commit 3114825e245f4ee670e8ba63e9662f89586d68b7
Merge: cad20e9 aec7359
Date:   Wed Sep 14 23:38:03 2016 -0700

    Merge pull request #1624 from RosettaCommons/everyday847/CA_rmsd_analogues
    
    RMSD for ribonucleoproteins

commit cad20e9c9d1c4609ad57af94e9480a8a2ec365e7
Merge: 7731a4e 0d11da8
Date:   Wed Sep 14 15:38:58 2016 -0600

    Merge pull request #1619 from RosettaCommons/sergey/binder
    
    Adding bindings generation for overriding functions that return reference to primitive types or std::string

commit 7731a4e413ed05b0fc53f887db234ad0b1a23086
Merge: 3828819 4fa7a49
Date:   Wed Sep 14 13:55:31 2016 -0400

    Merge pull request #1612 from RosettaCommons/Cyrus/mergetarget
    
    From Steven Lewis:
    
    These are mostly small changes, the code I meant to push today is waiting on RosettaCommons #1601.
    
    Cyrus PR 46: Smlewis/cyrus/score mover tweak: I read ScoreMover fairly closely to write a documentation page for it, and fixed some issues with the code / comments while I was at it.
    
    Cyrus PR 47: smlewis/cyrus/fix copyright headers: fixing copyright headers in new files post Rocco’s fixes. (This is most of the changes in protocols)
    
    -> % python ~/ROSETTA/Rosetta/tools/Check_header_guards_and_copyright.py src/protocols/ | grep "^/Users/smlewis" | sed "s/://" > find_header_these This grabs the files that need header fixes
    cat find_header_these| while read line do sed -i bak "s/UW TechTransfer,email:license@u.washington.edu./CoMotion, email: license@uw.edu./" $line done
    
    Cyrus PR 52: smlewis/cyrus/fix_IA_ctor Fixes issues with ignoring user-set options in XML for InterfaceAnalyzer

commit 38288194110dbf55a886a2a2dde21ab2affede1a
Merge: b4dca64 e087552
Date:   Wed Sep 14 12:29:22 2016 -0400

    Merge pull request #1616 from RosettaCommons/dougrenfrew/embrace_emplace
    
    Enabling new C++11 std::vector functions in utility::vectorL/0/1

commit b4dca6478e455c40b1e220fa848d69ac23f7ee04
Merge: bc26a55 3ee1252
Date:   Wed Sep 14 08:51:37 2016 -0700

    Merge pull request #1561 from RosettaCommons/everyday847/gradually_idealize
    
    RNA idealization app

commit bc26a55c0606012aded598bb34ac80650276831b
Merge: 4a8a31a 70fe21c
Date:   Tue Sep 13 21:53:05 2016 -0700

    Merge pull request #1622 from RosettaCommons/vmullig/fix_inttests
    
    Removing timing information from erraser_minimize integration test to stop the test from failing.

commit 4a8a31af2af357c83cc9cdf2285e6cd3cc7733e1
Merge: 20d953c d6083ab
Date:   Tue Sep 13 17:29:25 2016 -0700

    Merge pull request #1602 from RosettaCommons/kylebarlow/general_dev
    
    BackrubProtocol refactoring and parse_my_tag
    
    * Refactoring BackrubProtocol to not access global option data as it applies
    
    * This allowed me to add a new parse_my_tag option to BackrubProtocol. This BackrubProtocol mover is less complicated to use in Rosetta Scripts, as it represents the composition of movers that makes up the full backrub protocol as it is applied in the command line backrub application.

commit 20d953c474618b65204aed9966bdccee61c1e63a
Merge: 7909efc 7d807b8
Date:   Tue Sep 13 16:44:04 2016 -0700

    Merge pull request #1601 from RosettaCommons/kylebarlow/coupled_moves
    
    Allow coupled_moves to act on multiple ligands
    
    * New option: coupled_moves::number_ligands
    * Better behavior when the ligand_mode option is set to false; no longer also need to set the ligand_prob option to 0.0 to tell the code there is no ligand
    
    coupled_moves integration test changes expected

commit 7909efcc575a976c846fd844214a90c42064c0fc
Merge: 85c3572 079a6c0b
Date:   Tue Sep 13 15:53:01 2016 -0700

    Merge pull request #1605 from RosettaCommons/vmullig/bgfix3
    
    I think this fixes compilation on Blue Gene

commit 85c357237b120e65fc4987fe9e34299b0c76e5cb
Merge: 8667f38 8ff8e7b
Date:   Tue Sep 13 16:35:07 2016 -0500

    Merge pull request #1604 from RosettaCommons/roccomoretti/fix_cxx11_dep
    
    Fix some issues with modern compilers.
    
