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branch: master 「№58164」
Commited by: Andrew Watkins
GitHub commit link: 「68a6a189e8cbe3dd」
Difference from previous tested commit:  code diff
Commit date: 2015-09-19 14:54:57

Fixing library levels build; sorry!

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branch: master 「№58163」
Commited by: Andrew Watkins
GitHub commit link: 「791ade228547653e」 「№793」
Difference from previous tested commit:  code diff
Commit date: 2015-09-19 14:47:43

Merge pull request #793 from RosettaCommons/everyday847/deprecate_disulfide_exception Remove exception from annotated sequence

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branch: master 「№58162」
Commited by: Andrew Watkins
GitHub commit link: 「450d75095dfa6bb8」 「№798」
Difference from previous tested commit:  code diff
Commit date: 2015-09-19 09:32:01

Merge pull request #798 from RosettaCommons/everyday847/ssbond_input Use SSBOND records, if available, to prompt conformation::detect_disulfides. Integration test changes are all cosmetic/reflect that NtermConnect and CtermConnect are no longer silenced by CMDLINE_SELECTORs.

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branch: master 「№58161」
Commited by: Sergey Lyskov
GitHub commit link: 「1da8a4c0bcd96736」
Difference from previous tested commit:  code diff
Commit date: 2015-09-18 18:58:17

Updating HPC ‘execute’ so it uses test working dir for logs by default

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branch: master 「№58160」
Commited by: Andrew Watkins
GitHub commit link: 「0184b05294383990」 「№799」
Difference from previous tested commit:  code diff
Commit date: 2015-09-18 14:54:21

Merge pull request #799 from RosettaCommons/everyday847/branching_in_centroid Rudimentary centroid mode for branching

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branch: master 「№58159」
Commited by: Rhiju Das
GitHub commit link: 「dbcf6ff6e9024aa6」 「№806」
Difference from previous tested commit:  code diff
Commit date: 2015-09-18 12:26:02

Merge pull request #806 from RosettaCommons/rhiju/fa_stack_updates Rhiju/fa stack updates all changes are OK: +broken tests are the 'usual' ones in integration (pna, inverse_rotamer_remodel), which I'm fixing in a separate branch. + also saw a 'cosmetic' line ordering change in integration.release_debug for mm_params. + last, dna_interface_design is also broken, but only in integration.release_debug (not integration). seems to be affecting everyone.

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branch: master 「№58158」
Commited by: Rhiju Das
GitHub commit link: 「c0e92cf87b5ca648」
Difference from previous tested commit:  code diff
Commit date: 2015-09-17 18:47:17

goes with previous commit: fix possible bug in stepwise minimizer, setting of working_minimize_res

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branch: master 「№58157」
Commited by: Vikram K. Mulligan
GitHub commit link: 「edd9836c1d021bf7」 「№805」
Difference from previous tested commit:  code diff
Commit date: 2015-09-17 06:13:35

Merge pull request #805 from RosettaCommons/vmullig/genkic_minsolutions_bug Caught a bug in GenKIC. Expect GenKIC integration test changes.

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branch: master 「№58156」
Commited by: Sergey Lyskov
GitHub commit link: 「28c6ff884d5ee7a3」 「№802」
Difference from previous tested commit:  code diff
Commit date: 2015-09-16 17:57:57

Merge pull request #802 from RosettaCommons/benchmark Adding options to benchmark scripts for PyRosetta debug releases

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branch: master 「№58155」
Commited by: Tom Linsky
GitHub commit link: 「2e802cd97b75228f」 「№796」
Difference from previous tested commit:  code diff
Commit date: 2015-09-16 16:17:35

Merge pull request #796 from RosettaCommons/tlinsky/tlinsky/rcg_remove_exception RemodelConstraintGenerator now throws exception when constraints can't be removed

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branch: master 「№58154」
Commited by: Labonte
GitHub commit link: 「00ea0333284dbec7」 「№797」
Difference from previous tested commit:  code diff
Commit date: 2015-09-16 10:48:06

Merge pull request #797 from RosettaCommons/JWLabonte/patch_system Patch system: Adding PatchOperation for changing a bond type All tests pass, except for broken/unstable integration tests.

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branch: master 「№58153」
Commited by: P. Douglas Renfrew
GitHub commit link: 「4b45f173ea141bfc」 「№800」
Difference from previous tested commit:  code diff
Commit date: 2015-09-15 17:07:45

Merge pull request #800 from RosettaCommons/dougrenfrew/2-amino-octanoic_acid Adding 2-amino-octanoic acid the l-ncaa residue types. The `number_of_residuetypes` integration test expected to fail.

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branch: master 「№58152」
Commited by: davidekim
GitHub commit link: 「df73fb2c17bff247」
Difference from previous tested commit:  code diff
Commit date: 2015-09-14 18:42:36

Merging with remote

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branch: master 「№58151」
Commited by: Rhiju Das
GitHub commit link: 「a9c9dc6648889422」 「№794」
Difference from previous tested commit:  code diff
Commit date: 2015-09-14 15:58:36

Merge pull request #794 from RosettaCommons/rhiju/fix_match_test_instability2 trying again to fix instabilities in match_* integration tests broken tests are + ones that did not work previously (cppcheck & integration: pna & dna_interface_design) @everyday847 is *pna* yours? + match_* integration tests -- what this commit will hopefully stabilize. + The mm_params test also shows a cosmetic change in integration.release_debug where order of output changes -- don't know what's up with that.

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branch: master 「№58150」
Commited by: Labonte
GitHub commit link: 「bcc1a5fb03a6fb9b」
Difference from previous tested commit:  code diff
Commit date: 2015-09-14 14:22:14

silencing cpp complaint

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branch: master 「№58149」
Commited by: Labonte
GitHub commit link: 「7ab62678154ca8a3」 「№731」
Difference from previous tested commit:  code diff
Commit date: 2015-09-13 17:42:45

Merge pull request #731 from RosettaCommons/JWLabonte/sugars/general Carbohydrates: Refactoring CarbohydrateInfo to use singleton for static const data Unit tests pass. carbohydrate test changes expected because of expanded Gasteiger testing. All other integration test failures are from broken/unstable tests. cpp test change is not a true case.

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