commit f30827e2f49ecd83f073860286177e31de14a6db
Merge: 3d170be 2770435
Date:   Wed May 3 19:57:48 2017 -0700

    Merge branch 'master' of github.com:RosettaCommons/main

commit 3d170beb9f0fa0a4401cd37c0b0bbbe48e16fab0
Date:   Wed May 3 19:38:40 2017 -0700

    Checking in updated reference weights for beta_nov16.  These weights were fit using a novel scheme in which both native recovery and stability ddG calcs (Kellogg set) were optimized against, however, the native recovery tests had reference weights modulated to account for non-stability-related biases in AA composition of native proteins.

commit 1c192a93830f2b21c531affb75fce937513c0670
Date:   Wed May 3 19:21:48 2017 -0700

    Bugfix for make symmdef file in helix mode.

commit ead037f78b65328a200addb43bd6140b40700fb1
Merge: da548cf 057ce1c
Date:   Wed May 3 13:50:41 2017 -0600

    Merge pull request #2226 from RosettaCommons/sergey/binder
    
    Updating fmt lib, this should fix RosettaCommons/binder#19. Updating Binder so it generate bindings for basic_stringstream.

commit da548cfbb07844a7c674239fd09c0aeea55d22a7
Merge: bab9bc1 e04f11e
Date:   Wed May 3 07:53:36 2017 -0400

    Merge pull request #2225 from RosettaCommons/guffysl/constraint_generator_loader_pr
    
    Adds a data loader for ConstraintGenerator objects. They can now be specified in their own CONSTRAINT_GENERATORS block in a RosettaScript and can be passed to AddConstraints using the constraint_generators option. Also adds unit tests for several other data loaders.

commit bab9bc1b63fe4aa02c293e55239f8abb11ff4d55
Merge: a6f72d9 7c2f772
Date:   Tue May 2 15:32:35 2017 -0700

    Merge in pilot app bugfix to master.

commit a6f72d9450c25febff462c9203fc6703e58ec372
Date:   Tue May 2 14:46:30 2017 -0700

    Bugfix to fasol pilot app for when lk_ball is off.

commit b399b509c82010a64422bea5775b36f0d5d6729b
Merge: 867aa07 09c9404
Date:   Tue May 2 13:31:14 2017 -0500

    Merge pull request #2221 from RosettaCommons/roccomoretti/fixedarray_static_compile_fix
    
    Fix static mode GCC 4.9 error in fixedsizearray1.hh
    
    GCC isn't liking using a Size as a C-style array index in this situation. Do an explicit conversion to int first.
    
    Thanks to Aliza Rubenstein for pointing out the issue.

commit 867aa07ea65dae81ff1beee0586571b60948dffe
Merge: 64c90c8 bfc4cfc
Date:   Mon May 1 21:34:15 2017 -0600

    Merge pull request #2212 from RosettaCommons/sergey/binder
    
    1. Updating Binder to support binding for template member functions.
    2. Adding support for PyRosetta serialization build.
    3. Adding procedure to explicitly instantiate serialization save/load function during binding generation phase.
    4. Small refactoring to Rosetta source to allow easier extraction of instantiation macros.
    5. Adding support for Testing Server serialization build.
    6. Adding support for std::shared_ptr<void> types.

commit 64c90c89271ea96b863085358daee1510ee9499f
Merge: c3a37f8 c5eee7b
Date:   Mon May 1 19:50:26 2017 -0700

    Merge pull request #2220 from RosettaCommons/everyday847/hotfix_two
    
    our great national nightmare is over

commit c3a37f8b76cca71c1aef189cc04798594193aa71
Merge: d05722d6 5331125
Date:   Mon May 1 10:09:32 2017 -0700

    Merge pull request #2219 from RosettaCommons/everyday847/hotfix_integration_tests
    
    Hotfix integration tests

commit d05722d638b276fff3ce6e978680ddcaebacabf2
Merge: 3456b10 c939ff2
Date:   Sun Apr 30 14:39:33 2017 -0700

    Merge pull request #2217 from RosettaCommons/everyday847/fixup_lores_optimization
    
    Fix up lores optimization

commit 3456b10982d7c9312941673cdb01cd44b287bf41
Merge: e8e7858 a3e26ba
Date:   Sat Apr 29 13:16:15 2017 -0700

    Merge pull request #2214 from RosettaCommons/everyday847/atom_alias_lcaa
    
    ATOM_ALIAS lines for L-CAAs

commit e8e7858ab7c4ac3a52be02a8a433ef26692f7890
Merge: f564332 11b0250
Date:   Sat Apr 29 11:11:38 2017 -0700

    Merge pull request #2213 from RosettaCommons/everyday847/autocyclize
    
    Automatically set up cutpoint variants for LINK-cyclized poses

commit f564332fcd2a88c7b80237149bda3f2610b4ece3
Merge: e3f2cae 87c3a57
Date:   Fri Apr 28 01:37:56 2017 -0700

    Merge pull request #2141 from RosettaCommons/vmullig/xsd_types_for_taskoperations
    
    Add an XSD type for comma-separated task operation lists
    
    It is useful for a potential GUI to be able to differentiate between a Rosetta module that takes a general string and a Rosetta module that takes a comma-separated list of pre-defined task operations.  This adds an XSD type for task operation lists separated by commas.
    