    The C++11 update revealed some issues with modern compilers, mainly with deprecated constructs. This pull request should fix many of them.
    
    In particular, it fixes issues with gcc 6.2.0, clang 3.9.0, and ICC 14.0 on my Linux machine.
    
    This doesn't necessarily fix all issues: most notably Vikram is still experiencing issues on the Baker Lab machines. But those issues there can be addressed in a future pull request. (The fixes here are not contingent on fixing ICC 16.0.)

commit 8667f38ae616276c75b131bcbd2060a074435def
Merge: d82abc1 94abeb2
Date:   Tue Sep 13 09:14:45 2016 -0400

    Merge pull request #1614 from RosettaCommons/aleaverfay/add_srlz_funcs_for_lrecs
    
    Adding serialization routines for two long-range energy containers:
    
    ConstraintEnergyContainer
    DisulfideMatchingEnergyContainer

commit d82abc1b30d3e850d42606eb49688dd6cf9a0520
Merge: 3da71ed ba2f637
Date:   Mon Sep 12 21:17:55 2016 -0700

    Merge pull request #1615 from RosettaCommons/xingjiepan/fix_cppcheck_error_in_graph
    
    Fix the cppcheck errors in utility/graph/UpperEdgeGraph.hh

commit 3da71ed823e986a7dcb152ce14f81dfed8e800a4
Date:   Tue Sep 13 01:10:07 2016 +0000

    Fixing line endings.

commit 7b02bb37192bd4ceccbe7f73f8ed19211bfa0e62
Merge: 9bded6d 92f7dd4
Date:   Mon Sep 12 15:36:41 2016 -0700

    Merge pull request #1610 from RosettaCommons/vmullig/rosettascripts_template_script
    
    Have RosettaScripts print a template script whenever the input script is omitted
    
    Tasks:
    
    -    Remove the -print_template_script option.
    -    Update the output message.
    -    Update logic to decide whether to print output message (now, whenever -parser:protocol flag is omitted).
    -    Update documentation.
    -    Beauty.

commit 9bded6d84cc6e9c337bea8afa4fd60020bfc2d60
Merge: 28d0da0 5fae910
Date:   Mon Sep 12 12:44:45 2016 -0700

    Merge pull request #1582 from RosettaCommons/kylebarlow/pymol_observer
    
    Associate each PyMolObserver with a single Pose object

commit 28d0da0c28fbcf9795f6e1c40f54355eeb0364e9
Date:   Sun Sep 11 23:18:31 2016 -0700

    Beautifying master.

commit f61790c89e2fc447ff80cc80f025806c74c26bca
Merge: 575ad7e 5faf819
Date:   Sun Sep 11 13:24:23 2016 -0700

    Merge pull request #1593 from RosettaCommons/everyday847/ERRASER_to_main
    
    ERRASER python scripts should be part of main

commit 575ad7e5edee793b76f40b69fee51bc7c47eeb75
Merge: 62f5992 2998f02
Date:   Sun Sep 11 11:36:48 2016 -0600

    Merge pull request #1608 from RosettaCommons/sergey/binder
    
    Fixing PyRosetta so it could be compiled with latest Pybind11 master.

commit 62f59926235b075321039121a966b2c1a7abe573
Merge: 0ca4248 49808a3
Date:   Sun Sep 11 08:41:57 2016 -0700

    Merge pull request #1609 from RosettaCommons/everyday847/fix_erraser_whoops
    
    Fix ERRASER -- whoops!

commit 0ca4248d244ad1929a9b195d6730421130a12652
Merge: 4075d4c f65e1d1
Date:   Sat Sep 10 12:27:39 2016 -0500

    Merge pull request #1596 from RosettaCommons/roccomoretti/relax_centroid_native
    
    Fix issue with centroid poses and -relax:constrain_relax_to_native_coords
    
    -relax:constrain_relax_to_native_coords would only work if you also included the -in:file:fullatom flag. Otherwise, the native pose would get loaded as centroid mode. (By set_native_in_mover() in src/protocols/jd2/util.cc)
    
    That's terribly silly, as relax is a full-atom only protocol. (Doubly so, as the -s gets loaded as fullatom by default, but the -in:file:native is loaded as centroid.)
    
