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branch: scientific 「№26」
Commited by: Labonte
GitHub commit link: 「03208cbfaffeda72」 「№4068」
Difference from previous tested commit:  code diff
Commit date: 2019-07-04 11:00:19
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mhc_epitope_energy.debug scientific.mhc_epitope_energy scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_f19_decoy_discrimination.debug scientific.mp_f19_decoy_discrimination scientific.mp_f19_energy_landscape.debug scientific.mp_f19_energy_landscape scientific.mp_f19_sequence_recovery.debug scientific.mp_f19_sequence_recovery scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #4068 from RosettaCommons/JWLabonte/quick_fix Bug Fix: ligand_motif_design integration test This merge will hopefully correct the `ligand_motif_design` integration test, which I accidentally broke when adding ATP to the database. (:rat: is sorry.) The test formerly used its own ATP `.params` file, and Rosetta will not allow there to be two ATPs in a `ResidueTypeSet`. I am simply making the test use the database version, which also involves renaming the atoms in the input `.pdb` file to their correct PDB names. All tests pass, but there are naturally differences in the `ligand_motif_design` test.

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branch: scientific 「№25」
Commited by: Labonte
GitHub commit link: 「98bf209eda57a650」 「№4037」
Difference from previous tested commit:  code diff
Commit date: 2019-06-25 14:01:49
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mhc_epitope_energy.debug scientific.mhc_epitope_energy scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #4037 from RosettaCommons/Blair980728-patch-1 PTMs: Adding 2 more enzymes to database

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branch: scientific 「№24」
Commited by: Jack Maguire
GitHub commit link: 「d24aa6a89229a158」 「№4025」
Difference from previous tested commit:  code diff
Commit date: 2019-06-16 09:23:37
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #4025 from RosettaCommons/JackMaguire/ClangCxx14 Correcting extras=cxx... flags for clang #3992 added options to compile with std=c++1y and later versions of c++. To do this, I needed to remove std=c++1x from those builds but failed to notice that clang uses std=c++11 instead. This PR simply corrects the flag being removed. Thanks for the review Sergey!

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branch: scientific 「№23」
Commited by: Jaume Bonet
GitHub commit link: 「b0c18bd01c0dd36a」 「№4001」
Difference from previous tested commit:  code diff
Commit date: 2019-06-07 07:40:47
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #4001 from RosettaCommons/jaumebonet/coupledmovesRS CoupledMovesProtocol: fixed attribute definitions between parse_my_tag and provide_xml_schema

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branch: scientific 「№22」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「d8f9b4a90a8f2caa」
Difference from previous tested commit:  code diff
Commit date: 2019-05-30 13:47:16
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Fix EnergyMap::operator += (#3977) The convention for increment-and-assign type operators is to return a reference to the object that has just been incremented, thereby facilitating multiple increments in a single statement ``` a += ( b+= c ); ``` The original author* of the EMapVector class (aka EnergyMap) did not realize this and so this class does not return a reference, and instead returns void. This has never been a problem for C++ code as no one has seemingly wanted to chain increment-and-assign operations. PyBind11, however, will take the returned type and assign it to the original object: ``` emap1 += emap2 ``` is interpretted as: ``` emap1 = (emap1 += emap2) ``` so that this code: ``` emap1 += emap2 print("Surpise!", emap1) ``` will print ``` Surprise! None ``` This PR changes the signature of just the EMapVector's operator+= and similar methods, but surely there are other places in the code where operators are not conforming to the C++ conventions. *I am the original author of this code.

