commit d93921394aa5a1ee7d76b8044524c963ed706b55
Date:   Wed Aug 27 09:06:53 2014 -0700

    try to reduce changes in swa_rna_gagu_04_clustering by forcing std::endl at end of a tracer output.

commit 0bb0b7fc18ac01f2382007787a378299b9b74a97
Date:   Wed Aug 27 19:06:11 2014 +0300

    Corrected a problem is CutChainMover that refrenced a residue at position total_residue+1.\n In splice I reverted changed done to find_nearest_res calls inside Splice::aplly

commit 947325bea5981d74b8139b4552f828856ffee821
Date:   Wed Aug 27 18:01:58 2014 +0300

    corrected reference to non-existant residue

commit e3f73b470f54750b86c642d40a3049cc800720f4
Merge: 21cdd18 3ed6e05
Date:   Tue Aug 26 22:16:15 2014 -0600

    Fixing bug in PyMolMover introduced in r42695. Coloring by energy and sending custom colors should now work as expected.

commit 21cdd18c486fa81bdc29fa66054b308d1bd3c43b
Date:   Tue Aug 26 22:15:43 2014 -0600

    Fixing bug in PyMolMover introduced in r42695. Coloring by energy and sending custom colors should now work as expected.

commit 9c3d21f5901ecdd8a30c8234f91d439354b0a6a4
Date:   Tue Aug 26 18:10:24 2014 -0700

    in StepWiseMinimizer, doing vary_bond_geometry setup and restoration of constraints tightly around  run of minimizer, to prevent issues with atom indices changing after O2' packing. Introducing pack_polar_hydrogens step within StepWiseMinimizer

commit c96554a28dcb9408d7e0a8e51b3e95201677bfda
Date:   Tue Aug 26 18:08:28 2014 -0700

    making legacy output_silent_file overwrite by default

commit 5ec83449737afe00ee71d56a2fdbaa98d5d5b898
Date:   Tue Aug 26 18:08:05 2014 -0700

    softening distance constraint for hydrogen placement in -vary_polar_hydrogen_geometry mode.

commit 569f857edc33b45bbb77727f83ad5573ac7ae9e7
Date:   Tue Aug 26 18:07:27 2014 -0700

    promotion of some options from StepWiseBasicModelerOptions.cc to StepWiseBasicOptions.cc to allow their setting form command-line in stepwise

commit 3fb4e0df6ae24e2cf4c70b2e5605c99b34c90a65
Date:   Tue Aug 26 16:33:21 2014 -0700

    I think design_cycpeptide_MPI.cc now works with the new features needed for Per's application.  Compiles fiine; needs to be tested.

commit b4d22ab153ce686a4b7209eb9463ce03dc1939b9
Date:   Tue Aug 26 11:41:28 2014 -0700

    encapsulating pack_polar_hydrogens into PolarHydrogenPacker class.

commit 939c0785c300fca830a1ec1492418f60a33960ac
Date:   Tue Aug 26 10:31:35 2014 -0700

    remove verbose output from CCDLoopClosureMover when called from inside StepWiseProteinCCD_Closer

commit 2bd8661ccdec7a83f3ca5d90b972bfe649398f15
Merge: 6055614 3ed6e05
Date:   Tue Aug 26 10:26:55 2014 -0700

    Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev

commit 7f4ca32e435a8d534e7e91dc4d002f6702f6f82a
Merge: d2f313d 3ed6e05
Date:   Tue Aug 26 09:37:30 2014 -0700

    merge from master to get weitzner stepwise_ccd_slowdown fixes.

commit 3ed6e05f32ce1ae336ab77e375dbe6c58058d2e3
Date:   Tue Aug 26 09:38:46 2014 -0400

    Adding a funciton to ResidueGraph to regenerate the vertex and edge indices. This should be called when you are adding/removing nodes and edges to ResidueGraphs. Fixes bugs in smallest ring size detection algorithm.
    
