Pushed Revisions

branch: master 「№59461」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「0ebf4b56da6b623a」「№2211」
Difference from previous tested commit: code diff
Commit date: 2017-05-08 08:55:08

Merge pull request #2211 from RosettaCommons/aleaverfay/bugfix_chain_endings_in_pdb_reading Bugfix in Pose construction logic Fixing another chain-endings bug that is tripped when the Cterm of onechain (residue i) is missing some backbone atoms, AND the Nterm of the next chain is also missing some backbone atoms, so that Rosetta won't put a Cterm at residue i-1 nor an Nterm at i+2. As a result, a two chain PDB will get read in as a single chain. Super simple fix for this.

branch: master 「№59460」
Commited by: Andrew Watkins
GitHub commit link: 「12b7b0fc73ebe534」「№2243」
Difference from previous tested commit: code diff
Commit date: 2017-05-07 17:55:35

Merge pull request #2243 from RosettaCommons/everyday847/misc_pedantry A few loop refactors, and use of fixedsizearray1 for some suites

branch: master 「№59459」
Commited by: Rocco Moretti
GitHub commit link: 「5ed9d146a9ac3577」
Difference from previous tested commit: code diff
Commit date: 2017-05-07 17:48:03

Better annotation of ligand_database_io integration test. I can't replicate the test server changes locally, so hopefully more loging output will help track down the instability.

branch: master 「№59458」
Commited by: Vikram K. Mulligan
GitHub commit link: 「26d01defc0ed29bf」「№2224」
Difference from previous tested commit: code diff
Commit date: 2017-05-07 02:11:32

Merge pull request #2224 from RosettaCommons/vmullig/fix_pdbinfo_on_helix_append Fix issue with PDBInfo and appending helices to an existing pose with MakeBundle/BundleGridSampler

branch: master 「№59457」
Commited by: Sergey Lyskov
GitHub commit link: 「6c5f43317387c3bb」「№2188」
Difference from previous tested commit: code diff
Commit date: 2017-05-06 17:36:38

Merge pull request #2188 from RosettaCommons/atom-moyer/unfriend-function Unfriend xyzMatrix operators so they appear in PyRosetta

branch: master 「№59456」
Commited by: Andrew Watkins
GitHub commit link: 「a472443b479e3ad0」「№2242」
Difference from previous tested commit: code diff
Commit date: 2017-05-06 11:02:46

Merge pull request #2242 from RosettaCommons/everyday847/analogue_na_scoring A couple places to generalize torsion scoring based on analogue_na()

branch: master 「№59455」
Commited by: Brandon Frenz
GitHub commit link: 「8e64845ff2858d26」「№2237」
Difference from previous tested commit: code diff
Commit date: 2017-05-05 20:09:57

Merge pull request #2237 from RosettaCommons/bfrenz/ES_bugfixes added removal of terminal truncation types to safely append/prepend r…

branch: master 「№59454」
Commited by: Sergey Lyskov
GitHub commit link: 「d8a0897781ab9362」「№2238」
Difference from previous tested commit: code diff
Commit date: 2017-05-05 16:44:06

Merge pull request #2238 from RosettaCommons/sergey/binder Add-on to PyRosetta serialization support - Adding binding for std::stream classes. - Adding mapping-to-standard-name for std::stream classes. - Adding extra bytes method for std::*stringstream classes so they could be used in Python3. - Adding PyRosetta serialization test.

branch: master 「№59453」
Commited by: Andrew Watkins
GitHub commit link: 「740e0518dc72b64f」「№2234」
Difference from previous tested commit: code diff
Commit date: 2017-05-05 15:46:32

branch: master 「№59452」
Commited by: Tom Linsky
GitHub commit link: 「0b2fc781f0ee1f0d」「№2204」
Difference from previous tested commit: code diff
Commit date: 2017-05-04 20:53:26

branch: master 「№59451」
Commited by: F. Dimaio
GitHub commit link: 「f30827e2f49ecd83」
Difference from previous tested commit: code diff
Commit date: 2017-05-03 22:57:48

Rocco Moretti 8 years
Commit message from non-merge commit: "Checking in updated reference weights for beta_nov16. These weights were fit using a novel scheme in which both native recovery and stability ddG calcs (Kellogg set) were optimized against, however, the native recovery tests had reference weights modulated to account for non-stability-related biases in AA composition of native proteins."

branch: master 「№59450」
Commited by: Vikram K. Mulligan
GitHub commit link: 「2770435ee850777b」
Difference from previous tested commit: code diff
Commit date: 2017-05-03 22:34:49

branch: master 「№59449」
Commited by: Vikram K. Mulligan
GitHub commit link: 「daf44a635f6e5bd3」「№2227」
Difference from previous tested commit: code diff
Commit date: 2017-05-03 22:33:05

Merge pull request #2227 from RosettaCommons/vmullig/buried_apolar_area_filter Tweaking BuriedSurfaceArea filter. Tasks: - [x] Add option to use all atoms, hydrophobic atoms only, or polar atoms only. - [x] Add option. - [x] Update parse_my_tag(). - [x] Update XSD functions. - [x] Add to integration test. - [x] Switch BuriedSurfaceArea filter to use same SASA calculator used by TotalSASA filter. - [x] Update compute() function. - [x] Use Gabe's data tables for total area calculated with hydrophobic atoms only. - [x] Add Gabe's data tables for total area calculated with polar atoms only. - [x] Set minimum buried area to zero. - [x] Truth (add new option to documentation). - [x] Fix crash bug. - [x] Beauty (run the code beautifier).

branch: master 「№59448」
Commited by: F. Dimaio
GitHub commit link: 「1c192a93830f2b21」
Difference from previous tested commit: code diff
Commit date: 2017-05-03 22:21:48

branch: master 「№59447」
Commited by: Sergey Lyskov
GitHub commit link: 「ead037f78b65328a」「№2226」
Difference from previous tested commit: code diff
Commit date: 2017-05-03 15:50:41

Merge pull request #2226 from RosettaCommons/sergey/binder Updating fmt lib, this should fix RosettaCommons/binder#19. Updating Binder so it generate bindings for basic_stringstream.

branch: master 「№59446」
Commited by: Sharon Guffy
GitHub commit link: 「da548cfbb07844a7」「№2225」
Difference from previous tested commit: code diff
Commit date: 2017-05-03 07:53:36

Merge pull request #2225 from RosettaCommons/guffysl/constraint_generator_loader_pr Adds a data loader for ConstraintGenerator objects. They can now be specified in their own CONSTRAINT_GENERATORS block in a RosettaScript and can be passed to AddConstraints using the constraint_generators option. Also adds unit tests for several other data loaders.

Legend:

queued	Queued Test
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comparing	Test results is now comparing with previous results
finished	Test is finished without errors
failed	Test failed
build Failed	Test could not be run because build failed
script failed	Test results is unknow because test-script failed
canceled	Test was canceled