    This pull request bypasses the "is it centroid or not" logic, and always loads the native reference pose as fullatom.
    
    Integration test changes expected in relax_w_allatom_cst, as the native pose is now loaded as centroid (due to removing the -in:file:fullatom flag from the integration test),  even though the centroid version is not used.

commit 4075d4caf7624cc1bf6f04f9913d8ee9a2e948da
Merge: d742728 ed8cae2
Date:   Fri Sep 9 11:12:26 2016 -0500

    Merge pull request #1581 from RosettaCommons/jadolfbr/grafting_disulfides
    
    Fix antibody.cc
    
    This PR adds an option, optimal_graft, that fixes the grafting component of antibody.cc.  By fix, I mean that it uses the exact settings we have successfully used for antibody design - this results in 100% graft closure, clean disulfides, and lower energies.  By using other code for this option, we also fix a major bug in the grafting component of antibody.cc, which is responsible for much of the disulfide issues.
    
    We also add disulfide score terms for centroid mode in AnchoredGraftMover's default, smooth centroid score function.  They help to lessen the effects of the bug without the optimal_graft option, but do not alleviate it completely.
    
    This will change a few integration tests that use AnchoredGraftMover or CCDEndsGraftMover including antibody_designer and AnchoredPDBCreator due to the additional centroid score terms.
    
    Thanks to @lqtza for testing and debugging all this with me, as well as the work calling Relax directly for the final relax, instead of generating it from cmd-line options.

commit d74272886f8ea29a536e8be11b6cc7c6a96db6f2
Merge: 7b5bf62 94ef77c
Date:   Fri Sep 9 10:59:37 2016 -0500

    Merge pull request #1546 from RosettaCommons/jadolfbr/ab_numbering_converter
    
    Antibody numbering conversion
    
    Description
    =========
    
    * Add a mover and app for converting antibody structures from one numbering scheme to another.
    * Change numbering_scheme option to input_ab_scheme
    * Implement output_ab_scheme to every app that outputs antibodies, so users can use any scheme as input and get any scheme as output in antibody apps, including antibody.cc (well, at least for output).
    *Fix public app code_template.
    
     - [x] Add Mover to inter-convert numbering schemes: ```AntibodyNumberingConverterMover```
     - [x] Add app that does the conversion: ```antibody_numbering_converter```
     - [x] Add integration test for app
     - [x] Add RosettaScript Integration
     - [x] Test with structures numbered in AHo and convert to Chothia!  Woohoo! Reload the Chothia antibody in Rosetta, test clustering, CDRs, etc.
     - [x] Update intra-cdr numbering database file manually using 2001 AHo numbering paper and the numbering scheme atlas.
     - [x] Test crazy H3 antibodies and thoroughly write unit tests to interconvert all schemes and load back in.
    
    Requested:
    =========
    
    - [x] Change input flag from ```-numbering_scheme_``` to``` _-input_ab_numbering_```
    - [x] Change output flag from ```-output_numbering_scheme``` to ```-output_ab_numbering```.
    - [x] Remove ```_Scheme``` suffix for numbering schemes - at least in terms of string parsing.
    
    Current Use
    =========
    
    Just add the option, ```-output_ab_scheme``` to any antibody app that writes PDBs or the converter app.
    
    Note that the option ```-input_ab_scheme``` instructs which numbering scheme the current input pdb is (and that ```-numbering_scheme``` option has been deprecated in favor of this option).

commit 7b5bf62fea4002c0f3e30412a459b69c95078bca
Merge: 7cbc066 f2621d4
Date:   Fri Sep 9 10:55:18 2016 -0400

    Merge pull request #1590 from RosettaCommons/xingjiepan/move_Graph_from_core_to_utility
    
    Move graph from core to utility

commit 7cbc066119c5a9b47726bd2a5096275439471e09
Merge: fd221c2 5e4b5cd
Date:   Thu Sep 8 22:36:25 2016 -0700

    Merge pull request #1549 from RosettaCommons/everyday847/rna_thread_and_minimize
    
    No integration test changes (save what's expected, e.g. number_of_residuetypes)

commit fd221c21553532c61117ed4a7a4e814c46792859
Date:   Thu Sep 8 16:35:15 2016 -0700

    Updating the Xcode project template file to be compatible with the
    libxml2 in external.
    