    Tasks:
    - [x] Add the type (xsct_task_operation_comma_separated_list).
    - [x] Update the utility functions in protocols/rosetta_scripts that parse task operations lists to use xsct_task_operation_comma_separated_list instead of xs_string.
    - [x] Find and update any additional movers, filters, etc. that take comma-separated task operations lists, being mindful of those that might take multiple lists.
         - [x] Check in core.
         - [x] Check in protocols.
         - [x] Check in devel.
         - [x] Check in apps.
    - [x] Check tests.
    - [x] Think about the case of something that might take a _single_ task operation.
    - ~~Think about the case of things that take task factories.~~ --> Put off for a future pull request.
    - [x] Also: cherry-pick in some more utility functions in utility/xsd_util/.
    - [x] Beauty.
    
    Ultimately, I'll do this for things that take residue selectors, score functions, movers, filters, etc.
    
    **Note:** This does _not_ add any GUI elements to the Rosetta codebase.  This is just utility code that will make GUI development easier down the road.

commit e3f2cae19743fcd2ee7452da25072bb3b4a639f9
Merge: 8a38ce2 25c56a9
Date:   Thu Apr 27 12:09:33 2017 -0600

    Merge pull request #2209 from RosettaCommons/sergey/f
    
    Adding set/get global output_prefix functionality to Tracer

commit 8a38ce21d15c4a997c56983e9698cdfb19a549bf
Merge: dd56636 d3766fb
Date:   Wed Apr 26 22:41:59 2017 -0700

    Merge pull request #2208 from RosettaCommons/weitzner/match_xml_test
    
    Adding '-jd2:failed_job_exception false' to the match_xml integration test command

commit dd5663606b0dab9b2f678906bc0fac4f4ac0044c
Merge: 06c81a7 9e79e27
Date:   Wed Apr 26 16:06:50 2017 -0700

    Merge pull request #2207 from RosettaCommons/weitner/fix_calibur_test
    
    A missing '-' before 'nodally' causes the chain clustering test to fa…

commit 06c81a707244fa2d0558e2ddaab9e620acc86f1e
Merge: 87b1448 7889b7c
Date:   Tue Apr 25 21:54:22 2017 -0700

    Merge pull request #2190 from RosettaCommons/weitzner/match_cst_format
    
    Weitzner/match cst format

commit 87b144852b1670541cca9099b3a8dd2fa288a55b
Date:   Tue Apr 25 13:44:22 2017 -0700

    beautify ShortBackrubMover.cc

commit bd8403eaf53922ad96aebb49f379c89fdb1a4740
Merge: b4d9eff 709f61c
Date:   Mon Apr 24 13:34:06 2017 -0700

    Merge pull request #2194 from RosettaCommons/anumazam/fixbackrub
    
    Fix unsigned int bug

commit b4d9eff21f9a491b68761397a4f4fad436822af4
Merge: c1778f2 c4cf583
Date:   Mon Apr 24 09:23:57 2017 -0500

    Merge pull request #2183 from RosettaCommons/roccomoretti/restype_destructor_observer
    
    Add ResidueType destruction observer system
    
    For classes (mainly in scoring) which need to cache per-ResidueType data, but want to do it in a way that doesn't preserve the lifetime of the associated ResidueType, they can cache the data based on the (raw) pointer to the ResidueType. However, if the ResidueType is deleted, there's issues with an invalid pointer sticking around.
    
    To get around this, add an observer system (like the observer system in Pose), which is specifically for informing those classes about ResidueType destruction, so they can appropriately clear their cache of the soon-to-be-deleted ResidueType reference. This approach was decided on after a short discussion with @aleaverfay.
    
    In addition to cleaning up some raw ResidueType pointer uses which were not needed (which involved adding pointer accessors to Pose/Conformation/Residue in addition to the reference accessors), the following classes were hooked into the observer system: LKB_ResidueInfo, CartesianBondedEnergy, FA_ElecEnergy, FACTSPotential, and FullatomCustomPairDistanceEnergy.
    
    This fixes issues #2006 and #2021 .
    
    The only test changes expected are the central_class_modification, and a number of cosmetic changes resulting from when count pair data gets loaded.

commit c1778f28561486e69215a1bf752a671f431a1156
Merge: 885a843 eb525b1
Date:   Mon Apr 24 15:58:37 2017 +0300

    Merge pull request #1860 from RosettaCommons/orlypolo/DisulfideInsertionEnergyCheck
    
    Orlypolo/disulfide insertion energy check

commit 885a843dff22316f2070dbfca04fc95bee47c0bb
Merge: 20a5a5c df176a4
Date:   Sun Apr 23 23:51:21 2017 -0700

    Merge pull request #2196 from RosettaCommons/vmullig/gabe_science
    
    Add a filter to compute the longest continuous stretch of polar residues in a pose or selection
    
    Requested by @grocklin .
    