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branch: scientific 「№21」
Commited by: Sergey Lyskov
GitHub commit link: 「808795efd9a378a1」 「№3959」
Difference from previous tested commit:  code diff
Commit date: 2019-05-23 12:26:15
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #3959 from RosettaCommons/sergey/binder Updating PyRosetta so it could be build with Python-3.7 on Mac

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branch: scientific 「№20」
Commited by: Steven Lewis
GitHub commit link: 「cb17a85dd9b048bf」 「№3966」
Difference from previous tested commit:  code diff
Commit date: 2019-05-18 11:07:35
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #3966 from RosettaCommons/smlewis/fix_NamedAtomPairConstraint_type overrides for some constraint classes. Fix NamedAtomPairConstraint's type()

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branch: scientific 「№19」
Commited by: Vikram K. Mulligan
GitHub commit link: 「33e358d32e268bf5」 「№3953」
Difference from previous tested commit:  code diff
Commit date: 2019-05-09 13:30:25
scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #3953 from RosettaCommons/vmullig/bin_analysis_in_cluster_app Add bin string analysis to energy_based_clustering application This allows the number of unique ABOXYZ bin strings (with or without cyclic permutation, depending on whether cyclic permutations during clustering are allowed) to be counted. Completed tasks: - Add flag for this analysis. - Checks that this is only being applied to alpha-amino acids or to peptoids. - Add functions for computing bin strings. - Add counters for unique bin strings. - Add output: - Bin strings for every structure. - Bin strings for every cluster center. - Summary of number of unique bin strings (for structures and for cluster centers). - Summary of number of unique bin strings if strings and their mirror images are considered to be equivalent (for structures and for cluster centers). - Unit tests. - Beauty. - Documentation -- added to this page: https://www.rosettacommons.org/docs/latest/application_documentation/analysis/energy_based_clustering_application (though it may take a day or so to show up). - Integration test.

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branch: scientific 「№18」
Commited by: Jeliazko Jeliazkov
GitHub commit link: 「f46cd154940cbf78」 「№3839」
Difference from previous tested commit:  code diff
Commit date: 2019-04-27 15:45:49
scientific.cartesian_relax.debug scientific.cartesian_relax scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_docking.debug scientific.ligand_docking scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #3839 from RosettaCommons/lqtza/scs_blast_updates_for_auto_db Enable use of new antibody database (lives in additional_protocol_data).

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branch: scientific 「№17」
Commited by: TJ Brunette
GitHub commit link: 「0d2afa55e6960cae」 「№3924」
Difference from previous tested commit:  code diff
Commit date: 2019-04-19 12:49:49
scientific.cartesian_relax.debug scientific.cartesian_relax scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_docking.debug scientific.ligand_docking scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

Merge pull request #3924 from RosettaCommons/tjbrunette/junc_filter fix issue with rna_design uncommented. This code makes hbnet compatible with silent files. Thus the integration test change for hbnet. Also, this includes bug fixes for loop closure, and structProfile.

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Test: linux.clang.scientific.cofactor_binding_sites.debug

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Test: linux.clang.scientific.cofactor_binding_sites

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Test: linux.clang.scientific.ligand_docking.debug

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Test: linux.clang.scientific.ligand_docking

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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Test: linux.clang.scientific.rna_denovo_favorites.debug

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Test: linux.clang.scientific.stepwise_rna_favorites.debug

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branch: scientific 「№16」
Commited by: Vikram K. Mulligan
GitHub commit link: 「b30ab1b187951c48」
Difference from previous tested commit:  code diff
Commit date: 2019-04-11 21:59:56
scientific.cartesian_relax.debug scientific.cartesian_relax scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_docking.debug scientific.ligand_docking scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites

beautifying

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Test: linux.clang.scientific.cofactor_binding_sites.debug

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Test: linux.clang.scientific.cofactor_binding_sites

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Test: linux.clang.scientific.ligand_docking.debug

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Test: linux.clang.scientific.ligand_docking

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Test: linux.clang.scientific.mp_dock.debug

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Test: linux.clang.scientific.mp_domain_assembly.debug

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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Test: linux.clang.scientific.rna_denovo_favorites.debug

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Test: linux.clang.scientific.stepwise_rna_favorites.debug

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Test: linux.clang.scientific.stepwise_rna_favorites