    Xcode users: you will need to remove the project file and regenerate it
    using the following command:
    
    $ cd Rosetta/main/source/xcode && rm Rosetta.xcodeproj/project.pbxproj
    && python make_project.py all

commit 04fe2fd313463a27ba6bb8a6076389a61d393411
Merge: dba6351 a81bcc5
Date:   Thu Sep 8 11:51:50 2016 -0700

    Merge pull request #1568 from RosettaCommons/everyday847/better_ERRASER_minimization
    
    All of you who really love refining RNA structures: the first stage of doing so just got a lot faster!

commit dba6351aa665ff0d3eff950a670078170661bf31
Merge: 0f89e0f f719d68
Date:   Thu Sep 8 09:42:30 2016 -0700

    Merge pull request #1584 from RosettaCommons/everyday847/deprecate_n_residue
    
    Merging! We seem to have come to a consensus, after all.

commit 0f89e0f6f76faf7d68e891123fc37610eafc4d7f
Merge: 01a57f1 d33dff9
Date:   Wed Sep 7 16:51:58 2016 -0700

    Merge pull request #1595 from RosettaCommons/everyday847/post_modernization_beauty
    
    Post-modernization beautification

commit 01a57f1001de159f3b3ce074f50b6034f05f869a
Merge: 567e481 f4b8269
Date:   Wed Sep 7 15:05:29 2016 -0700

    Merging actual fix

commit 567e481eb4f6f3d60d972129380253e665f9e10e
Merge: c2abaa4 2187be2
Date:   Wed Sep 7 14:47:36 2016 -0700

    Merge pull request #1594 from RosettaCommons/everyday847/loop_convert
    
    Modernizations, for real this time

commit c2abaa478349e3871704a847a5fff57d11d7a555
Date:   Tue Sep 6 16:44:06 2016 -0400

    Fixing the cxx11thread,serialization build

commit 17bff4be27ded4ed027f390afebf3ae9df349f0b
Merge: fd7733e 466eda8
Date:   Tue Sep 6 14:19:44 2016 -0400

    Merge pull request #1527 from RosettaCommons/aleaverfay/cxx11_as_default
    
    c++11 as default
    
    These commits flip the switch on C++11, so that we can now use its nice features (auto, lambda functions) in developing code, without having to nest that code in hard-to-read #ifdef blocks.
    
    Lots of expected integration test changes -- a lot of low-level utility classes are now going to behave differently, and the compilers themselves are using a different standard meaning they may have to produce different code.

commit fd7733eb89ea33a565b920eba6590a2cc234d850
Merge: 6dace0b 24db7c1
Date:   Tue Sep 6 11:30:26 2016 -0400

    Merge pull request #1583 from RosettaCommons/lqtza/cdr_regex_update
    
    cdr regex in antibody.cc is loaded from the database now

commit 6dace0b774a15197b55060860756a0087e20f00a
Merge: 60f4b54 b492d39
Date:   Mon Sep 5 22:33:13 2016 -0500

    Merge pull request #1588 from RosettaCommons/jadolfbr/packstat
    
    Fix packstat score test.
    
    So, the packstat score test was crazy with the JD2 merge (76 to >100k cycles or something).  Turns out that for packstat to SCORE, it needs to write out a PDB file to the output stream to turn it into a SimplePDB.  This caused the energies to fail when it tried to access the weights DURING scoring (which are now output by default).
    
     * Use StructFileRepOptions to turn off output of the energies table (as well as any pose cache). This should fix the test.
     * Use StructFileRepOptions to remove global setting of OptionSystem data Yay! @aleaverfay
    
    
    Turns out that packstat is only really tested in the score performance test.  If you care about packstat, you should add a proper test for it (and probably refactor it to not output an entire PDB from a pose at each score cycle).
    