    Added regenerate graph index to assign_gasteiger_atom_types(). This will regenerate graph indices (see above) before trying to assign atom types. Bug fix for proline patches

commit 22524dcf59617757e979fcb03f6434c718d54ccc
Merge: 97f9b88 7fcdfd9
Date:   Tue Aug 26 15:01:18 2014 +0300

    Forgot to add constant_seed flag to the integartion tests, (which caused them to fail):
    splice_out_generic
    splice_out_longer
    splice_out_shorter_loop
    
    	modified:   tests/integration/tests/splice_out_generic/flags
    	modified:   tests/integration/tests/splice_out_longer/4JB9.pdb
    	modified:   tests/integration/tests/splice_out_longer/flags
    	modified:   tests/integration/tests/splice_out_shorter_loop/flags

commit 97f9b88e3f476506c58925f355385caaefdf8251
Date:   Tue Aug 26 15:01:18 2014 +0300

    Forgot to add constant_seed flag to the integartion tests, (which caused them to fail):
    splice_out_generic
    splice_out_longer
    splice_out_shorter_loop
    
    	modified:   tests/integration/tests/splice_out_generic/flags
    	modified:   tests/integration/tests/splice_out_longer/4JB9.pdb
    	modified:   tests/integration/tests/splice_out_longer/flags
    	modified:   tests/integration/tests/splice_out_shorter_loop/flags

commit 7fcdfd9b796ceb0b86f1cb1a3a7d96279b91dd85
Merge: f6d4fcf 5f9adda
Date:   Tue Aug 26 07:49:20 2014 -0400

    Merge pull request #69 from RosettaCommons/weitzner/stepwise_ccd_slowdown
    
    Weitzner/stepwise ccd slowdown: The CCD update resulted in a slowdown in some cases. Rhiju noticed that the Ramachadran data files were being read in from the disk multiple times, which, in the way it was written before, would happen when constructing a new CCDLoopClosureMover. This problem would then be exacerbated when CCDLoopClosureMover was created on the stack in a for loop.
    
    This revision fixes that by getting a COP to the Ramachandran potential stored in the ScoringManager. Additional changes are introduced to the Ramachandran2B potential to allow arbitrary conformations to be evaluated, and the RamaCheck2B class  is updated to use this new interface. This means you can now use two-body Ramachandran checks during CCD closure!
    
    Finally, this change set updates StepWiseProteinCCD_Closer to have a CCDLoopClosureMoverOP as a data member instead of creating it on the stack to reduce the number of times "new" is called in that protocol.
    
    This should improve the runtime of integration tests that use CCDLoopClosureMover, and all of those tests will change due to the lack of tracer output associated with reading the Ramachandran data files. See http://benchmark.graylab.jhu.edu/revision?id=115&branch= for the full list of changed tests.

commit 5bdb226649ed5a370a0562ea82388f7348589dee
Date:   Tue Aug 26 00:57:26 2014 -0700

    Working on design_cycpeptide_MPI.cc

commit 26075ece5aceadc759ee904b6cc19c13c6e3918f
Date:   Tue Aug 26 00:41:47 2014 -0700

    Working on design_cycpeptide_MPI.cc

commit 23519daae65ff09ab97df644b34910dcb655aaf6
Date:   Tue Aug 26 00:24:38 2014 -0700

    Added support for having residues that don't repack in design_cycpeptide_MPI.cc.  Someday I'll do all of this properly, with resfiles and whatnot.

commit f6d4fcf1efded4f1f4cebcaf59bdb07ed8d32429
Date:   Mon Aug 25 23:39:50 2014 -0400

    Fixing some PyRosetta compilation errors on clang platform

commit 43854b4093647201ff869d3cc60ad3319dbef99d
Date:   Mon Aug 25 21:24:11 2014 -0600

    Fixing some compilation on clang platform

commit f3ad3a19d0568fe89bb017c2b89abeec354c62ff
Merge: a39bec2 8b45c0d
Date:   Mon Aug 25 20:22:38 2014 -0700

    merge from master to test brian's update.

commit a39bec26a666b2b24be4db3c8fd1db1bff467c73
Merge: 8e0a41c 5f9adda
Date:   Mon Aug 25 20:05:49 2014 -0700

    testing brian's speedup of StepWiseCCDCloser after CCD accelerations...

commit d2f313d1b22a700dd555d1e600184f2b7dbc874e
Date:   Mon Aug 25 19:04:46 2014 -0700

    adding improper torsion constraints for polar hydrogens.