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branch: scientific 「№15」
Commited by: Andy Watkins
GitHub commit link: 「c5c5824d14987f1a」 「№3897」
Difference from previous tested commit:  code diff
Commit date: 2019-04-03 14:39:30
scientific.cartesian_relax scientific.cofactor_binding_sites scientific.enzyme_design scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_docking_ddg scientific.ligand_docking scientific.mp_dock scientific.mp_domain_assembly scientific.mp_lipid_acc scientific.mp_relax scientific.mp_symdock scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites scientific.stepwise_rna_favorites

Merge pull request #3897 from RosettaCommons/everyday847/recover_broken_silent Read slightly broken silent files gracefully

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Test: linux.clang.scientific.cartesian_relax

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Test: linux.clang.scientific.cofactor_binding_sites

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Test: linux.clang.scientific.enzyme_design

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Test: linux.clang.scientific.fast_relax_5iter

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Test: linux.clang.scientific.fast_relax

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Test: linux.clang.scientific.ligand_docking_ddg

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Test: linux.clang.scientific.ligand_docking

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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branch: scientific 「№14」
Commited by: Vikram K. Mulligan
GitHub commit link: 「0175401f13308587」 「№3886」
Difference from previous tested commit:  code diff
Commit date: 2019-03-27 12:20:28
scientific.cartesian_relax scientific.cofactor_binding_sites scientific.enzyme_design scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_docking_ddg scientific.ligand_docking scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites scientific.stepwise_rna_favorites

Merge pull request #3886 from RosettaCommons/vmullig/split_unit_tests_2 Split the test suite that is ACTUALLY timing out. I split the wrong one previously. Whoops.

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Test: linux.clang.scientific.cofactor_binding_sites

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Test: linux.clang.scientific.ligand_docking_ddg

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Test: linux.clang.scientific.ligand_docking

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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Test: linux.clang.scientific.rna_denovo_favorites

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branch: scientific 「№13」
Commited by: Stacey Gerben
GitHub commit link: 「dca9f7c22c03de87」 「№3835」
Difference from previous tested commit:  code diff
Commit date: 2019-03-19 14:15:15
scientific.cartesian_relax scientific.cofactor_binding_sites scientific.enzyme_design scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_docking_ddg scientific.ligand_docking scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites scientific.stepwise_rna_favorites

Merge pull request #3835 from RosettaCommons/srgerb/poses_to_silent Adding Ability To Easily Output Poses As Silent Files To PyRosetta

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Test: linux.clang.scientific.cofactor_binding_sites

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Test: linux.clang.scientific.ligand_docking_ddg

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Test: linux.clang.scientific.ligand_docking

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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branch: scientific 「№12」
Commited by: Sergey Lyskov
GitHub commit link: 「8832fec1a1cf8dd0」 「№3846」
Difference from previous tested commit:  code diff
Commit date: 2019-03-11 13:51:01
scientific.cartesian_relax scientific.cofactor_binding_sites scientific.enzyme_design scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_docking_ddg scientific.ligand_docking scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites scientific.stepwise_rna_favorites

Merge pull request #3846 from RosettaCommons/sergey/f Increasing default unit tests timeout if clean-clone detected

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Test: linux.clang.scientific.cofactor_binding_sites

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Test: linux.clang.scientific.ligand_docking_ddg

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Test: linux.clang.scientific.ligand_docking

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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branch: scientific 「№11」
Commited by: Steven Lewis
GitHub commit link: 「0e576faa1ca146a6」 「№3619」
Difference from previous tested commit:  code diff
Commit date: 2019-02-22 11:08:58
scientific.cartesian_relax scientific.enzyme_design scientific.fast_relax_5iter scientific.fast_relax scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites scientific.stepwise_rna_favorites

Merge pull request #3619 from RosettaCommons/smlewis/update_PDBdiagnostic_refs PDB diagnostic: update reference lists. Reformat readme per Julia's formatting (This was left open forever, merging it now so I can make a new one to update the refs again)

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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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