    @smlewis @roccomoretti @willsheffler
    
    Thanks for the help in sleuthing Steven!

commit 60f4b548cde5e77656347a83c90cfff885a3b5dc
Merge: e7ebbc5 a2de367
Date:   Sat Sep 3 20:00:13 2016 -0700

    Merge pull request #1199 from RosettaCommons/everyday847/terpenes
    
    Simple addition of terpene support

commit e7ebbc56ce8ab05a8a6d36b1a08bf6d0948d6b77
Merge: f4e430c 28fe898
Date:   Sat Sep 3 00:50:40 2016 -0500

    Merge pull request #1586 from RosettaCommons/smlewis/mmCIFJobOutputter
    
    Fix JD2 profile test perma-fail
    
    Thanks @roccomoretti for pointing this out. The directories changed with the new JD2 integration tests and there was a dependent symbolic link for the profile test
    
    @smlewis

commit f4e430c5bd1a56e8f2f1c9a533e6a132fd8c6ec1
Merge: 6f92f00 9f6aab9
Date:   Fri Sep 2 10:39:29 2016 -0500

    Merge pull request #1575 from RosettaCommons/nikoniko90/exemplar2.0
    
    Changed exemplar generation to create more compact exemplars. Added flags to restore prior functionality, these flags will cause the make_exemplar integration test to fail. Other completely unrelated integration tests and profile tests are failing, but they look to be "usual suspects" that are failing frequently.

commit 6f92f0006be6dba39aee9b78abc43e4a9650e3e2
Date:   Thu Sep 1 19:04:09 2016 -0400

    Fixing link in PyRosetta documentation template

commit ad34a4dacec897d5497c788d9ea89cab6b70b844
Merge: 9f96294 e97c6c0
Date:   Thu Sep 1 17:52:56 2016 -0400

    Merge pull request #1534 from RosettaCommons/Cyrus/mergetarget
    
    From Cyrus via Steven Lewis:
    
    Four items in this PR, mostly from Steven Lewis (@smlewis), with assist from Indigo King (@indigogo):
    
    Cyrus PR 40: smlewis/cyrus/FilterReportAsPoseExtraScoresMover; adds new class to dump Filter values mid-protocol; it seems bizarre that this didn’t exist already and/or isn’t how Filters already worked, but the list didn’t say one existed.
    
    Cyrus PR 39: smlewis/cyrus/re_fix_beta15_catch: When I added the tool to get upset at beta_15 score functions without their requisite command line flag, it worked only for weights files with the .wts extension; now it works extensionless. Praise be to the integration tests, which caught a huge bug in the second version of this (you’re getting the third).
    
    Cyrus PR 36: Trivial fix to the code template for Filters.
    
    Cyrus PR 30: Updates old LoopAnalyzerMover to be RosettaScriptable. Creates LoopAnalyzerFilter, which is what it sounds like. Also Cyrus PR 40 because some of it went into a testing branch after the integration tests caught a bug, and the lack of cxx11 made me sad.

commit 9f962940a6b56a7ffa84cc0c23c0b2c5acf49601
Merge: 8a08f71 423fd71
Date:   Thu Sep 1 12:50:01 2016 -0700

    Merge pull request #1587 from RosettaCommons/everyday847/fix_cartbonded_bug_i_created
    
    Don't exit early if called with bad atom ids

commit 8a08f7173240c73641349c5ca3575f5136c96d86
Merge: 5f4f34f 04f248e
Date:   Wed Aug 31 20:20:55 2016 -0700

    Merge pull request #1580 from RosettaCommons/everyday847/beta_bb_app
    
    Some functionality for working with beta amino acids

commit 5f4f34fdc28c9ab99e845c5f9c21114e4eb4389e
Merge: a8a15af b0d66bb
Date:   Wed Aug 31 16:49:51 2016 -0700

    Merge pull request #1585 from RosettaCommons/calebgeniesse/everyday847/stepwise_performance
    
    Small performance boost to stepwise

commit a8a15afd9455efd21c49b01cc5c2838aa7af6d5f
Merge: cfe75a7 ce48681
Date:   Wed Aug 31 13:05:41 2016 -0500

    Merge pull request #1071 from RosettaCommons/smlewis/mmCIFJobOutputter
    
    mmCIF JD2 output compatibility - chemXRW leftover
    Steven Lewis and Jared Adolf-Bryfogle
    