    Tasks:
    - [x] Add the filter from code templates.
    - [x] Write parse_my_tag:
         - [x] Option to exclude terminal stretches.
         - [x] Filter high or low.
         - [x] Cutoff.
         - [x] Optional residue selector.
    - [x] Write XSD function.
    - [x] Write apply function.
    - [x] Add ResidueSelector support.
    - [x] Add option to treat glycine as a polar residue.
    - [x] Unit tests:
        - [x] Counting in a pose.
        - [x] Excluding termini.
        - [x] Counting in a selected region.
        - [x] All of the above with multiple chains.
    - [x] Integration test.
    - [x] Documentation.
    - [x] Beauty.

commit 20a5a5c29594b52ad381805411845dfd22349d00
Date:   Sun Apr 23 23:44:47 2017 -0700

    Beautifying files that are currently causing beautifier failure in master.

commit ed814bb236038ef6ecb8bdd5ebb39206fb5760dd
Merge: 6028bc0 6a17b00
Date:   Thu Apr 20 21:05:17 2017 -0700

    Merge pull request #2150 from RosettaCommons/sboyken/improve_hbnet
    
    improve hbnet

commit 6028bc076a19d0acf9e6d93e4eb14aa12dc910a7
Merge: d1b7279 2633428
Date:   Thu Apr 20 19:58:36 2017 -0700

    Merge pull request #2195 from RosettaCommons/dimaio/lk_bridge_deriv_fix
    
    Fix deriv discontinuity in lk_ball_bridge.  Score changes in beta_nov16 expected.

commit d1b7279819db552e916124694e6ea05ff9fb0ea4
Date:   Thu Apr 20 16:23:27 2017 -0500

    Fix glycan_relax integration test command file
    
    There was a spurious backslash, resulting in odd grep behavior

commit 972acb0608f0e00f70932dcc0757a45e57c0a081
Date:   Thu Apr 20 14:12:35 2017 -0400

    beautifying bad lines added by Mayukh

commit 706d425d4e9ac6720f68114fe0cedd9898fd19af
Date:   Wed Apr 19 14:56:14 2017 -0700

    Hotfix to serialization build

commit d637c167c3939648a10a9df06a5dbbc104ecf64d
Merge: b511374 3ced404
Date:   Wed Apr 19 09:59:35 2017 -0400

    Merge pull request #2191 from RosettaCommons/JWLabonte/sugars/database
    
    Carbohydrates: A gift for @raemisch
    
    All unit tests pass. Beautifier is complaining about code that isn't ugly. Integration test changes are all reporting on a new ResidueType.

commit b511374b3b7d3394e5ef71ba5251becf84050386
Merge: 4fbaf10 6553c90
Date:   Tue Apr 18 16:11:05 2017 -0700

    Merge pull request #2178 from RosettaCommons/everyday847/bp_classification
    
    A tiny bugfix modification to model and native base pair statistics

commit 4fbaf1079be57d86cfd557c4802af84e5dd05bfc
Merge: c44784f d5d4526
Date:   Tue Apr 18 11:10:58 2017 -0700

    Merge pull request #2187 from RosettaCommons/weitzner/fix-hbond-set
    
    Fix an issue that could produce a segfault in residue_hbonds

commit c44784f56d4109f04af2cd48b8b68cb571df40d3
Merge: 7db6f23 bdfcc79
Date:   Tue Apr 18 08:08:21 2017 -0700

    Merge pull request #2186 from RosettaCommons/weitzner/more-py3
    
    And... now the unit tests also run python 3

commit 7db6f2322d225b5ff6df844b8f895c02d320cedf
Merge: 7aecc1b e459215
Date:   Tue Apr 18 10:37:37 2017 -0400

    Merge pull request #2185 from RosettaCommons/mchakra8/UDP
    
    Carbohydrates: Adding UDP-sugars
    
    This merge will add UDP parameters to load UDP-sugars and non-conjugated UDP.
    
    All unit tests passed. All integration tests indicate a change in output due to the addition of a residue type (with the exception of the Carbohydrate integration test, where the output is as expected).

commit 7aecc1b4d1961333280b48ab652a9ed8a3bca380
Merge: 6167457 7cf71c8
Date:   Mon Apr 17 15:11:43 2017 -0400

    Merge pull request #2171 from RosettaCommons/guffysl/hbond_residue_selector
    
    This commit adds two new residue selectors, BondedResidueSelector and HBondSelector.
    
