branch: master 「№58036」
Commited by: Vikram K. Mulligan
GitHub commit link: 「650e766d8d5c184c」 「№691」
Difference from previous tested commit:  code diff
Commit date: 2015-08-07 19:23:09

Merge pull request #691 from RosettaCommons/vmullig/gellman_helix Fixed a minor bug with helical bundle generation Fixed a minor bug with helical bundle generation when the repeating unit is more than one residue. The number of mainchain atoms in the last (overhang) residue was being checked incorrectly. Also, adding a feature to the fit_helixparams app that lets the user specify that certain bond angles or bond lengths are non-ideal. ...Aaaaand in the process I caught two more bugs in the BundleGridSampler.

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branch: master 「№58035」
Commited by: Tom Linsky
GitHub commit link: 「a8ad342e141a2dae」 「№679」
Difference from previous tested commit:  code diff
Commit date: 2015-08-07 14:05:08

Merge pull request #679 from RosettaCommons/tlinsky/tomponents API improvements to denovo_design base classes

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branch: master 「№58034」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「657466faf43bfb28」 「№686」
Difference from previous tested commit:  code diff
Commit date: 2015-08-07 14:00:36

Merge pull request #686 from RosettaCommons/jadolfbr/antibody_design Jadolfbr/antibody design A few small changes that should be merged. Antibody Related ---------------------- 1) Disable cartesian min during graft adaptation in the designer. To close 100% of grafts, it is not needed and can cause downstream effects from the inaccurate G. From now on, this is off to increase stability of large cluster runs. 2) Change CDR length max to 25, which is reasonable. Really, this only effects H3. 3) Add optional output of monte carlo acceptance rates to PDB file during antibody design runs. 4) Change docking during design from LH_A to A_LH so that LH is moving relative to A. Non-Antibody Related --------------------------- 1) Remove the text of what the '-correct' option should do. Its all BS. Even the defaults in the options file can be overruled through code. At least this is more clear and points people to score_function_corrections.cc. Test Changes ------------------ Expected in antibody design mover due to the change in defaults.

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branch: master 「№58033」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「010540855af75acc」 「№684」
Difference from previous tested commit:  code diff
Commit date: 2015-08-07 13:49:50

Merge pull request #684 from RosettaCommons/jadolfbr/proto_cdr4 DE Loop/Proto CDR4 analysis for the Antibody Features Reporters ----------------------------------------------------------------------------------------- Much of this work, especially in terms of the Features R framework was done by Simon Kelow (@skelow). This merge enables the Antibody Features Reporter and associated R scripts to analyze the DE loop of antibodies, what we are also calling proto_cdr4. Both names are not ideal, but for now, this is the way they are. A few functions in AntibodyInfo were refactored in order to return information on this loop as if it was a CDR. This will enable the full antibody framework to work with this loop, and has allowed us to use the implemented feature reporters without too many changes. A set of antibody-specific options have been added to the features R framework to enable global use of these loops during antibody analysis. Documentation on the wiki will be updated as this merge happens. No integration or unit test changes seen except the currently failing ones.

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branch: master 「№58032」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「2e5d1c155a3a328a」 「№682」
Difference from previous tested commit:  code diff
Commit date: 2015-08-07 13:43:39

Merge pull request #682 from RosettaCommons/jadolfbr/ab_rs_debug Merge jadolfbr/ab_rs_debug This fixes Rosetta Script integration for the AntibodyDesignMover and the antibody TaskOps.

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branch: master 「№58031」
Commited by: Sergey Lyskov
GitHub commit link: 「4b1ffe616bd4a7cd」 「№689」
Difference from previous tested commit:  code diff
Commit date: 2015-08-07 10:52:51

Merge pull request #689 from RosettaCommons/PyRosetta Refactoring PyRosetta monolith linking so it use shorter command line. This should fix recent PyRosetta build errors on Mac.

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branch: master 「№58030」
Commited by: Sarel
GitHub commit link: 「ec5754152c0509e3」 「№685」
Difference from previous tested commit:  code diff
Commit date: 2015-08-07 01:24:38

Merge pull request #685 from RosettaCommons/sjf/symm_filterscan_fix Sjf/symm filterscan fix

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branch: master 「№58029」
Commited by: Vikram K. Mulligan
GitHub commit link: 「5cca4e1e24e89534」 「№690」
Difference from previous tested commit:  code diff
Commit date: 2015-08-06 17:01:40

Merge pull request #690 from RosettaCommons/vmullig/d_workflow Adding integration test for D-amino acid workflow. Tests LayerDesign, the BundleGridSampler, MutateResidue, resfiles, and PDB output.