commit 81025292a3e5a78c4908f6417f802ad17505ca5d
Date:   Mon Aug 25 19:00:39 2014 -0700

    Temporarily removing the ROTAMER_AA TYR line from the BoronateLDopa params file, since this is creating errors.  I need to debug the fa_dun scoring term and see why it's having problems with this residue type.

commit 4e05cc714bf50b69779f6529de4620a1f840b26c
Merge: 2ccf580 69174c2
Date:   Mon Aug 25 18:53:37 2014 -0700

    Merging remote vmullig/cycpep into local.

commit 2ccf5801483f6ff935a533cc72b23cca2e3ca432
Date:   Mon Aug 25 18:28:51 2014 -0700

    Tweaking LYX.params file.

commit 57b2c456bc671822b398cd814b1f4cc932c6bf7f
Date:   Mon Aug 25 17:16:53 2014 -0700

    pilot app for packing polar hydrogens -- will convert this to class next.

commit 0ce191075aeb306febed5627b8504987f0698e82
Date:   Mon Aug 25 17:16:33 2014 -0700

    fix author name to rna_rotamer_building_functions.cc

commit bd81125335d0738e86145674473c16ce3d0676f6
Date:   Mon Aug 25 17:16:07 2014 -0700

    fix to extraction from silent files with full_model_info

commit 5f9addaa98e3b571031e286ed1af605cf2a48b57
Date:   Mon Aug 25 17:36:31 2014 -0400

    Whoops. I had accidentally unincluded the class's forward header. Fixed.

commit 74c9f664d66f35b6f280a56b307f6374bfabbb96
Date:   Mon Aug 25 17:07:50 2014 -0400

    Making sure the loop and movemap instances in CCDLoopClosureMover are always in sync with those in StepWiseProteinCCD_Closer.

commit 4ecef28d694d6cced5bbceb33a19c73022c0567b
Date:   Mon Aug 25 17:03:51 2014 -0400

    Making CCDLoopClosureMover a data member of the StepWiseProteinCCD_Closer class. This will prevent 'new' from being called in each iteration to instantiate a RamaCheck instance to accompany the CCDLoopClosureMover.  Instead, the CCDLoopClosureMover is instantiated lazily and configured once.

commit 1cded732992f5ff01b8683ba72ec2da29a5be8fa
Date:   Mon Aug 25 16:44:09 2014 -0400

    Updating RamaCheck2B to use the new methods in Ramachandran2B. Now trial conformations will be evalulated properly.

commit fb5eb6b9f9088a3e31dabb910347145351ab6d92
Date:   Mon Aug 25 16:42:36 2014 -0400

    Making the spacing the way I like it in the methods I modified in Ramachandran2B

commit 7ef30ebdec548f8bb5ded2aad3b2559b87523174
Date:   Mon Aug 25 16:39:19 2014 -0400

    Adding an interface that will arbitray sequences and conformations to be evaluated in Ramachandran2B. Previously a residue instance would have to be passed in, which made it difficult to evaluate trial conformations before setting the conformation to the pose. Now you can pass through phi, psi and three chemical::AAs and get back a number.  Aww yeah.

commit a3d12e1c6170ac389755b8645b50efcaf4b10f2e
Date:   Mon Aug 25 13:29:34 2014 -0700

    fixing angle constraint setup by ConstrainToIdealMover (previously was not working at all for polar hydrogens! oops!). Allowing command-line specification of -bond_angle_sd_polar_hydrogen

commit 8e0a41ca383637c627eceba7485e4cfa58d73406
Merge: 6e0e5eb c5db9a9
Date:   Mon Aug 25 12:59:34 2014 -0700

    merge into daslab branch of latest from rhiju/stepwise_benchmark, including removal of verbaige and tests of polar_hydrogen_geometry. Also an assert that Hpos_polar == Hpol_idx in ResidueType. If so, will get rid of one of these -- super-confusing.

commit c5db9a9a8ed68aa51f7e2aa24b342f105032ea17
Date:   Mon Aug 25 12:58:46 2014 -0700

    assertion that Hpos_polar and Hpol_idx are the same. If true across all integration tests, I will deprecate one of them.

commit 4c2cf5db12b33d039150c1f5ab32f08a3c1e7a17
Date:   Mon Aug 25 15:54:08 2014 -0400