    
    Currently, cif output is supported directly by cif_writer.hh, but not by JD2.  This adds classes to enable that, plus lots of other smaller changes in extra output, dump pdb, etc.
    
    mmCIF JD2 Options
    ============
    
    Two options will now control JD2 and mmCIF:
    -out:mmCIF and -out:mmCIF_gz
    
    Output Options
    ============
    Extra PDB and mmCIF output is now controlled through these options (listed with their current defaults):
    
    -output_pose_energies_table true
    -output_pose_cache_data true
    -output_pose_fold_tree false
    
    
    mmCIF Extra Tables
    ===============
    Extra output is now refactored to be part of SFR and extracted in PoseToSFRConverter (as it should be) and can be output by the CIF writer as well.  As far as we can tell, extra tables are ignored by programs, including PyMol.  SO we should be in the clear. Each extra set of output is a new table for mmCIF.  These are controlled by options, some of which only print out in JD2, as before, or are only output if the SFR has this info.
    
    These new tables consist of the following:
     - pose_energies
     - pose_cache_data
     - pose_comments
     - rosetta_remarks
     - rosetta_additional
    
    The rosetta_additional table has two columns - type and output.  Thats it.  For now, the fold_tree is one type if we output it, and etc is another type for additional_string_output not covered by the tables above.
    
    The Pose energies and cache table can be -not- output to a cif through options above.  Alternatively, -cif_extra_data_separate_file specifies to put the scores in a separate file instead of in the cif file.
    
    mmCIF Line Length
    ===============
    -CIF files will have the 80 line length.  It seems that the same cifparse file is used to read in and output CIF files, and it looks like you need to specify the line length in both.  I'm not sure how EXTERNAL programs will respond to cif files having a maximum line length of the computer writing it out.  It would be nice, but I am tabling this.  What needs to happen, is that it changes with the PDB directly!
    
    Additional Changes
    ==============
    dump_pdb now does not have an available function where you can pass a 'tag' string, which, in reality, does absolutely nothing.  This is fixed in every file that passed this bogus 'tag'.
    
    Test Changes
    ==========
    From what Steven and Jared can tell, we are dealing with purely cosmetic changes here for the integration tests.  An extra line ending separating [extra-pdb-output] components (that were before one giant string internally).
    
    Most deletions of lines are just lines moving around in a file.  Some integration tests have their pose energies table DISAPPEAR, instead of appear - but the old state was unscored poses with empty energies tables, so that loss is still cosmetic.
    
    Please look over your own integration tests just to double check.
    
    Happy Wednesday!

commit cfe75a7278b6aeda897d24c35bbc9a2f012eb1ba
Merge: 40ccfaf 64f1edc
Date:   Wed Aug 31 13:29:53 2016 -0400

    Merge pull request #1573 from RosettaCommons/revert-1572-revert-1571-sofibali/sofia_summer_work
    
    Reinstate "Sofibali/sofia summer work"
    
    carbohydrate test changes expected

commit 40ccfaf8273337b4eb91cd59f05ccbfceef78c87
Merge: 47cd4c5 56310b3
Date:   Tue Aug 30 16:18:01 2016 -0500

    Merge pull request #1574 from RosettaCommons/roccomoretti/mover_status_doc
    
    Add in-code documentation for MoverStatus codes
    
    Also add error handling for unused MoverStatus code (MS_FAIL) in JD2.

commit 47cd4c594b62090acc955c9283be26eeb834ce29
Merge: 1b99e81 29a0075
Date:   Tue Aug 30 09:47:34 2016 -0700

    Merge pull request #1576 from RosettaCommons/dimaio/mg_cartmin_issue2
    
    This PR addresses the same issue in #1566 (unfortunately, that PR did not completely fix the problem), with bondangle/bondlength minimization of Mg-containing poses. The issue arises due to the input_stub logic selecting three collinear atoms to build the stub.
    