    BondedResidueSelector requires either an input residue selector or list of residue numbers and selects all residues with chemical bonds to the input set. HBondSelector optionally takes an input residue selector or list of residue numbers. If provided, it selects all residues that form hydrogen bonds with residues in the input set given that those hydrogen bonds meet a specified energy requirement (default -0.5 REU). If no selector is provided, all residues in the pose that form hydrogen bonds are selected. By default, backbone-backbone hydrogen bonds are ignored.

commit 61674572ec6cdb89c254fd9746a334630df8bc1a
Date:   Sun Apr 16 16:54:32 2017 -0400

    beautifying

commit 93759c10b0b747506c84fcd69eff175dc14d86f5
Merge: 19e433d cff73d1
Date:   Sun Apr 16 08:55:30 2017 -0700

    Merge pull request #2181 from RosettaCommons/weitzner/more-py3
    
    Weitzner/more py3 -- a beautification test (related to LK Ball) and one integration test (ligand_database_io ) failed on this PR, but I only touched some python code related to testing, so I'm merging this thing in.

commit 19e433d24038f0d50c7f5bc2004687a505989a26
Date:   Sat Apr 15 13:08:00 2017 -0700

    Making the integration test script work with pyhon 2 and 2. Also making clang the default compiler on macs.

commit 10c7c9bbb01c0a082956d55bf06274134c290006
Merge: 2ffd2c1 076b89e
Date:   Sat Apr 15 12:40:15 2017 -0700

    Merge pull request #2180 from RosettaCommons/weitzner/py3-compat
    
    Weitzner/py3 compat

commit 2ffd2c1c7e600daf94e94920cbfe92f83e9796a3
Merge: f1f12f0 069d56a
Date:   Fri Apr 14 22:42:33 2017 -0600

    Merge pull request #2179 from RosettaCommons/sergey/f
    
    beautifying

commit f1f12f001f6f5ffb193147ce5174fb2be0b92365
Merge: 3e6426b 7a16b5d
Date:   Fri Apr 14 18:57:32 2017 -0700

    Merge pull request #2125 from RosettaCommons/dimaio/more_beta_nov16_bugfixes
    
    This pull request fixes several minor bugs with beta_nov16 (mostly lk_ball_bridge):
    
    1) The ramp widths for lk_ball_bridge and lk_ball (which are different) were used incorrectly in places, ultimately leading to derivative discontinuities in lk_ball_bridge.  Also modifying ramp widths to best match the shape of lk_ball_bridge that was previously used.
    2) The heavyatom-heavyatom interaction radius for lk_ball_bridge is a tiny bit larger than that of fa_sol; reusing fa_sol's minimizer graph missed some interactions.  Modifying to have lk_ball create its own minimizer graph.
    3) countpair was not correctly applied for lk_ball_bridge_uncpl in scoring (but was in packing/minimization) ... this has also been corrected.  Also fixed a small countpair inconsistency with lk_ball across non-polymer connections.
    
    This change only effects beta_nov16 scoring with one exception: beta_nov15 will report slightly different scores in disulfide-containing structures.  This leads to several beta_nov15 integration test failures: disulfidize_beta_cys, genkic_ramaprepro_sampling, simple_cycpep_predict_tbmb, ppi_*

commit 3e6426b7509c2c54cfb469d3bc8458097ee9c79f
Merge: 856195a b652cd0
Date:   Fri Apr 14 17:06:12 2017 -0600

    Merge pull request #2175 from RosettaCommons/sergey/f
    
    Moving bison files into separate dir so they do not confuse qmake

commit 856195aabe59b68600cd346ec32eab607b2dc523
Date:   Thu Apr 13 17:41:45 2017 -0400

    beautifying

commit 2d34bec79b8ff8c12d5bbc9c2dd3d0c77118e325
Date:   Thu Apr 13 17:26:42 2017 -0400

    Updating ‘beautifying’ test log

commit 067c5dce24aa88723a88bedf3111892b32eb26cb
Date:   Thu Apr 13 17:17:13 2017 -0400

    beautifying

commit 6e5f46ce56f80371f34adda4e7151e184723f746
Date:   Thu Apr 13 16:10:19 2017 -0400

    dummy commit

commit 8e3d56b73b55065f044c8117cc41bb7ec4b492a4
Date:   Thu Apr 13 15:46:05 2017 -0400

    Updating 'beautify' test so it now use user info for commit author

commit 7ddf0b1b8e3a3279d0317e07661165f8e5e96b5b
Merge: c27ba1f 7db9d2a
Date:   Thu Apr 13 14:38:25 2017 -0400

    Merge remote-tracking branch 'origin/master' into benchmark

commit c27ba1f5540258cc68e620b373703a981d02c050
Date:   Thu Apr 13 00:14:34 2017 -0400

    beautifying

commit d4c816693cebd545ae8445f4f345e1c1166dd9c7
Date:   Wed Apr 12 23:54:18 2017 -0400

    Adding output of ‘git diff’ to beautify test log

commit 08956e26da20500eef459040a1b469789f73ecd8
Date:   Wed Apr 12 18:22:40 2017 -0400

    beautifying

commit c9ef9221e2e177b1a67328930eb0e851c201cc90
Merge: f2642a8 91d43f0
Date:   Wed Apr 12 18:22:20 2017 -0400