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branch: master 「№58028」
Commited by: Rebecca Alford
GitHub commit link: 「075aaa1e1f1413cb」 「№681」
Difference from previous tested commit:  code diff
Commit date: 2015-08-06 11:22:48

Merge pull request #681 from RosettaCommons/rfalford12/remove_membrane_types Remove core/conformation/membrane/types.hh Part II of pull requests that remove hardcoded values from the membrane framework Previously, the types.hh file included static variables that were placed throughout the code. However, this discouraged use of MembraneInfo and lead to inconsistency. New convention: The defaults should be initialized in AddMembraneMover and MembraneInfo only If you need & expect these values, grab them from the pose if you can Otherwise, the values you are created are likely not related to the pose so initialize them from scratch (rare case) I also ended up removing a huge code block from MembranePotential during my parsing.... because impulse to keep the code clean :) Note - this pull requests depends on #677!!!!

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branch: master 「№58027」
Commited by: Labonte
GitHub commit link: 「34a9ced5b3953b4c」 「№687」
Difference from previous tested commit:  code diff
Commit date: 2015-08-06 02:30:22

Merge pull request #687 from RosettaCommons/JWLabonte/scripts_directory_move Consolidating directories where one can place Pythons scripts per discussion at PreRosettaCON 2015... no test changes

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branch: master 「№58026」
Commited by: Sergey Lyskov
GitHub commit link: 「2062f13a4477b9c4」
Difference from previous tested commit:  code diff
Commit date: 2015-08-05 19:26:18

Fixing performance tests comparison so it does not accumulate old info. Adding ‘profile’ benchmark script. Increasing performance tests runtime to improve stability.

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branch: master 「№58025」
Commited by: Vikram K. Mulligan
GitHub commit link: 「54452ada07377524」
Difference from previous tested commit:  code diff
Commit date: 2015-08-05 18:44:25

Switching all instances of "Size" to "core::Size" in one of Andy's pilot apps. This was tripping up my version of gcc for some reason. (I had the same problem with one of Julia's pilot apps a while back.) Don't know why this doesn't get flagged in any of the test server builds.

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branch: master 「№58024」
Commited by: Rebecca Alford
GitHub commit link: 「f8e9eedf161e0437」 「№677」
Difference from previous tested commit:  code diff
Commit date: 2015-08-05 08:57:12

Merge pull request #677 from RosettaCommons/rfalford12/change_default_normal2 Change membrane normal to be a unit vector by default --------------------------------------------------------------------------------- Change the default membrane normal to keep unit length instead of normalizing to 15Å. This pull request accomplishes two main goals: = Decouple the concept of the membrane normal, which represents orientation of the bilayer and the thickness of the bilayer. This is important for upcoming developments in the membrane representation = Remove hardcoding of the membrane thickness throughout the code An option is added to file_data.cc for outputting data for MEM where the normal is scaled to the thickness for visualization purposes only. To use this option, pass the flag -mp:output:normalize_to_thk. This change is now tracked by the mp_loadtime integration test. This pull request preceeds another pull request that will completely remove core/conformation/membrane/types.hh to discoruage hard-coding and increase reliance on the MembraneInfo object. Anticipated Test Changes: Fingerprint Tests: No score changes, just prints the updated normal coords. Unit Tests: Commits in this pull request update unit tests to check for a normal of unit length. Integration Tests: Anticipated changes due to changed normal length. Coordinates change in mp_relax, mp_relax with ligand, mp_dock and mp_dock_setup. We have resolved this is due to an instability in the test server and not our code. mp_loadtime also changes due to the addition described above. The following integration tests are expected to change: mp_loadtime, mp_relax, mp_relax_w_ligand, mp_dock, mp_dock_setup, mp_find_interface, mp_mutate_relax, mp_quick_relax, mp_score_jd2, mp_symdock, mp_symmetry_load, mp_transform The documentation has also been updated to reflect this change here: https://www.rosettacommons.org/docs/wiki/application_documentation/membrane_proteins/RosettaMP-KeyElements-MembraneRsd

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branch: master 「№58023」
Commited by: havranek
GitHub commit link: 「584bd5fbed21f60d」 「№671」
Difference from previous tested commit:  code diff
Commit date: 2015-08-02 13:24:21

Merge pull request #671 from RosettaCommons/havranek/amoeba_options Adjusting patches for DNA terminii to reflect actual molecules by adding

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branch: master 「№58022」
Commited by: havranek
GitHub commit link: 「88213f63ba4b63f0」 「№670」
Difference from previous tested commit:  code diff
Commit date: 2015-07-31 17:34:05

Merge pull request #670 from RosettaCommons/havranek/amoeba_options Adding commandline options for polarizable multipole electrostatics.

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branch: master 「№58021」
Commited by: Vikram K. Mulligan
GitHub commit link: 「5a3ef6da42f33dd0」 「№668」
Difference from previous tested commit:  code diff
Commit date: 2015-07-30 20:18:06

Merge pull request #668 from RosettaCommons/vmullig/mpitest_off Disabling the bundlegridsampler_design_nstruct_mode MPI test until Disabling the bundlegridsampler_design_nstruct_mode MPI test until I can track down the cause of the instability. Sorry to have had this on for so long -- I was kind of hoping that one of Andy's cppcheck fixes would magically fix the instability, but no dice. Note: this means that MPI integration test failures should NOT be ignored any longer. The other MPI integration test DOES work without instability.

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