    This PR fixes this issue by choosing alternate atoms if the selected stub atoms are collinear.

commit 1b99e817685751799ae5524c169ce6cbef65279f
Merge: 5c02664 2ce48e8
Date:   Mon Aug 29 15:27:26 2016 -0700

    Merge pull request #1565 from RosettaCommons/hahnbeom/cart_bonded_update
    
    Hahnbeom/cart bonded update

commit 5c026642365e0ca8b9b908f730ea74b65cfceaae
Merge: 4039cd0 3d6f03b
Date:   Mon Aug 29 13:26:29 2016 -0700

    Merge pull request #1569 from RosettaCommons/everyday847/handle_insertions_pdbinfo
    
    Unit test added--note that I'm setting up the unit test so that it tests only the unit I'm interested in, i.e., how this function works on the PDBInfo. So I'm setting up a PDBInfo with the exact defect I want to repair and then repairing it. Actually inserting a residue via a call from Conformation, then repairing the result, would be an integration test!

commit 4039cd0a57142b2e934053921f99ad9bf3ee9418
Merge: 773e8f4 6437f22
Date:   Mon Aug 29 09:55:37 2016 -0700

    Merge pull request #1545 from RosettaCommons/tlinsky/ppi_integration_test
    
    Add integration test for PPI benchmark

commit 773e8f42fe3f70f8f509cd9a67920a2815b170b2
Merge: 8c9420b 77ccaac
Date:   Mon Aug 29 03:33:35 2016 -0700

    Merge pull request #1572 from RosettaCommons/revert-1571-sofibali/sofia_summer_work
    
    Revert "Sofibali/sofia summer work"
    
    This merge caused the following problems:
    
    -    The PyRosetta C001_Carbohydrates_Demo01 unit test failed to run.
    -    Several integration tests were complaining about the INAME line in the changed params file (a typo).
    -    The carbohydrates integration test failed to run.

commit 8c9420b7271371a14d1ffa7807240908a565851f
Merge: 491a10f 32feeb4
Date:   Sun Aug 28 17:36:43 2016 -0400

    Merge pull request #1571 from RosettaCommons/sofibali/sofia_summer_work
    
    Sofibali/sofia summer work Modified carbohydrate params files

commit 491a10fe65302e8872006f8b3325c54a683e685b
Merge: 06e7b35 bc66957
Date:   Sun Aug 28 12:27:14 2016 +0200

    Merge pull request #1364 from RosettaCommons/ch.norn@gmail.com/evolution
    
    Ch.norn@gmail.com/evolution. Contains code for simulating evolution: NucleotideMutatationMover to mutate between amino acids, but restrained by the codon table (single nucleotide mutations), and EvolutionaryDynamicsMover to accept and reject mutations, not according to the boltzmann function, but according to evolutionary dynamics.

commit 06e7b35e1ca0aa940b590d137f58bfaced3b0759
Merge: 1a29679 9835e95
Date:   Sat Aug 27 09:43:41 2016 -0700

    Merge pull request #1570 from RosettaCommons/everyday847/phosphohis
    
    Parameters for phosphorylated histidine

commit 1a29679b2c5960a44cf29ad95487952f80183e7e
Merge: cf0b69c 73d5727
Date:   Fri Aug 26 21:35:24 2016 -0400

    Adding platform info to PyRosetta-4.documentation release path

commit cf0b69ca99a0bba3acab52258475dc1e132855da
Merge: 4d2e945 6ec0c27
Date:   Fri Aug 26 16:27:22 2016 -0600

    Merge pull request #1562 from RosettaCommons/sergey/binder
    
    Adding release.PyRosetta4.documentation test. Refactoring rosetta release source/binary tests so they use new release API.

commit 4d2e9450373fd7aec50978bb64977a313042cf29
Merge: 5ecd351 475530c
Date:   Fri Aug 26 16:36:52 2016 -0400

    Merge pull request #1567 from RosettaCommons/dougrenfrew/2-amino-3-methylamino-propanoic_acid
    
    Adding 2-amino-3-methylamino-propanoic acid (also know as beta-methylamino-alanine, BMAA) to the NCAAs.

commit 5ecd3518d9037f354449811d5f7e9033bc895690
Merge: 5234551 702dadd
Date:   Fri Aug 26 10:37:22 2016 -0400

    Merge pull request #1563 from RosettaCommons/dougrenfrew/C-linked-glycosolation
    
    Adding C-mannosyl tryptophan patch. TRP can now be mannosylated at the delta-carbon.
    