    Merge commit '91d43f0b1efc5c8d4906a2637450544b20d717c6' into benchmark

commit f2642a8183ab3a7dc3bf88e20a4c1e6411a93989
Merge: ba51e67 6099aae
Date:   Wed Apr 12 13:38:09 2017 -0600

    Merge pull request #2163 from RosettaCommons/sergey/binder
    
    Updating PyRosetta Job Distributer and MPI Job distributer

commit ba51e675f75aa8b96e1b9e48a27269bced1d6f02
Merge: f146a71 a7b712a
Date:   Wed Apr 12 10:43:55 2017 -0400

    Merge pull request #2165 from RosettaCommons/aleaverfay/npd_hbond
    
    Fix off-rotamer-packer bugs w/ LK_Ball term

commit f146a7183f725d84d09bfe830e890bd6a8c7382c
Merge: 961fb96 e2c3e4c
Date:   Tue Apr 11 15:36:24 2017 -0700

    Merge pull request #2170 from RosettaCommons/rhiju/hotfix_polymerbondedenergycontainer
    
    hotfix to PolymerBondedEnergyContainer

commit 961fb96ae3a0b4887bdf50a8d1a682f047c78f2b
Merge: 3d8292e 4fcd948
Date:   Tue Apr 11 08:01:51 2017 -0400

    Merge pull request #2168 from RosettaCommons/aleaverfay/rotsets_offsets_bug
    
    bugfix w/ deleting and adding rotamers
    
    There's a bug in the way the RotamerSets class handles the addition
    and deletion of Rotamers from the RotamerSet objects it holds. This fix here
    cause the RotamerSets object to make sure its rotamer-count and offset data
    is up to date before setup_for_packing is called, (and therefore, before
    simulated annealing begins).
    
    I had been really hoping this bugfix would have turned up more integration test changes, as I have another PR in the works (#2165) that produces quite a few trajectory changes, and I'm not yet certain why.

commit 3d8292ea8d4da2341929615130fc3293b1c4ee86
Merge: 2948c6a 02a0fbf
Date:   Tue Apr 11 02:08:48 2017 -0700

    Merge pull request #2169 from RosettaCommons/vmullig/fix_zerolength_bug
    
    Fixing an error in Conformation::rebuild_polymer_bond_dependent_atoms
    
    Fixing an error in Conformation::rebuild_polymer_bond_dependent_atoms() in the edge case that this function is called on an open terminus.  (This was creating problems with using the DeclareBond mover to create terminal disulfide bonds).
    
    @csykang : This should fix the problem with your script, and allow you to build disulfide-cyclized peptides without extra tail glycine residues.

commit 2948c6af1560d82c8ad07c4a374e45a4f78a1662
Merge: a257fe0 d0cba13
Date:   Mon Apr 10 23:11:52 2017 -0700

    Merge pull request #1508 from RosettaCommons/vmullig/support_nmethyl
    
    Adding support for N-methyl amino acids
    
    # **Background and Rationale:**
    
    N-methyl amino acids can be used during peptide synthesis to confer various desirable properties on a synthetic peptide.  N-methylation removes a hydrogen bond donor, in many cases promoting solubility in hydrophobic environments and helping with membrane permeability.  It also greatly alters the conformational preferences of an amino acid residue.
    
    ![nmethylpeptide](https://cloud.githubusercontent.com/assets/4205776/17455648/a2aa4124-5b73-11e6-8f32-9e7c63ae7ef2.png)
    
    We want to be able to design with N-methyl amino acids, and this pull request is intended to add support for:
    - Modelling N-methyl amino acid geometry (adding a patch for N-methylation).
    - Properly scoring N-methyl amino acid-containing peptides (permitting the loading of custom Ramachandran and p_aa_pp tables for N-methyl amino acids).
    
    Following the implementation of PackerPalettes (pull request #1047), a future pull request will add:
    - Support for designing with N-methyl amino acids (_i.e._ getting the packer decide whether to N-methylate a position or not).
    