    Changing RamaCheck to use the instance of the Rama potentials contained in the ScoringManager to prevent additional reads from the filesystem.

commit dfb47776250189093c3e708c8afc64d6ed6d761e
Merge: 515134d 8b45c0d
Date:   Mon Aug 25 13:27:16 2014 -0600

    Merge branch 'master' into PyRosetta

commit 60556143ffac593f3dceca9389932f1755fd8e7d
Merge: 5ba608f 2cfbd4c
Date:   Mon Aug 25 12:14:40 2014 -0700

    Merge branch 'kylebarlow/general_dev' of github.com:RosettaCommons/main into kylebarlow/general_dev
    
    Conflicts:
    	tests/integration/tests/Werror_check/command

commit 8b45c0d3c33c0fc58eeeeb1a2dda14842a226f7e
Date:   Mon Aug 25 14:04:12 2014 -0500

    Add error checking on -out:levels
    
    Additional error checking on -out:levels settings such that
    we don't segfault for bad options (e.g. ones missing a colon,
    or options with more than one colon.)
    
    Also change behavior such that if a tracer is listed twice,
    the second time takes precedence over the first.

commit 9cc1ab785d85e9b0a7d7e7f1ab01c385ccc354ab
Merge: 5ba608f 2e88c3d
Date:   Mon Aug 25 14:39:52 2014 -0400

    Merge pull request #68 from RosettaCommons/JWLabonte/Atom_output
    
    This branch has made a number of (I think) improvements to the `show()` methods of several classes. In particular:
    - [x] Added `conformation/Atom.cc`.
    - [x] Added `conformation::Atom::show()` (and an `operator<<`).
    - [x] Renamed `chemical::Atom::print()` to `chemical::Atom::show()`.
    - [x] `Residue::show()` now calls `conformation::Atom::show()`.
    - [x] Added optional parameters to `Residue::show()` and `ResidueType::show()` to cause the latter to call `chemical::Atom::show()` for each atom.
    - [x] Expanded what is output by `chemical::Atom::show()`.
    
    I also cleaned up the Doxygen in the files.
    
    I also added `GasteigerAtomType`s to sugar residues and ouput the results in the carbohydrates integration test to both test these new `show()` modifications and to test Gasteiger typing of sugars.
    
    no unit test changes
    Only the carbohydrates integration test changes, as expected.

commit cec730ee78aac6f63168d55b22afea10226208a3
Date:   Mon Aug 25 14:28:13 2014 -0400

    Adding methods to SocringManager to get a COP to Ramachandran and Ramachandran2B

commit 81f928a0067acd6266b9e8b34f3f207c581d950f
Date:   Mon Aug 25 14:15:33 2014 -0400

    Various little fixes to StepWiseProteinCCD_Closer's header to make it comply with the coding conventions.

commit c1f600d557f0e6e93ba8cc70705fbf940a5106ed
Date:   Mon Aug 25 13:40:40 2014 -0400

    Adding comments that explain what's going on.

commit c6c1ce536677247d0456dadf6d0d17e3ad5d05ed
Date:   Mon Aug 25 09:16:15 2014 -0500

    DARC version2 updates

commit 5ba608fed49bc2de9ab9c90dbf55697aabedfb34
Date:   Mon Aug 25 16:09:02 2014 +0300

    Applied the follwoing changes:
    
        Updated the Splice* integration tests to test for newly introduced changes to Splice mover
    
        Corrected a problem with arguments passed to find_nearest_res in Splice mover. Before it only looked for nearest res in chain A, now looks in all chains.
    
        I Changed LoopLengthChange mover so it now respects the cut_chain input. meaning: if the input cut_chain is X then it will remain X after llc mover is apllied.
    
