Pushed Revisions

branch: master 「№61160」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「4c30495e98c5caa2」「№4537」
Difference from previous tested commit: code diff
Commit date: 2020-03-02 17:50:46

branch: master 「№61159」
Commited by: Vikram K. Mulligan
GitHub commit link: 「531ac226da23042c」「№4527」
Difference from previous tested commit: code diff
Commit date: 2020-03-02 14:35:29

Merge pull request #4527 from RosettaCommons/vmullig/disable_multithreading_unless_turned_on Changing default thread count for the RosettaThreadManager to 1. Users must turn ON multi-threading by specifying a value different than 1. There seemed to be consensus among those using multi-threading that the current default (using all available processors) wasn't ideal. The option of using all processors still exists, but this PR makes it no longer the default. This was a change made in the vmullig/multithreaded_scoring2 branch (PR #4342), but since that branch is taking a while to optimize, I'm cherry-picking this into its own PR. @javierbq @lyskov @asford @weitzner TODO: - [x] Double-check whether any tests need to be updated for this change. They probably do. --> They seem fine. - [x] Update documentation.

branch: master 「№61158」
Commited by: Vikram K. Mulligan
GitHub commit link: 「5a16ef8795a6afe9」「№4539」
Difference from previous tested commit: code diff
Commit date: 2020-03-02 13:27:25

Merge pull request #4539 from RosettaCommons/vmullig/fix_galigandock_parse Fix parsing of "sample_ring_conformers" option in GALigandDock. This was being parsed as a Real rather than as a bool.

branch: master 「№61157」
Commited by: Vikram K. Mulligan
GitHub commit link: 「7dd556d5f2dcec89」「№4535」
Difference from previous tested commit: code diff
Commit date: 2020-03-02 01:55:33

Merge pull request #4535 from RosettaCommons/vmullig/float_not_int Allow Rotate mover to accept floats for the number of degrees, rather than ints. For some reason, the Rotate mover was set to take an integer for the rotation in degrees rather than a float. Fixing this.

branch: master 「№61156」
Commited by: Daniel Farrell
GitHub commit link: 「bc690c0a4f2e4b33」「№4491」
Difference from previous tested commit: code diff
Commit date: 2020-02-29 13:09:07

branch: master 「№61155」
Commited by: Teun Hoevenaars
GitHub commit link: 「6d80962f7244a1ac」「№4366」
Difference from previous tested commit: code diff
Commit date: 2020-02-27 03:07:28

Merge pull request #4366 from RosettaCommons/teunhoevenaars/jacobi_loop_closure_1 Jacobi loop closure protocol and Jacobian analysis modules

branch: master 「№61154」
Commited by: Labonte
GitHub commit link: 「659d2ccf7448e968」「№4069」
Difference from previous tested commit: code diff
Commit date: 2020-02-26 15:23:43

Merge pull request #4069 from RosettaCommons/JWLabonte/PTMs/parsing EnzymaticMovers: Adding parsing of nucleic acid sequences to the EnzymaticMover system This merge allows the EnzymeManager to parse nucleic acid sequons, allowing for EnzymaticMovers that simulate such enzymes as DNA methyltransferases. This merge will also add a VARIANT_OF record type for .params files such that one can specify the base ResidueType of a VariantType that is defined by a .params file instead of by a patch file, as is typical. thanks to @everyday847 for teaching me the 1-letter NA code thanks to @roccomoretti for the code review All tests pass.

branch: master 「№61153」
Commited by: Steven Lewis
GitHub commit link: 「adb1b1b57207541a」「№4528」
Difference from previous tested commit: code diff
Commit date: 2020-02-26 13:03:31

Merge pull request #4528 from CyrusBiotechnology/smlewis/foldtree_nc remove foldtree nonconst begin/end for compile improvements. Resolves #4517

branch: master 「№61152」
Commited by: Labonte
GitHub commit link: 「517cd6424af46820」「№4497」
Difference from previous tested commit: code diff
Commit date: 2020-02-26 12:00:56

Merge pull request #4497 from RosettaCommons/JWLabonte/PTMs/EnzymaticMovers EnzymaticMovers: Adding NTerminalAcetyltransferaseMover This merge will add an EnzymaticMover for N-terminal acetylation. All tests pass. Thanks to Xiyao Long for reviewing. (Are you new to Rosetta coding? You should review a pull request too. :) )

branch: master 「№61151」
Commited by: Jason C. Klima
GitHub commit link: 「c163738ff8dc6b49」「№4489」
Difference from previous tested commit: code diff
Commit date: 2020-02-24 14:59:08

branch: master 「№61150」
Commited by: Steven Lewis
GitHub commit link: 「2db736690b286275」「№4518」
Difference from previous tested commit: code diff
Commit date: 2020-02-24 13:22:47

Merge pull request #4518 from RosettaCommons/smlewis/template_prot_8 Update generate_templates.py Updating to account for protocols.8 change, credit to @marzolf-daniel for spotting it

branch: master 「№61149」
Commited by: Labonte
GitHub commit link: 「ab71f4a039511598」「№4039」
Difference from previous tested commit: code diff
Commit date: 2020-02-22 16:39:21

Merge pull request #4039 from RosettaCommons/JWLabonte/PTMs/OGT PTMs: a more strict consensus for OGT This merge makes the sequon for human OGT more specific.

branch: master 「№61148」
Commited by: Sergey Lyskov
GitHub commit link: 「06ef18135023cf26」「№4512」
Difference from previous tested commit: code diff
Commit date: 2020-02-21 23:51:10

Merge pull request #4512 from RosettaCommons/sergey/binder refactoring testing scripts so termination on timeout in PyRosetta4.unit could be logged

branch: master 「№61147」
Commited by: Rocco Moretti
GitHub commit link: 「6c476c50555eed04」「№4508」
Difference from previous tested commit: code diff
Commit date: 2020-02-20 11:11:40

Merge pull request #4508 from RosettaCommons/roccomoretti/more_diagnostics_for_venv_tests Save diagnostic information for VirtualEnv-using integration tests. We're seeing some issues with drrafter_setup_real_test_H_no_init in the ubsan tests. It looks like the issue is happening during the VirtualEnv setup. Attempt to save the logging/error information from the virtual env setup steps. (But don't diff on it.)

branch: master 「№61146」
Commited by: Daniel Farrell
GitHub commit link: 「cb1cabafd7463ab7」「№4482」
Difference from previous tested commit: code diff
Commit date: 2020-02-20 10:29:09

branch: master 「№61145」
Commited by: Rocco Moretti
GitHub commit link: 「9dc9936130ea42be」「№4516」
Difference from previous tested commit: code diff
Commit date: 2020-02-20 10:23:31

Legend:

queued	Queued Test
queued for comparison	Test finished running but not yet compared
running	Test is Running right now
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