    **Tasks (note that many of these changes have already been merged into master in incremental merges):**
    - [x] Add a N-methylation VariantType.
    - [x] Add a patch for this.
      - [x] Figure out a way to allow custom rama_prepro maps to be specified for the patched amino acids.
      - [x] Figure out a way to allow custom rotamer libraries to be specified for the patched amino acids.
      - [x] Debug the rotamer libraries -- there's something wrong there.
    - [x] Add support for lazily loading custom scoring tables.
      - [x] For _rama_prepro_.
        - ~~Think about thread-safety.~~ <i>Put off to a future pull request.  The lazily loaded objects are in ScoringManager, which contains a bunch of stuff that needs to be made thread-safe.  It's all in one place, in any case.</i>
    - [x] Expand mainchain scoring tables to permit N-dimensional data (for future support for beta-amino acids).
    - [x] Add support for specifying the dimension, resolution, and grid offset in the database file (so that we're no longer hardcoding 5-degree bins and whether we have grid points in bin centres or on edges).
    - [x] Add support for comments in the database file.
    - [x] Comment the database files explaining the columns.<br/>
      ~~\- Possibly add support for variable-resolution mainchain torsion tables (_e.g._ with finer sampling in alpha-helix and beta-strans wells).  This has been talked about in the past, and now might be a time to do it.~~ _Beyond the scope of this pull request, though it should be easier to do now._
    - [x] For all of the above, add a MainchainTorsionScoringTable class.
      - [x] Support symmetrization of gly/ACHRIAL tables.
      - [x] Support polycubic interpolation.<br/>
      - ~~Support linear interpolation.~~ <i>Put off to a future pull request, since </i>rama_prepro<i> uses exclusively polycubic interpolation.</i>
    - [x] Unit tests for _rama_prepro_ scoring with N-methylation --> RamaPrePro tests AND cyclic geometry tests.
    - [x] Unit tests for _fa_dun_ scoring and rotamer generation with N-methylation --> Covered in cyclic geometry tests and protocols::cyclic_peptide::N_methylation tests.
    - [x] Beauty.
    - [x] Documentation.
      - [x] RAMA_PRE_PRO lines in params files.
      - ~~Rotamer lines in patch files.~~  --> We have no documentation for patch files.  Grr.
      - ~~RamaPrePro lines in patch files.~~
    - [x] Figure out how to add sampling tables / CDFs for arbitrary mainchain potentials.
    - [x] Add function to produce random mainchain torsion vectors biased by probability distribution.
      - [x] Unit test.
      - [x] Debug why we don't seem to be using the N-methyl rama map currently.
    - [x] Add option to use rama_prepro instead of rama tables in GenKIC when sampling.
      - [x] Document this.
      - [x] Unit test.
      - [x] Integration test.
      - [x] Add rama_prepro GenKIC filter.
      - [x] Document this.
      - [x] Add to unit test.
      - [x] Add to integration test.
    - [x] Add option to GenKIC to correct polymer bond-dependent atoms.
         - [x] Document this.
         - [x] Turn this on in simple_cycpep_predict.
    - [x] Add support for N-methylation to _simple_cycpep_predict_.
      - [x] Add option (true by default) to use rama_prepro for sampling instead of rama.
      - [x] Document the new option (rama_prepro instead of rama).
      - [x] Interface for specifying N-methylated positions.
      - [x] Documentation.
      - [x] Integration test.
      - [x] Use rama_prepro cutoff energy instead of rama cutoff energy.
    - [x] Move tryptophan rotamers into database for unit tests.
    - [x] Move the rest of the rotamers into the rotamer library.
    - [x] Unit test with N-methyl-tryptophan rotamers. --> Covered in protocols::cyclic_peptide::N_methylation tests.
    - [x] Move generic N-methyl-L-alpha-amino acid rama table into database.
    - [x] Cyclic N-methyl amino acid scoring unit test.
         - [x] Regular NMe.
         - [x] For beta_nov15 NMe.
         - [x] For beta_nov16 NMe.
         - [x] Non-NMe beta_nov16 unit test while I'm at it.
         - [x] Two-chain NMe.
         - [x] Two-chain beta_nov15 NMe.
         - [x] Two-chain beta_nov16 NMe.
         - [x] Non-NMe beta_nov16 two-chain unit test while I'm at it.
    - [x] Mirror image N-methyl amino acid scoring unit test.
    - [x] Note to self: @twcraven will regenerate the N-methyl map (and add maps for pre-proline, and for sarcosine and sarcosine pre-pro).  I need to add and test those.
         - [x] Need sarcosine.
         - [x] Need sarcosine_prepro.
         - [x] Sarcosine unit tests.
    - [x] Fix problem with rebuilding polymer bond-dependent atoms (methyl group).
         - [x] Document new option ("update_polymer_bond_dependent_atoms") in ModifyVariantTypeMover.
         - [x] Unit test for recursive identification of connection-dependent atoms.
         - [x] Fix issue with rebuilding polymer bond dependent methyl group when it's at a terminus.
         - [x] Figure out why first output in simple_cycpep_predict_nmethyl integration test has crooked N-methyl group.
         - [x] OK, figured it out: it's the packer.  When rotamers are constructed, backbone atom coordinates are preserved, by the N-methyl group is not considered to be a set of backbone atoms.  Add recursive check for polymer bond dependencies in Residue::place to correct this.
    - [x] Add option to MutateResidue mover to update polymer bond-dependent atoms.
         - [x] Document this.
    
    Also:
    - [x] Updating HydroxylTorsionPotential for D-amino acids.
    - [x] Add params files for noncanonical amino acids found in cyclosporin A.
    - [x] Add AIBparams  #file.
    
    For a future pull request:
    - Update _rama_ as _rama_prepro_ was updated.
    - Update _p_aa_pp_ as _rama_prepro_ was updated.

commit a257fe0ac80b3e705345693d5a4d4d4826d5aec2
Merge: ab165a1 df128c1
Date:   Mon Apr 10 17:31:24 2017 -0500

    Merge pull request #2167 from RosettaCommons/roccomoretti/boron_fix
    
    Fix Boron typing
    
    The atom type used for boron in the sdf/CCD C++ code was mis-specified (it was correct in molfile_to_params.py). Change to the correct type and add a unit tests which covers boron.
    