        Added source PDB 3UMT to the H3 PSSM database
    
        Added to CutChainMover a functions that finds a chainbreak between input residues

commit 515134dbb6c8a0fd9a2a3a5efed14039a9f01651
Merge: debacd2 f8dcbf4
Date:   Mon Aug 25 09:06:03 2014 -0400

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

commit debacd2ed74d2433bf0cae790a6a6ef83e136ed6
Merge: 0747a2f d4e7d5e
Date:   Mon Aug 25 09:04:35 2014 -0400

    Merge branch 'PyRosetta' of github.com:RosettaCommons/main into PyRosetta

commit e2caf9cf097be07d214d36cbd3a5e7d49ccb9e9d
Merge: c834778 f8dcbf4
Date:   Mon Aug 25 14:44:21 2014 +0300

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

commit c8347780ebed6b1a18bae204399d0fba272a75c2
Date:   Mon Aug 25 14:42:26 2014 +0300

    Corrected a problem with arguments passed to find_nearest_res in Splice mover. Will cause integration test changes in all Splice* integration tests

commit d5c8a947cea14a4eb3db2eb6ebb9b2d5a5395423
Date:   Sun Aug 24 20:23:53 2014 -0700

    fix some variable names to protocols/stepwise/sampler/README (RotamerSampler --> StepWiseSampler)

commit c14e96a4bf1c465f9e423fbab4896a061045efed
Date:   Sun Aug 24 20:23:28 2014 -0700

    copying over StepWiseMonteCarloOptions to StepWiseModelerOptions using StepWiseBasicOptions = operator -- should prevent mistakes from overlooking manual setting.

commit 0acfb12ef7692d2dcc610759de7cbc93df32659b
Date:   Sun Aug 24 12:24:15 2014 -0700

    In stepwise output_silent_file(), do not do rms_fill calculation unless asked for explicitly. Saves time in make_movie mode.

commit 114a24c9857a773fd024ac82d2b716850428083c
Date:   Sun Aug 24 12:23:38 2014 -0700

    get rid of verbose scoring output from StepWiseMinimizer

commit df47cfac0a23a4b531447c922890861e152bee87
Date:   Sun Aug 24 12:10:28 2014 -0700

    get rid of green debugging output for SWA_MoveSelector

commit c3f0ddf818af4af2ae421ba2f1e84e0372bd8dda
Date:   Sun Aug 24 12:10:12 2014 -0700

    quick fix so that -vary_polar_hydrogen_geometry flag works for proteins.

commit a7fad2a8613e74158450c0a65e25c082409894a8
Date:   Sun Aug 24 12:02:10 2014 -0700

    including <ctime> for linux compile.

commit 00a2c27924ab3606e7e62c8eff30dce82af9d28a
Date:   Sun Aug 24 12:01:02 2014 -0700

    fixing bug in silent file output of string-valued tags (was adding an extra space after the tag, silly).

commit a78c06672f29c9d233ccc94b9221eb7d0c698bf9
Date:   Sun Aug 24 11:38:22 2014 -0700

    renaming superimpose_pose and create_alignment_id_map with _legacy tags -- reminder that in the future these should be deprecated in favor of centralized choices for pose alignment held in StepWisePoseAligner

commit aa7c7a0bb81ea0e93d9cb90a430548f6d7bd9be4
Date:   Sun Aug 24 11:37:35 2014 -0700

    fixing silly modeler->sampling name change (happened with a find/replace from earlier this year); caught while writing documentation.

commit 2d49382f7be4d11062c6b6a480b19251f726c76a
Date:   Sun Aug 24 11:36:05 2014 -0700

    -save_times option allows clocking of models in stepwise monte carlo runs.

commit eff25a11ba8d9563febfc701cfe14c9dd9ed4dc1
Merge: 72d64bb f8dcbf4
Date:   Sun Aug 24 10:26:09 2014 -0700

    merging latest from master to see if verbiage from CCD is reduced.

commit 72d64bb887f434d6d4b74e91e149e9f3d9f835f4
Date:   Sun Aug 24 09:53:42 2014 -0700

    applying tools/coding_util/artistic_spacing.py to ConstrainToIdealMover.??

commit 75216ba73c94d43400eca2f4c8b24bc8b5bde246
Date:   Sun Aug 24 09:52:09 2014 -0700

    changing name of set_AllowInsert to set_allow_insert to match conventions that we use elsewhere.

commit 6f8c344a429aa284cc91030658a5bd914c9c79e1
Date:   Sun Aug 24 09:49:40 2014 -0700

    cleanup of ConstrainToIdealMover, which sets up bond_geometry constraints -- now movemap is passed in rather than a member function; makes clear that this is an object that will be updated (whereas AllowInsert is const and used to figure out which atoms move).

