Pushed Revisions

branch: master 「№58868」
Commited by: David E Kim
GitHub commit link: 「d9fd19ad2d3c4886」「№1554」
Difference from previous tested commit: code diff
Commit date: 2016-08-24 17:27:55

branch: master 「№58867」
Commited by: Vikram K. Mulligan
GitHub commit link: 「d96fc823f03680e4」「№1556」
Difference from previous tested commit: code diff
Commit date: 2016-08-24 16:36:09

Merge pull request #1556 from RosettaCommons/vmullig/sample_cispro Add an option to simple_cycpep_predict to sample cis-omega values preceding D/L proline This can be expanded later to include positions preceding N-methyl positions, too. Tasks: - Add option. - Add code to do the sampling (the sample_cis_peptide_bond GeneralizedKICPerturber). - Add integration test. - Documentation. - Beauty. All tests pass except for the following integration tests: - bridge_chains (known instability that Tom's fixing) - simple_cycpep_predict_cispro (just added)

branch: master 「№58866」
Commited by: TJ Brunette
GitHub commit link: 「d6cc30cb0ce7f73f」「№1551」
Difference from previous tested commit: code diff
Commit date: 2016-08-24 12:47:54

Merge pull request #1551 from RosettaCommons/tjbrunette/fix_link_res fixes seg fault in Rotamer links. Also, adds the ability to define template rotamers.

branch: master 「№58865」
Commited by: Hahnbeom Park
GitHub commit link: 「16041aaa72eda300」「№1555」
Difference from previous tested commit: code diff
Commit date: 2016-08-23 21:15:57

Merge pull request #1555 from RosettaCommons/hahnbeom/fix_symm_residue_selector fixing error in integration test "symmetrical_residue_selector"

branch: master 「№58864」
Commited by: Rocco Moretti
GitHub commit link: 「cae4c00333842887」「№1552」
Difference from previous tested commit: code diff
Commit date: 2016-08-23 16:48:42

Merge pull request #1552 from RosettaCommons/roccomoretti/integration_test_mode Adjust integration.py to allow for other modes in demos tests. e.g. release_debug

branch: master 「№58863」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「733da1cab7b67984」「№1484」
Difference from previous tested commit: code diff
Commit date: 2016-08-23 16:30:00

Merge pull request #1484 from RosettaCommons/jadolfbr/LCM LinkageConformerMover improvements Make LinkageConformerMover use only carbohydrate residues if no move map is supplied. Why I didn't have this in the first place, is beyond me. Make LCM/GlycanRelax not crash if a default, all-true (default-constructed) MoveMap is supplied (where the iterator returned is basically infinite or something strange) Explicitly state what should be done on new inputs, better handling multiple apply calls for different structures/jobs/etc (This is where integration test changes were coming from - now they are gone. Yay for the testing server and the PR system!)

branch: master 「№58862」
Commited by: Tom Linsky
GitHub commit link: 「dfa9b4c2aa9ebb0f」「№1502」
Difference from previous tested commit: code diff
Commit date: 2016-08-22 13:51:39

Merge pull request #1502 from RosettaCommons/tlinsky/tomponents Updates to denovo classes. Integration test changes expected for bridge_chains

branch: master 「№58861」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「3ab7d06d5fcce9f3」「№1547」
Difference from previous tested commit: code diff
Commit date: 2016-08-22 12:49:28

Merge pull request #1547 from RosettaCommons/jadolfbr/remove_initial_pert small update for antibody design

branch: master 「№58860」
Commited by: Rocco Moretti
GitHub commit link: 「2f2b80c9ace3bc0d」「№1548」
Difference from previous tested commit: code diff
Commit date: 2016-08-20 11:45:09

Merge pull request #1548 from RosettaCommons/roccomoretti/molfile_to_params_chain Add option to change chain letter in molfile_to_params.py Allows different chain designations to be made for output PDBs.

branch: master 「№58859」
Commited by: Tom Linsky
GitHub commit link: 「f84a3c40fa20fd5c」「№1544」
Difference from previous tested commit: code diff
Commit date: 2016-08-18 21:04:29

Merge pull request #1544 from RosettaCommons/tlinsky/extract_asymm_secstruct When extracting asymmetric subunit, also extract/set pose.secstruct CXX11 unit test failed initially, but passed when I resubmitted: http://benchmark.graylab.jhu.edu/revision?id=4574&branch=

branch: master 「№58858」
Commited by: Rocco Moretti
GitHub commit link: 「c2e3285917dca339」「№1543」
Difference from previous tested commit: code diff
Commit date: 2016-08-18 10:26:12

Merge pull request #1543 from RosettaCommons/roccomoretti/fix_pyrosetta_copyright Fix broken PyRosetta from copyright fixes In updating the copyright headers, I accidentally messed up the docstring on one of the PyRosetta files, leading to breakage of the PyRosetta unit tests (with a Python parse error).

branch: master 「№58857」
Commited by: Rebecca Alford
GitHub commit link: 「f6a6d5a14bc2f118」「№1539」
Difference from previous tested commit: code diff
Commit date: 2016-08-18 08:30:44

Merge pull request #1539 from RosettaCommons/rfalford12/single-TM-span-option Automatic Topology for Single TM Alpha Helical Proteins --- Adding an option to AddMembraneMover to automatically determine the transmembrane spanning topology for a single TM helix (accessible via command line and RosettaScripts)

branch: master 「№58856」
Commited by: Tom Linsky
GitHub commit link: 「a8a0602976cb23c0」「№1460」
Difference from previous tested commit: code diff
Commit date: 2016-08-17 14:09:48

Merge pull request #1460 from RosettaCommons/tlinsky/sheet_cst_gen Refactor SheetConstraintGenerator for easier selection of pairings and ss

branch: master 「№58855」
Commited by: Tom Linsky
GitHub commit link: 「cbe4bab73a3cc168」「№1542」
Difference from previous tested commit: code diff
Commit date: 2016-08-17 13:26:49

Merge pull request #1542 from RosettaCommons/tlinsky/fix_ssene_ss Fix SetSecStructEnergies Mover for case when input pose is empty Initial testing showed unit test failures, but they disappeared after retesting, so this should be fine: http://benchmark.graylab.jhu.edu/revision?id=4560&branch=

branch: master 「№58854」
Commited by: jkleman
GitHub commit link: 「fef88e1b827640cb」「№1445」
Difference from previous tested commit: code diff
Commit date: 2016-08-17 11:23:14

Merge pull request #1445 from RosettaCommons/jkleman/mp_updates_toolkit Jkleman/mp updates toolkit = made HelixFromSequence app into a Mover = added PDB numbering support for spanfile input, new spanfile format will automatically be detected = added PDB numbering support for MPMutateRelaxMover = added integration tests for PDB file format in spanfile and MPMutateRelaxMover

branch: master 「№58853」
Commited by: Tom Linsky
GitHub commit link: 「f21bc8bbd60fe13d」「№1517」
Difference from previous tested commit: code diff
Commit date: 2016-08-16 19:43:55

Merge pull request #1517 from RosettaCommons/tlinsky/binary_silent_comment Make BinarySilentStruct use same comment-parsing as other silent structs

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queued	Queued Test
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