037a4 Merge: cf67eca d3f4184 Date: Sun Mar 13 13:59:18 2016 -0400 Merge pull request #1189 from RosettaCommons/everyday847/use_ss_min_with_bb_grid_sampler I introduced a cppcheck error that I now have fixed. Merging. commit cf67ecafcc9919bee14bad07050aba69a7651d63 Merge: e1b0646 dd146e6 Date: Sun Mar 13 05:56:12 2016 -0700 Merge pull request #1190 from RosettaCommons/revert-1176-vmullig/genkic_tweaks2 Revert "Add a low-memory mode option to GenKIC" Whoops! Merged too soon -- there were some integration test failures. commit e1b0646ec5b95ffc2272f4477e2802887661ca95 Merge: c7e31c2 de014c0 Date: Sun Mar 13 05:53:31 2016 -0700 Merge pull request #1176 from RosettaCommons/vmullig/genkic_tweaks2 Add a low-memory mode option to GenKIC I modified GenKIC a while back to store full solution poses rather than just solution DoF vectors. This was to accommodate the pre-selection mover, which could modify the pose in complicated ways that would not be captured by just storing DoFs. However, this can create problems for users who want to do a lot of sampling: memory becomes an issue. This adds an option to restore the old behaviour. Tasks: -- Add the option. -- Modify GeneralizedKIC::add_solution() to store either a vector of solution poses (default mode) or a vector of loop DoFs (low-memory mode). -- Modify final selection to use either the vector of solution poses (default mode) or the vector of loop DoFs (low-memory mode). -- Modify selection logic. -- Add warning if low-memory mode is used with a preselection mover. -- Debug. -- Integration test. -- Unit test. -- Documentation. -- Beauty. commit c7e31c28628af3fc1104e937406a7b6636c78f81 Merge: f39be5c dbbf4d1 Date: Sat Mar 12 22:16:21 2016 -0500 Merge pull request #327 from RosettaCommons/aleaverfay/lbfgs_as_default Unit test failures have been rectified. Integration test failures are expected, seeing as they each use minimization that is now lbfgs. commit f39be5c97b8c3125c728cf835cce94b155d031e2 Merge: 437d2bd c07a385 Date: Sat Mar 12 18:53:12 2016 -0800 Merge pull request #1187 from RosettaCommons/vmullig/add_talaris2014_tests Adding sfxn_fingerprint tests for talaris2014. Our default scorefunction should have a regression test to ensure that it doesn't change beneath us. (Granted, all but one of the terms are shared with talaris2013 -- but still, we should test it.) commit 437d2bd4c9107c190b5bfa150f2b05d63dc1c5d0 Date: Sat Mar 12 16:23:01 2016 -0500 Update RotamerSet.cxxtest.hh Again, fixing unit test build commit e0c92d8b8bec711e2b43a80713cb693e8013c988 Date: Sat Mar 12 15:13:18 2016 -0500 Accidentally broke unit test build; sorry commit be890a9da1a7c2fbe737eb017562f9352d1ea58d Merge: bec6bae c7b041b Date: Sat Mar 12 14:52:51 2016 -0500 Merge pull request #1175 from RosettaCommons/talaris2014_default Set talaris2014 as default scoring function commit bec6bae3640ab4f9e1304bb57cba82396ed2895b Merge: a9fef9a 998320e Date: Sat Mar 12 10:24:08 2016 -0800 Merge pull request #1160 from RosettaCommons/sjbertolani/unrecognized_atom_record_in_pyrosetta This adds a python wrapper for the std:vector< core::pose::UnrecognizedAtomRecords> container. You can now access the data and iterate on the container in pyrosetta. No test changes expected. commit a9fef9aed8c32a69be7b3994dfcbe91e28c77c41 Merge: 4becdbe ba9c97c Date: Fri Mar 11 16:30:13 2016 -0500 Merge pull request #1177 from RosettaCommons/remove_cc_includes No more .cc includes (anywhere but, potentially, pilot apps). Integration test changes are only the Known Bad Changers. No issues elsewhere. commit 4becdbee2101f074bd45ddb6f96b95b3dff2ee7d Merge: 3eb2837 7ccd6a3 Date: Fri Mar 11 13:12:42 2016 -0800 Merge pull request #1174 from RosettaCommons/vmullig/genkic_tweaks Tweaking GenKIC defaults to avoid memory issue Changing default closure_attempts for GenKIC to 100 (from 2000). Users reported memory issues with default settings. commit 3eb2837039425dec50d3e64132a7755684a41b6e Merge: 093e71a 50183e8 Date: Fri Mar 11 09:56:12 2016 -0800 Merge pull request #1171 from RosettaCommons/tlinsky/constraint_generator Add ConstraintGenerator base class Integration test changes expected for inverse_rotamer_remodel and pna integration tests due to different tracer output (because a class name changed) commit 093e71a1bc2872d8ba9dc2b185035faece3d5cfe Merge: 412581f 2e7fe2f Date: Fri Mar 11 08:37:25 2016 -0800 Merge pull request #1173 from RosettaCommons/vmullig/fix_irritating_error_message Fix "false" error messages in GenericMonteCarlo mover. The GenericMonteCarlo mover throws an error message that only reads, "false", if the user provides certain bad inputs. This is completely non-informative. This fixes that. commit 412581f296e79f9c12dc27bbfad57e3871710d60 Merge: aede021 00513c7 Date: Thu Mar 10 14:40:13 2016 -0800 Merge pull request #1172 from RosettaCommons/dimaio/lkb_trie_v_trie_bugfixes Two minor bugfixes for trie-vs-trie scoring with lk-ball. commit aede021688fe1d9b41d257d44a4e124d316ed654 Merge: 25d18d0 20822e6 Date: Wed Mar 9 18:06:37 2016 -0800 Merge pull request #1170 from RosettaCommons/tlinsky/ss_selector_xml_option Change name of 'dssp' xml option in SecondaryStructure selector commit 25d18d039c296f6c17eaa294ab44883261e618e1 Merge: a8d45b2 af6762f Date: Wed Mar 9 18:05:33 2016 -0800 Merge pull request #1163 from RosettaCommons/tlinsky/matcher_resselector Improved residue selector usage in MatcherMover commit a8d45b2c71c5233c5773a73037218e536e0a69e3 Merge: 9c4389d 79028a3 Date: Wed Mar 9 10:21:43 2016 -0800 Merge pull request #1167 from RosettaCommons/dimaio/SymmInfo_bugfix Fixing a long-standing bug in the intra-subunit remapping logic in SymmetryInfo::update_nmonomer_jumps. commit 9c4389d3cb09d9ab84ab82b9eff883569bb25ec9 Date: Wed Mar 9 10:03:15 2016 -0800 Another mistake in pilot app fixed. commit f078d324ea7d249e5aaf1769a549af471978bdbd Date: Wed Mar 9 09:58:39 2016 -0800 Mistake in pilot app fixed. commit a16337e2111b79fcd9772bbe4d19f48284f82624 Date: Wed Mar 9 09:46:22 2016 -0800 Adding some options to a pilot app. No test changes expected (or possible). commit 334dba6e140730c577f40174b046ff46c08890a3 Date: Tue Mar 8 18:33:06 2016 -0800 Tweaking a pilot app.