    Carbohydrate integration test is expected to change.

commit 5234551a7ae3088a059c0f4c529ab17e84cfe67f
Merge: b3140f6 98a0ce8
Date:   Fri Aug 26 00:04:11 2016 -0700

    Merge pull request #1564 from RosettaCommons/vmullig/calc_pnear
    
    Minor bugfix to BinTransitionData, and small tweak to PNear output in simple_cycpep_predict (MPI mode)
    
    
    
    The BinTransitionData module was using utility_exit instead of throwing an exception, which brought down MPI jobs since it couldn't be handled by a try/catch block to kill the current job without bringing everything down. Also, PNear output was happening even if no native structure was provided.
    
    Minor, cosmetic changes expected to MPI-mode integration test output.

commit b3140f63790e669a1d94a9ab6f4efd15dc18a2ce
Merge: 1d98440 3c3bacc
Date:   Thu Aug 25 18:35:11 2016 -0700

    Merge pull request #1560 from RosettaCommons/yhsia/quasi
    
    Yhsia/quasi

commit 1d98440e2877fc1b70f8a19fa5716774c6bf6e32
Merge: ce62d10 7fe965d
Date:   Thu Aug 25 17:01:32 2016 -0700

    Merge pull request #1566 from RosettaCommons/dimaio/mg_cartmin_issue
    
    Rosetta crashes when bondangles were minimized with an Mg-containing pose.  The issue arises due to the input_stub logic selecting three collinear atoms to build the stub. As a quick and dirty fix, reorder the Mg atoms so this does not happen.

commit ce62d10b3afc5a9d2b6096dec750755a9338302c
Merge: 576a820 66ba686
Date:   Thu Aug 25 06:03:51 2016 -0700

    Merge pull request #1557 from RosettaCommons/tlinsky/fix_bridgechains_integration
    
    Make BridgeChains outputting pdbs off by default.  Should fix integration test

commit 576a82073736dd4167ba214f3c8aa6d773dbacf5
Merge: d9fd19a 7eed4a1
Date:   Thu Aug 25 02:30:25 2016 -0700

    Merge pull request #1558 from RosettaCommons/vmullig/calc_pnear
    
    Adding support for calculating PNear (funnel quality metric) to SimpleCycpepPredictApplication_MPI.
    
    This will eliminate a manual calculation step from the SSMs that @hssnzdh2 and I want to do on Blue Gene.
    
    Tasks:
    -    Add calculation.
    -    Add output.
    -    Add options for controlling Gaussian breadth (lambda) and Boltzmann temperature (kbt).
    -    Check integration test changes in MPI mode. (New output lines should appear.)
    -    Beauty.
    -    Documentation.

commit d9fd19ad2d3c48863626a6a9e58599feeda3ae85
Merge: d96fc82 152403e
Date:   Wed Aug 24 14:27:55 2016 -0700

    Merge pull request #1554 from RosettaCommons/davidekim/ss_updates
    
    Davidekim/ss updates

commit d96fc823f03680e4b79ab3c22ed98082b6799714
Merge: d6cc30c 01b157a
Date:   Wed Aug 24 13:36:09 2016 -0700

    Merge pull request #1556 from RosettaCommons/vmullig/sample_cispro
    
    Add an option to simple_cycpep_predict to sample cis-omega values preceding D/L proline
    
    This can be expanded later to include positions preceding N-methyl positions, too.
    
    Tasks:
    
    -    Add option.
    -    Add code to do the sampling (the sample_cis_peptide_bond GeneralizedKICPerturber).
    -    Add integration test.
    -    Documentation.
    -    Beauty.
    
    All tests pass except for the following integration tests:
    
    -    bridge_chains (known instability that Tom's fixing)
    -    simple_cycpep_predict_cispro (just added)

commit d6cc30cb0ce7f73f51c81c22ca6e6204f4e1813d
Merge: 16041aa 0e7cdb2
Date:   Wed Aug 24 09:47:54 2016 -0700

    Merge pull request #1551 from RosettaCommons/tjbrunette/fix_link_res
    
    fixes seg fault in Rotamer links. Also, adds the ability to define template rotamers.

commit 16041aaa72eda3006ef26975ea1ce5b98fa8859d
Merge: cae4c00 3ae6cdc
Date:   Tue Aug 23 18:15:57 2016 -0700

    Merge pull request #1555 from RosettaCommons/hahnbeom/fix_symm_residue_selector
    
    fixing error in integration test "symmetrical_residue_selector"