Pushed Revisions

branch: master 「№58340」
Commited by: Labonte
GitHub commit link: 「413b66359998f504」「№969」
Difference from previous tested commit: code diff
Commit date: 2015-12-11 05:50:56

Merge pull request #969 from RosettaCommons/JWLabonte/sugars/input Bug Fix: I was stupidly accessing map data before checking if they existed. All unit tests pass. carbohydrates integration test changes expected, because I had also added output of pdbs to the tests on this branch

branch: master 「№58339」
Commited by: Vikram K. Mulligan
GitHub commit link: 「776e287b8be8d139」「№965」
Difference from previous tested commit: code diff
Commit date: 2015-12-09 22:15:09

Merge pull request #965 from RosettaCommons/vmullig/tj_bundle_issue Fixing a minor problem in MakeBundle, identified by TJ TJ discovered that reading my documentation and following the instructions produces a cryptic failure. I'm fixing this. - Adding a runtime_assert and error message if z1=0 to generate_atom_positions() in the helical bundle code. - Updating documentation to make it clear that z1 and omega1 are not options that the user should normally set manually, unless he/she really knows what he/she is doing. No unit or integration test changes expected. @tjbrunette

branch: master 「№58338」
Commited by: Rhiju Das
GitHub commit link: 「09c7cdf08d4ba8ec」「№936」
Difference from previous tested commit: code diff
Commit date: 2015-12-09 20:10:19

Merge pull request #936 from RosettaCommons/calebgeniesse/SubMotifInfo Calebgeniesse/sub motif info [only tests that fail are the ones that keep having numerical instabilities.]

branch: master 「№58337」
Commited by: Rhiju Das
GitHub commit link: 「db86b0c3f9589e64」「№957」
Difference from previous tested commit: code diff
Commit date: 2015-12-09 12:26:29

Merge pull request #957 from RosettaCommons/rhiju/farna_output_resnum_chain handle output of chain along with resnum in FARFAR.

branch: master 「№58336」
Commited by: Frank DiMaio
GitHub commit link: 「d741e9540f12e66e」
Difference from previous tested commit: code diff
Commit date: 2015-12-08 19:33:20

branch: master 「№58335」
Commited by: Rhiju Das
GitHub commit link: 「a73b1f4d14a9fe3b」「№959」
Difference from previous tested commit: code diff
Commit date: 2015-12-08 13:52:37

Merge pull request #959 from RosettaCommons/rhiju/remove_time_in_stepwise_lores_test HOTFIX: remove time from stepwise_lores integration test.

branch: master 「№58334」
Commited by: Jeliazko Jeliazkov
GitHub commit link: 「bf6e248381e50639」「№960」
Difference from previous tested commit: code diff
Commit date: 2015-12-08 09:36:23

Merge pull request #960 from RosettaCommons/lqtza/fix_xcode_make_project fixing xcode project script which pull request #672 broke

branch: master 「№58333」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「c0acc462593441eb」
Difference from previous tested commit: code diff
Commit date: 2015-12-07 21:44:25

branch: master 「№58332」
Commited by: Sergey Lyskov
GitHub commit link: 「2c7cf19f8d265616」
Difference from previous tested commit: code diff
Commit date: 2015-12-06 16:16:20

branch: master 「№58331」
Commited by: Sergey Lyskov
GitHub commit link: 「62e859ea30b54994」
Difference from previous tested commit: code diff
Commit date: 2015-12-06 00:34:36

branch: master 「№58330」
Commited by: Rhiju Das
GitHub commit link: 「5a674b7a01973f2f」「№950」
Difference from previous tested commit: code diff
Commit date: 2015-12-05 20:44:58

Merge pull request #950 from RosettaCommons/rhiju/farna_renovation Rhiju/farna renovation A few integration tests change -- all are traceable to small numerical instabilities in stepwise apps, which are compiled within the same library as the farna stuff (protocols.d_5).

branch: master 「№58329」
Commited by: Sergey Lyskov
GitHub commit link: 「f92dafe39386dd20」
Difference from previous tested commit: code diff
Commit date: 2015-12-04 15:54:39

branch: master 「№58328」
Commited by: Tom Linsky
GitHub commit link: 「87db6810d459cc80」「№940」
Difference from previous tested commit: code diff
Commit date: 2015-12-03 21:09:47

Merge pull request #940 from RosettaCommons/tlinsky/ss_selector_dssp Add always_use_dssp option to SecondaryStructure residue selector

branch: master 「№58327」
Commited by: Tom Linsky
GitHub commit link: 「94850a779f9fd004」「№941」
Difference from previous tested commit: code diff
Commit date: 2015-12-03 21:09:24

Merge pull request #941 from RosettaCommons/tlinsky/tomponents Updates to make FoldGraph and StructureData more robust and reliable

branch: master 「№58326」
Commited by: Rebecca Alford
GitHub commit link: 「f592c7d1adf43d15」「№949」
Difference from previous tested commit: code diff
Commit date: 2015-12-03 08:15:46

Merge pull request #949 from RosettaCommons/rfalford12/fix_multi_mem_bug Rfalford12/fix multi mem bug This pull request fixes a 'once feature now bug.' Initially, I wanted to prevent the user from incorporating multiple membrane residues due to ambiguity in tracking. Now, since a single MEM can be easily tracked and changed, it makes sense to allow multiple MEM residues. This change revises IO case 2 (AddMembraneMover lines 544-605) which deals with multiple MEM residues detected in AddMembraneMover: - Old Behavior: throw an exception as a result of multiple membrane residues - New Behavior: - If the user doesn't point to a MEM, accept the first MEM in sequence by default - If the user does point to a MEM, accept that MEM I also added two new unit tests to the AddMembraneMover test suite to cover these test cases

branch: master 「№58325」
Commited by: jkleman
GitHub commit link: 「60eedc55ba463259」「№952」
Difference from previous tested commit: code diff
Commit date: 2015-12-03 03:33:13

Merge pull request #952 from RosettaCommons/jkleman/fixing_option fixing option to get rid of InterfaceAnalyzer and constel issues

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