commit cae4c003338428878c06f0f42683180cbf75b18c
Merge: 733da1c f110e6e
Date:   Tue Aug 23 15:48:42 2016 -0500

    Merge pull request #1552 from RosettaCommons/roccomoretti/integration_test_mode
    
    Adjust integration.py to allow for other modes in demos tests.
    
    e.g. release_debug

commit 733da1cab7b67984dd88d8d3bbaa43e86625d952
Merge: dfa9b4c 64a3c66
Date:   Tue Aug 23 15:30:00 2016 -0500

    Merge pull request #1484 from RosettaCommons/jadolfbr/LCM
    
    LinkageConformerMover improvements
    
    Make LinkageConformerMover use only carbohydrate residues if no move map is supplied.  Why I didn't have this in the first place, is beyond me.
    Make LCM/GlycanRelax not crash if a default, all-true (default-constructed) MoveMap is supplied (where the iterator returned is basically infinite or something strange)
    
    Explicitly state what should be done on new inputs, better handling multiple apply calls for different structures/jobs/etc (This is where integration test changes were coming from - now they are gone.  Yay for the testing server and the PR system!)

commit dfa9b4c2aa9ebb0ff9a0a6fc3e1c4bc9b913b4d4
Merge: 3ab7d06 68a1d35
Date:   Mon Aug 22 10:51:39 2016 -0700

    Merge pull request #1502 from RosettaCommons/tlinsky/tomponents
    
    Updates to denovo classes.  Integration test changes expected for bridge_chains

commit 3ab7d06d5fcce9f34c1912c04823d7828e0b7def
Merge: 2f2b80c 7dfb87d
Date:   Mon Aug 22 11:49:28 2016 -0500

    Merge pull request #1547 from RosettaCommons/jadolfbr/remove_initial_pert
    
    small update for antibody design

commit 2f2b80c9ace3bc0d81426e27d9c8aaa5fd3e6876
Merge: f84a3c4 1ac9088
Date:   Sat Aug 20 10:45:09 2016 -0500

    Merge pull request #1548 from RosettaCommons/roccomoretti/molfile_to_params_chain
    
    Add option to change chain letter in molfile_to_params.py
    
    Allows different chain designations to be made for output PDBs.

commit f84a3c40fa20fd5ce256ad56b606dce62336ffec
Merge: c2e3285 36a0883
Date:   Thu Aug 18 18:04:29 2016 -0700

    Merge pull request #1544 from RosettaCommons/tlinsky/extract_asymm_secstruct
    
    When extracting asymmetric subunit, also extract/set pose.secstruct
    
    CXX11 unit test failed initially, but passed when I resubmitted: http://benchmark.graylab.jhu.edu/revision?id=4574&branch=

commit c2e3285917dca3398f28cea1bcf1811b06bce20b
Merge: f6a6d5a 11c5b09
Date:   Thu Aug 18 09:26:12 2016 -0500

    Merge pull request #1543 from RosettaCommons/roccomoretti/fix_pyrosetta_copyright
    
    Fix broken PyRosetta from copyright fixes
    
    In updating the copyright headers, I accidentally messed up the docstring on one of the PyRosetta files, leading to breakage of the PyRosetta unit tests (with a Python parse error).

commit f6a6d5a14bc2f1182cfffb21dce54869af977a0e
Merge: a8a0602 b58e33c
Date:   Thu Aug 18 08:30:44 2016 -0400

    Merge pull request #1539 from RosettaCommons/rfalford12/single-TM-span-option
    
    Automatic Topology for Single TM Alpha Helical Proteins
    ---
    Adding an option to AddMembraneMover to automatically determine the transmembrane spanning topology for a single TM helix (accessible via command line and RosettaScripts)

commit a8a0602976cb23c09f7a70b2cc2a7fb2a31fc393
Merge: cbe4bab 1e8e8ff
Date:   Wed Aug 17 11:09:48 2016 -0700

    Merge pull request #1460 from RosettaCommons/tlinsky/sheet_cst_gen
    
    Refactor SheetConstraintGenerator for easier selection of pairings and ss

commit cbe4bab73a3cc1686939ce4cf3ad6898b7d0371d
Merge: fef88e1 2cc7f58
Date:   Wed Aug 17 10:26:49 2016 -0700

    Merge pull request #1542 from RosettaCommons/tlinsky/fix_ssene_ss
    
    Fix SetSecStructEnergies Mover for case when input pose is empty
    
    Initial testing showed unit test failures, but they disappeared after retesting, so this should be fine: http://benchmark.graylab.jhu.edu/revision?id=4560&branch=

commit fef88e1b827640cb3d13d982e4c6766424b53c5d
Merge: f21bc8b af31e6f
Date:   Wed Aug 17 11:23:14 2016 -0400

    Merge pull request #1445 from RosettaCommons/jkleman/mp_updates_toolkit
    
    Jkleman/mp updates toolkit
    
    = made HelixFromSequence app into a Mover
    = added PDB numbering support for spanfile input, new spanfile format will automatically be detected
    = added PDB numbering support for MPMutateRelaxMover
    = added integration tests for PDB file format in spanfile and MPMutateRelaxMover

commit f21bc8bbd60fe13df8d27e683ab83086700bb1fd
Merge: 5d64745 56c45fe
Date:   Tue Aug 16 16:43:55 2016 -0700

    Merge pull request #1517 from RosettaCommons/tlinsky/binary_silent_comment
    
    Make BinarySilentStruct use same comment-parsing as other silent structs

commit 5d647453b0fdc32d32d8fed37a13bf6facdbc7fa
Merge: eb24f99 f7ed579
Date:   Tue Aug 16 14:36:25 2016 -0500

    Update Copyright headers in main.
    
    TechTransfer -> CoMotion
    license@u.washington.edu -> license@uw.edu
    
    Other associated normalizations of headers.
    
    Merging directly to avoid massive pull request on GitHub.

commit eb24f99335599d1fe319788dc209a2c2135398c7
Date:   Tue Aug 16 14:36:11 2016 -0500

    Remove the remaining 'TechTransfer' instances from main

commit f9365e66881b0a30d7ec3165c05b613725a05be4
Date:   Tue Aug 16 12:45:04 2016 -0500

    Update headers: tests and python scripts.

commit ee163d51ef06e1bfc57fe8094a2121e0cf859406
Date:   Tue Aug 16 11:19:26 2016 -0500

    Update licensing header for current contact.

commit 3ec589b8a980068e5f3492e8cb5e2f934d566272
Date:   Tue Aug 16 11:13:13 2016 -0500

    Update copyright headers to the old one.