Pushed Revisions

branch: master 「№59076」
Commited by: jkleman
GitHub commit link: 「bf3526f01b7b07a1」「№1769」
Difference from previous tested commit: code diff
Commit date: 2016-11-10 14:07:02

Merge pull request #1769 from RosettaCommons/jkleman/lipid-acc Jkleman/lipid acc updates to lipid accessibility calculation

branch: master 「№59075」
Commited by: Vikram K. Mulligan
GitHub commit link: 「8f28abe28c371338」「№1780」
Difference from previous tested commit: code diff
Commit date: 2016-11-10 04:10:21

Merge pull request #1780 from RosettaCommons/vmullig/support_nmethyl_merge4 Incremental merge #3 for supporting N-methylation Full list of changes is in pull request #1508 .

branch: master 「№59074」
Commited by: Frank DiMaio
GitHub commit link: 「fdcbb83b9efb1c3b」「№1774」
Difference from previous tested commit: code diff
Commit date: 2016-11-09 16:31:33

Merge pull request #1774 from RosettaCommons/dimaio/hyb_fix_boundserror Fix out of bounds error in hybridize

branch: master 「№59073」
Commited by: Rhiju Das
GitHub commit link: 「6238c7e203310702」「№1779」
Difference from previous tested commit: code diff
Commit date: 2016-11-08 22:25:49

Merge pull request #1779 from RosettaCommons/rhiju/linear_chainbreak_shrink_cutoff reducing distance cutoff for computing linear_chainbreak deriv from 0… + Tests that change are ones that use linear_chainbreak. + In most cases, minimizer now reaches lower energy and spouts fewer 'Inaccurate G' warnings (though there are still some).

branch: master 「№59072」
Commited by: Rhiju Das
GitHub commit link: 「85b7168cddb3169c」「№1777」
Difference from previous tested commit: code diff
Commit date: 2016-11-08 16:01:49

Merge pull request #1777 from RosettaCommons/rhiju/chainbreak_energy_generalize Rhiju/chainbreak energy generalize Only test changes are aesthetic (or previously broken cppcheck & thermal_sampler).

branch: master 「№59071」
Commited by: Rhiju Das
GitHub commit link: 「441415b91d37956b」「№1776」
Difference from previous tested commit: code diff
Commit date: 2016-11-07 11:21:12

Merge pull request #1776 from RosettaCommons/rhiju/make_dna_via_patched_rna Handle DNA in FARFAR (rna_denovo) [Only failing checks are thermal_sampler & cppcheck, both broken previously.]

branch: master 「№59070」
Commited by: Rhiju Das
GitHub commit link: 「8739b57ef2cf651f」「№1775」
Difference from previous tested commit: code diff
Commit date: 2016-11-06 18:54:34

Merge pull request #1775 from RosettaCommons/rhiju/declare_chemical_bond_at_loop_cutpoints declare chemical bond when CUTPOINT_UPPER and CUTPOINT_LOWER are assigned at a chainbreak Only tests that change are ones that failed before (cppcheck; thermal_sampler in debug_release), and bridge_chains gets a much lower energy due to absence of repulsion between the atoms bonded across the chainbreak.

branch: master 「№59069」
Commited by: Brahm Yachnin
GitHub commit link: 「f9fc0305175b872c」「№1765」
Difference from previous tested commit: code diff
Commit date: 2016-11-03 19:42:56

Merge pull request #1765 from RosettaCommons/BYachnin/Fix_Segfault_after_Execution Removed tracer output in destructor to fix segfault. Several integration tests lose the tracer output core.chemical.ResidueType: Residue dstor as expected, including integration.release-debug (cyclization, ddG_of_mutation, fiber_diffraction_fad, fold_and_dock) and integration (cyclization, ddG_of_mutation, fiber_diffraction, and fold_and_dock). mac.clang.integration.features_parallel failed due to different sqlite versions on the test servers.

branch: master 「№59068」
Commited by: Andrew Watkins
GitHub commit link: 「5d54dd7ccc45bb30」「№1768」
Difference from previous tested commit: code diff
Commit date: 2016-11-03 19:35:21

Merge pull request #1768 from RosettaCommons/everyday847/stepwise_performance_two Minor stepwise performance improvements and loop conversions

branch: master 「№59067」
Commited by: Andrew Watkins
GitHub commit link: 「bda5dbf6ac9204da」「№1760」
Difference from previous tested commit: code diff
Commit date: 2016-11-03 17:38:33

Merge pull request #1760 from RosettaCommons/everyday847/issue_with_virtual_atoms RNA cutpoint torsion issue + some miscellany

branch: master 「№59066」
Commited by: Sergey Lyskov
GitHub commit link: 「1ccd4b449eb2791c」「№1766」
Difference from previous tested commit: code diff
Commit date: 2016-11-03 17:14:27

Merge pull request #1766 from RosettaCommons/sergey/binder Updating PyRosetta documentation generation script so it now generate docs for pyrosetta.* sub-modules. Refactoring toolbox modules so they could be imported in Python-3.

branch: master 「№59065」
Commited by: Andrew Watkins
GitHub commit link: 「c28dabb55571830b」「№1767」
Difference from previous tested commit: code diff
Commit date: 2016-11-03 12:17:06

Merge pull request #1767 from RosettaCommons/everyday847/base_pair_constraint Base pair constraint mechanism

branch: master 「№59064」
Commited by: Rhiju Das
GitHub commit link: 「cb14486eaf0a6dd8」「№1762」
Difference from previous tested commit: code diff
Commit date: 2016-11-03 12:07:08

Merge pull request #1762 from RosettaCommons/rhiju/make_dna_via_patched_rna creating patch Deoxy_O2prime to convert RNA to DNA residues only broken tests (cppcheck, integration for erraser_minimize, thermal_sampler) were broken before and watkins is on it.

branch: master 「№59063」
Commited by: Rhiju Das
GitHub commit link: 「6922a68c56c0a3c5」「№1761」
Difference from previous tested commit: code diff
Commit date: 2016-11-02 13:42:41

Merge pull request #1761 from RosettaCommons/rhiju/make_7DA_UNP_not_RAD making 7DA.params an UNP aa so that it does not get designed Looks OK -- only rna_design changes, as expected -- no longer allowing 7-deaza-A in standard fixed-backbone RNA design. A few tests were previously broken (cppcheck; and integration for erraser_minimize & thermal_sampler were broken before -- @everyday847 please checkout).

branch: master 「№59062」
Commited by: Vikram K. Mulligan
GitHub commit link: 「8273fa01111f43a5」「№1759」
Difference from previous tested commit: code diff
Commit date: 2016-11-01 21:05:58

Merge pull request #1759 from RosettaCommons/vmullig/temporarily_revert_rama_table_from_tim Temporarily reverting Tim's change to the custom Rama tables, which broke some stuff. Sorry folks -- we meant to commit this to a branch, not to master yet.

branch: master 「№59061」
Commited by: Andrew Watkins
GitHub commit link: 「aa7e97ec73a3ffba」「№1757」
Difference from previous tested commit: code diff
Commit date: 2016-11-01 15:22:20

Merge pull request #1757 from RosettaCommons/everyday847/fix_new_delete_mismatch Fix an issue with a new[] / delete (no []) mismatch

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queued	Queued Test
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