    Thanks to Greg Sliwoski for pointing out the issue.

commit ab165a1dbe7950d25452f4e337bcaf3ec15b86d1
Merge: 56800e6 8fde4fc
Date:   Mon Apr 10 13:53:48 2017 -0700

    Merge pull request #2162 from RosettaCommons/bfrenz/RosettaES_buildfix
    
    Changed function calls to .residue_cop instead of .residue_op that changed between my previous PR and merge.

commit 56800e6c074a9c7ea90d7dab990a74ebada118e8
Merge: ef96883 080f7cf
Date:   Mon Apr 10 12:55:40 2017 -0600

    Merge pull request #2164 from RosettaCommons/ui
    
    Setting up UI project

commit ef96883e15a8fde741ee5998c0e35e6b05aaa6b0
Merge: f77b42f f714663
Date:   Sun Apr 9 22:02:57 2017 -0400

    Merge pull request #106 from RosettaCommons/arubenstein/mean_field_alg
    
    Implementation of mean-field algorithm to predict rotamer or amino acid probability. Can be used to determine preorganization of residues or predict specificity profile for protein-protein or protein-peptide interactions.
    
    All tests pass except ligand_database_io (known to be unstable) and the new tests that I added.

commit f77b42fbdc96687c0377f3f7c7f426dcab794bfb
Merge: 0a42a69 dc26dfa
Date:   Thu Apr 6 20:48:03 2017 -0700

    Merge pull request #2149 from RosettaCommons/everyday847/base_pair_classification
    
    Base pair classification that extends to modified residues

commit 0a42a69c6160670a9f4314de4c4f9a2f6d8eaab4
Merge: f096571 f986520
Date:   Thu Apr 6 17:28:45 2017 -0400

    Merge pull request #2157 from RosettaCommons/JWLabonte/XRW/LINK_records
    
    PDB IO: Stop loading LINK records that cross crystal cells
    
    LINK (and SSBOND) records include two codes that allow one to describe a link between atoms in two crystal cells using symmetry operations. To the best of my knowledge, there is no way we can handle this in Rosetta, and I believe it is simply safe to not load in such LINK records.
    
    Please see the pull request for a full description.
    
    All tests pass, (except for the ligand_database_io test, which is unstable.)

commit f096571efb7f5a099064031f0b7d70ef18b70506
Merge: 88c567d 5f6b96f
Date:   Thu Apr 6 16:12:57 2017 -0500

    Merge pull request #2161 from RosettaCommons/roccomoretti/grid_integration_fixes
    
    ScoringGrid Integration Test fixes
    
    Some of the integration tests using ScoringGrids had settings which were very sub-optimal. Change these such that they are not so unreasonable. (Though not necessarily "ideal".)
    
    Changes to ligand_dock_grid and hts_io integration tests expected.

commit 88c567dd8ce263729698f93523629c6763148f93
Merge: 9e5746d 0755556
Date:   Thu Apr 6 07:59:49 2017 -0700

    Merge pull request #2156 from RosettaCommons/everyday847/polymeric_ccd
    
    Automatically recognize polymeric residues from the CCD

commit 9e5746d55be739b769f7911a97006635652cbc1e
Date:   Thu Apr 6 01:34:45 2017 -0700

    Wow -- master really hasn't been beautified in a while.  Beautifying.

commit 30c7f16cfba8c4d29322627b705decc8fb5b2b6d
Merge: 9d4bb75 840e642
Date:   Wed Apr 5 23:26:26 2017 -0700

    Merge pull request #2158 from RosettaCommons/revert-2071-bfrenz/RosettaES
    
    Revert "Bfrenz/rosetta es"

commit 9d4bb75ff0cd2318594c7e12d0197e8c73514762
Merge: b6d3550 e8c4072
Date:   Wed Apr 5 22:19:40 2017 -0700

    Merge pull request #2071 from RosettaCommons/bfrenz/RosettaES
    
    Bfrenz/rosetta es

commit b6d3550dc69533b050bc31f5d494dc5a164fc6c8
Merge: 5432513 e7f0c3f
Date:   Wed Apr 5 10:34:43 2017 +0200

    Merge pull request #2155 from RosettaCommons/bazzoli/make_shobuns_public
    
    Moves app shobuns from pilot to public/analysis.

commit 543251380bad79f761a1ac79bf34b28b1f5c964f
Merge: 26a98a5 cd1c919
Date:   Mon Apr 3 15:40:06 2017 -0700

    Merge pull request #2153 from RosettaCommons/hpark/more_TMscore_fix
    
    Fixing typing issues in d0_ equation change

commit 26a98a5a272912c3fcb9c806d29ce3c6d2661e13
Merge: a5c2c34 e52f63f
Date:   Mon Apr 3 15:32:17 2017 -0700

