branch: master 「№57748」
Commited by: Andrew Watkins
GitHub commit link: 「34f1e311842178ae」
Difference from previous tested commit:  code diff
Commit date: 2015-03-28 13:56:10

Typo fix--null commit to test performance tests

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branch: master 「№57747」
Commited by: Andrew Watkins
GitHub commit link: 「57e281b0bfa3551c」
Difference from previous tested commit:  code diff
Commit date: 2015-03-28 13:55:04

Updating performance benchmarks to hopefully achieve stability at last

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branch: master 「№57746」
Commited by: Frank DiMaio
GitHub commit link: 「5de348c48f3da7e5」
Difference from previous tested commit:  code diff
Commit date: 2015-03-27 20:48:40

Merge PyRosetta build fixes.

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branch: master 「№57745」
Commited by: davidekim
GitHub commit link: 「ff6efcfe28efe136」 「№419」
Difference from previous tested commit:  code diff
Commit date: 2015-03-27 19:11:14

Merge pull request #419 from RosettaCommons/davidekim/boinc_build Davidekim/boinc build. Updates are for the BOINC builds.

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branch: master 「№57744」
Commited by: Frank DiMaio
GitHub commit link: 「d3d1dbb805c57098」
Difference from previous tested commit:  code diff
Commit date: 2015-03-27 17:54:07

Missed a file in my previous commit

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branch: master 「№57743」
Commited by: Frank DiMaio
GitHub commit link: 「14bce6aa1f4b2187」
Difference from previous tested commit:  code diff
Commit date: 2015-03-27 17:48:12

Another set of updates for RosettaCM. - updated logic for fragment placement in stage 1 - updated domain parsing logic in realign_domains - fixing bug in realign_domains where templates would accumulate drift over time (thanks Rocco!) - better handing of realignment of ligand-containing poses - removing more unused or redundant options - small changes to smoothing kernel for fragment-derived constraints - removing extraneous output accidently checked in in the previous commit Hybridize and mr_protocols integration test changes expected.

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branch: master 「№57742」
Commited by: Tom Linsky
GitHub commit link: 「aa5247d80cd6f601」 「№418」
Difference from previous tested commit:  code diff
Commit date: 2015-03-26 23:11:37

Merge pull request #418 from RosettaCommons/tlinsky/jd2_format Make jd2 follow its typical %04d format in MultiplePoseMover tags

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branch: master 「№57741」
Commited by: Tom Linsky
GitHub commit link: 「0e9cd5ac094853f1」 「№417」
Difference from previous tested commit:  code diff
Commit date: 2015-03-26 20:25:12

Merge pull request #417 from RosettaCommons/tlinsky/multiplepose Prepare MultiplePoseMover for overriding.

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branch: master 「№57740」
Commited by: Rebecca Alford
GitHub commit link: 「847d777e5980d988」 「№416」
Difference from previous tested commit:  code diff
Commit date: 2015-03-26 08:52:05

Merge pull request #416 from RosettaCommons/rfalford12/add_ddG_script Add PyRosetta script for membrane protein ddG Predictions

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branch: master 「№57739」
Commited by: Andy Watkins
GitHub commit link: 「e0894f519515dcd5」
Difference from previous tested commit:  code diff
Commit date: 2015-03-25 13:34:29

Reverting 57732

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branch: master 「№57738」
Commited by: Rebecca Alford
GitHub commit link: 「9b655a83d65f2932」 「№408」
Difference from previous tested commit:  code diff
Commit date: 2015-03-25 09:19:09

Merge pull request #408 from RosettaCommons/rfalford12/add_var_thk Add thickness/steepness setters to MembraneInfo - Allow the user to adjust the membrane hydrophobic thickness and transition steepness, symmetrically about the center along the normal axis. This can be done programmatically and via the command line. Additionally, the thickness used by the PyMOL viewer is now linked to MembraneInfo (can also be changed separately) No test changes expected

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branch: master 「№57737」
Commited by: Andrew Watkins
GitHub commit link: 「f6d177a956bdb5d6」
Difference from previous tested commit:  code diff
Commit date: 2015-03-25 01:17:24

Update FastRelax.cc I am doomed to forever break master when I quickly fix bugs online. Curses.

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branch: master 「№57736」
Commited by: Andrew Watkins
GitHub commit link: 「80704780adfad85b」
Difference from previous tested commit:  code diff
Commit date: 2015-03-25 01:01:38

Embarrassing error turned nrchi_min on by default

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branch: master 「№57735」
Commited by: sboyken
GitHub commit link: 「dbd801b32fee2c62」
Difference from previous tested commit:  code diff
Commit date: 2015-03-24 21:56:06

Updating Xcode project.pbxproj.template so that core.1 properly links to basic and Xcode compile now works. Because I'm only changing this one file, and it only affects Xcode and no other builds, I am pushing to master without pull request or test servers

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branch: master 「№57734」
Commited by: Labonte
GitHub commit link: 「8ad359fff21c4fc0」 「№400」
Difference from previous tested commit:  code diff
Commit date: 2015-03-24 17:38:41

Merge pull request #400 from RosettaCommons/JWLabonte/sugars/ring_conformers Code clean-up and refactoring of the `RingConformerSet`-related code. NEWS: This merge should allow one to use the `RingConformationMover` on NCAAs with aliphatic, saturated rings, provided the `.params` files are set up properly. This merge also allows one to specify the lowest and low-energy conformers in the topology files for residues with rings, if this information is known. The `RingConformationMover` will by default only select ideal ring conformers from among this set. no unit test changes carbohydrates and rings integration test changes expected In addition, this merge makes the following improvements to the ring conformer system: * `RingConformationMover` should now work with RosettaScripts. * All static const `RingConformer` data that a `RingConformerSet` uses is accessed via the singleton `RingConformerManager`, so everything should now be thread-safe. * An option flag `-sample_high_energy_conformers` allows the `RingConformationMover` to do exactly that. * Unit tests for ring-related things are more robust.

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branch: master 「№57733」
Commited by: Sergey Lyskov
GitHub commit link: 「0cd8b276db0192b6」 「№412」
Difference from previous tested commit:  code diff
Commit date: 2015-03-24 16:46:39

Merge pull request #412 from RosettaCommons/benchmark Adding scientific test templates

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