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branch: master 「№57764」
Commited by: Labonte
GitHub commit link: 「5691274637793572」 「№432」
Difference from previous tested commit:  code diff
Commit date: 2015-04-02 21:14:34

Merge pull request #432 from RosettaCommons/JWLabonte/clean-up Code Clean-Up: Removing Large Chunks of Blank Lines & Commented-Out Code This merge removes a couple tens of thousands of blank lines or commented out code from Rosetta. It also corrects some common Doxygen errors. See the pull request for more details. All unit tests pass. jscore and score_jd2 integration tests change because they output a line number. The Windows PyRosetta build was already broken. :rat:

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branch: master 「№57763」
Commited by: Fang-Chieh Chou
GitHub commit link: 「8cbc27070a98693e」 「№435」
Difference from previous tested commit:  code diff
Commit date: 2015-04-02 15:12:06

Merge pull request #435 from RosettaCommons/fcchou/turner Fcchou/turner

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branch: master 「№57762」
Commited by: Andrew Watkins
GitHub commit link: 「c657bb506f014ec3」
Difference from previous tested commit:  code diff
Commit date: 2015-04-02 13:00:15

Revising performance benchmark to do min of several (shorter) averaged trials

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branch: master 「№57761」
Commited by: Sergey Lyskov
GitHub commit link: 「c01d81815e02ee2e」
Difference from previous tested commit:  code diff
Commit date: 2015-04-01 23:17:24

PyRosetta.build test: disabling re-run with single CPU on Windows platform.

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branch: master 「№57760」
Commited by: Kale Kundert
GitHub commit link: 「76fb514eeeb8d142」 「№434」
Difference from previous tested commit:  code diff
Commit date: 2015-04-01 19:58:08

Merge pull request #434 from RosettaCommons/kalekundert/loop_modeling Properly build missing atoms in loop modeling

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branch: master 「№57759」
Commited by: TJ Brunette
GitHub commit link: 「a45d0f0d5f9cd93e」 「№420」
Difference from previous tested commit:  code diff
Commit date: 2015-04-01 12:49:33

Merge pull request #420 from RosettaCommons/tjbrunette/repeat_code Tjbrunette/repeat code This is the code for our repeat protein paper. I needed to move ABEGO manager from core/util to core/sequence to get the levels right. Because I have a score function that uses ABEGO manager. I still need to add an integration test. Will do that later this week.

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branch: master 「№57758」
Commited by: Frank DiMaio
GitHub commit link: 「59e92a2d36c2d5d6」
Difference from previous tested commit:  code diff
Commit date: 2015-03-31 19:33:36

Merging spherical harmonic code in numeric/fourier/SHT

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branch: master 「№57757」
Commited by: Fang-Chieh Chou
GitHub commit link: 「af28a92848ca0c9b」 「№430」
Difference from previous tested commit:  code diff
Commit date: 2015-03-31 18:31:56

Merge pull request #430 from RosettaCommons/fcchou/turner Fcchou/turner

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branch: master 「№57756」
Commited by: Andrew Watkins
GitHub commit link: 「d1bc5af287d3bb60」
Difference from previous tested commit:  code diff
Commit date: 2015-03-31 15:54:02

Update ScoreEach.bench.hh Increasing length of tests for scoreterms that seem to fail because their potential variance is higher than 5% of the test length.

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branch: master 「№57755」
Commited by: Tom Linsky
GitHub commit link: 「1c0f4089cbc4f4eb」 「№423」
Difference from previous tested commit:  code diff
Commit date: 2015-03-31 13:17:49

Merge pull request #423 from RosettaCommons/tlinsky/tlinsky/remodelloop_sealfoldtree Add "seal_foldtree" option to RemodelLoopMover

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branch: master 「№57754」
Commited by: Steffen Möller
GitHub commit link: 「aae51e5adfd62ab7」 「№421」
Difference from previous tested commit:  code diff
Commit date: 2015-03-31 05:05:41

Merge pull request #421 from RosettaCommons/smoe/find_python_modules_also_as_symlink Excluding MacOS X from readlink PyRosetta setup.sh

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branch: master 「№57753」
Commited by: Vikram K. Mulligan
GitHub commit link: 「f7cf37f8b590e4df」 「№425」
Difference from previous tested commit:  code diff
Commit date: 2015-03-30 22:35:00

Merge pull request #425 from RosettaCommons/vmullig/genkic_sampling Vmullig/genkic sampling Small change to GenKIC output requested by Gaurav. This might cause some cosmetic integration test changes to one of the GenKIC integration tests.

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branch: master 「№57752」
Commited by: F. Dimaio
GitHub commit link: 「6aa1e2295dcf61d2」
Difference from previous tested commit:  code diff
Commit date: 2015-03-30 21:44:39

A few more options to hybrid - bugfix for starting from extended chain - change add_non_init_chunks to integer parameter indicating the mean number of off-template chunks to steal (Poisson distribution) - max_contig_insertion is now applied in stage 1 in addition to stage 2

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branch: master 「№57751」
Commited by: Tom Linsky
GitHub commit link: 「50d8c93daa00fbfc」 「№405」
Difference from previous tested commit:  code diff
Commit date: 2015-03-30 15:34:10

Merge pull request #405 from RosettaCommons/tlinsky/disulfidize Improvements to disulfidize mover

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branch: master 「№57750」
Commited by: Tom Linsky
GitHub commit link: 「8f13df1821e0eab6」 「№422」
Difference from previous tested commit:  code diff
Commit date: 2015-03-30 05:27:04

Merge pull request #422 from RosettaCommons/tlinsky/remodelrevert Revert change to remodel that caused problems for repeat proteins

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branch: master 「№57749」
Commited by: Rhiju Das
GitHub commit link: 「77ccc95fa250d61d」 「№368」
Difference from previous tested commit:  code diff
Commit date: 2015-03-29 15:33:13

Merge pull request #368 from RosettaCommons/rhiju/stepwise_benchmark integrating stepwise_benchmark

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