    Merge pull request #2152 from RosettaCommons/hpark/fix_TMscore_d0
    
    Fixing incorrect d0_ in TMscore equation

commit a5c2c34e9c1e1c1089c6f5e16ddf5e9a12ac36ed
Merge: b73a11e ee3b8de
Date:   Mon Apr 3 16:25:59 2017 -0400

    Merge pull request #2129 from RosettaCommons/aleaverfay/fix_rtmin_after_setup_for_scoring_for_res_change
    
    Adding the residue's datacache to setup_for_minimizing_for_residue
    I introduced a bug into rtmin after merging in the offort_w_lkball branch (PR 1972) that @fdimaio found. This PR fixes this bug

commit b73a11e825db6ca54cebe8e74d60f55d69e731d1
Merge: e21a7a0 cf6e6a8
Date:   Mon Apr 3 12:51:11 2017 -0700

    Merge pull request #2146 from RosettaCommons/davidekim/boinc_android
    
    Davidekim/boinc android

commit e21a7a02d95d3aa1a6a981c28312eda383f53d6b
Merge: 134ffe4 86b6f54
Date:   Sun Apr 2 20:39:41 2017 -0700

    Merge pull request #2140 from RosettaCommons/rhiju/rna_motifs
    
    RNA motif annotation/scoring
    All tests preserved except expected ones.
    @everyday847 note change to `rna_noncanonical_hairpin`  test due to use of `na_analogue()` in `get_base_coordinate_system` in FARFAR base pair and stack scoring.

commit 134ffe479262044c8f22ddb4ecb02636b96e6134
Merge: c4b4473 60d24b6
Date:   Sun Apr 2 13:11:23 2017 -0700

    Merge pull request #2148 from RosettaCommons/rhiju/hotfix_generate_6Dloopclose
    
    Rhiju/hotfix generate 6d loopclose

commit c4b44739fc89064e7d45c88a29b60381d82b3ee2
Merge: df2bae3 7750e10
Date:   Fri Mar 31 18:03:24 2017 -0700

    Merge pull request #2144 from RosettaCommons/everyday847/superposition_defaults
    
    Change the default superposition behavior for RNA structure prediction

commit df2bae39b22db997cc24e6b0b12cc578f38d23a6
Merge: 7bc6810 ff784c8
Date:   Fri Mar 31 11:28:52 2017 -0400

    Merge pull request #2091 from RosettaCommons/rfalford12/enumerate-polar-rotamers
    
    Dump Rotamers into PDB files at a single position
    ---------------------------------------------------
    At a given residue position, this mover dumps the rotamers for the residue into individual PDB files and prints rotamer probabilities to standard output. I'm using it for other analyses, but Jeff may want to use it in class on Monday so it would be great to add to PyRosetta.

commit 7bc68107cf6d5b5371e031a206acb0f5d46f3102
Merge: 778c5f0 592c0ae
Date:   Wed Mar 29 11:30:22 2017 -0500

    Merge pull request #2128 from RosettaCommons/roccomoretti/auto_rebuild_dunbrack_binaries
    
    Add autogeneration of Dunbrack binaries as part of the build process
    
    Coming off a comment by Vikram:: put (re)generation of the Dunbrack binaries into the build process.
    
    * A new application (generate_database_cache) has been added which runs through the major Dunbrack libraries and loads them, generating the Dunbrack binaries if they don't already exist.
        - Associated with this are a number of de-globalization changes to the dunbrack::RotamerLibrary and associated code to allow for loading multiple RotamerLibraries in the same program from different OptionCollections
        - The normal usage (packing, etc.) still uses a single global object constructed from the default option set -- the alternate ones are really only useful for direct usage at this point.
    * Add a hook to Scons to run the generate_database_cache application for release mode compiles
    
    The hook only runs on release mode compiles (and only on Scons), and only if bin/generate_database_cache.etc link is being (re)generated. So it should run with most standard "installation" compiles (./scons.py mode=release bin) but will not be triggered for many of the time-sensitive testing compiles (e.g. unit test compiles, or compiles of just specific executables). That said, the no-regeneration-needed run of the release mode generate_database_cache application only takes about a second or so on my machine, which is dwarfed by the overhead of scons scanning.

commit 778c5f01b1dccdad7985108a271284ec13e56b98
Merge: 3cad483 3aabcf9
Date:   Wed Mar 29 11:28:28 2017 -0500

    Merge pull request #2138 from RosettaCommons/roccomoretti/chain_in_InterfaceScoreCalculator
    
    InterfaceScoreCalculator fixes
    
    Previously, the ligand docking InterfaceScoreCalculator, while it takes a set of chain letters as the specification of the chain to use, instead bounced the chain specification through chain IDs, jump numbers, and even residue numbers. This resulted in difficulties when attempting to score poses which aren't set up with precise chain letter/chain ID/jump number/residue number correspondence, particularly with RMSD calculations on structures with differing numbers of (non-ligand) residues.
    
    Rework the InterfaceScoreCalculator associate functions, so they work directly on chain letters (what the user is specifying). As an added bonus, reduce (but don't eliminate yet) the dependence on JD2.