commit 59113b8775defed27d306c041f559b43dd98a5e1
Date:   Sun Aug 24 09:37:01 2014 -0700

    for vary_bond_geometry, making bond_angle_sd_ and bond_length_sd_ const parameters of ConstrainToIdealMover -- really need to integrate this with cart_bonded.

commit af572612b38fb77e732e30962846bd0947244901
Date:   Sun Aug 24 09:27:28 2014 -0700

    creating score_type bond_geometry to hold info on varying bond angles/lengths of, e.g., polar hydrogens or other moieties in stepwise modeling.

commit 6e0e5eb15279688243972e137d67c2fbf37e9f2f
Merge: 9a426a9 c805e89
Date:   Sun Aug 24 09:01:26 2014 -0700

    Merging latest from rhiju/stepwise_benchmark, incl. hopefully fixes to swa_rna_mai integration tests.

commit 301aa5395069a95039a51185abce3b06a81cbd9d
Date:   Sun Aug 24 16:48:17 2014 +0300

    I Changed LoopLengthChange mover so it now respects the cut_chain input. meaning if the input cut_chain is X then it will remain X after llc mover is apllied.

commit 31efd13718c9c81285dbe5ca5b76b1408161bac9
Date:   Sun Aug 24 15:00:00 2014 +0300

    Added source PDB 3UMT to the H3 PSSM database

commit c805e893ec9507b5e01fe97ed136f9bcd8986816
Date:   Sat Aug 23 17:06:16 2014 -0700

    refactor of ConstrainToIdealMover; fixed setting of DOFs to really move anything with AllowInsert true; creating options to -rna:vary_geometry and -vary_polar_hydrogen_geometry in stepwise.

commit 313a1c946c1a72d828cd92929955709062838ee7
Date:   Sat Aug 23 19:56:00 2014 -0400

    Adding Luki's JD2 patch for adding rmsd's to score_jd2

commit 94b4db12a509f030972f89662b65d596d0bff5ae
Date:   Sat Aug 23 14:54:52 2014 -0700

    slight refactoring of vary_bond_geometry code -- creating a single "easy" setup_vary_bond_geometry() function in ConstrainToIdealMover. Changing AllowInsert in that mover to be const.

commit 714799838a453c37ba600f8aa0e10b2fb826ca23
Date:   Sat Aug 23 14:54:02 2014 -0700

    completing merge from daslab into branch rhiju/stepwise_benchmark

commit a7d3dbeccb10cd459703c0f3c113ed26bdd983b6
Merge: fc1016a 041b35a
Date:   Sat Aug 23 14:53:42 2014 -0700

    completing merge from daslab into branch rhiju/stepwise_benchmark

commit 9a426a95b66fc8e1e054cbedf5a0b585b321a953
Date:   Tue Aug 19 14:59:31 2014 -0700

    fixing error for unused variable

commit 041b35aba9b176402c51deb5a05a8c05b0c8b6e5
Merge: 2799feb f2d6674
Date:   Sat Aug 23 13:59:56 2014 -0700

    merge from master into daslab branch; resolving issues with CCDLoopClosureMover, hopefully

commit da20e9ee542ecc9265887b6984d67a3f50ae7765
Date:   Sat Aug 23 16:36:00 2014 -0400

    basic membrane relax application compiles

commit 838bba054d8e2bd72d72e8eabe3d2344eb85419b
Date:   Sat Aug 23 16:25:08 2014 -0400

    Adding membrane relax executable (oops)

commit 9536e165376e3666f56fb75c1f6917b214183eb0
Date:   Sat Aug 23 14:47:08 2014 -0400

    Starting to put together finished C++ version of the relax application

commit fbe6a5f9c431f06f1e27c91022876d5e76c28206
Date:   Sat Aug 23 14:31:39 2014 -0400

    Commenting out ddG for now - will do in pyrosetta?

commit 5135bbedfec7d2a12fcd2e74d2773221dd4c47fc
Date:   Sat Aug 23 14:22:14 2014 -0400

    Fixing pilot apps settings to match new pilot apps directory structure

commit c904d1f1bd1e43df4a7619f414947f79d8d6767b
Date:   Sat Aug 23 14:18:50 2014 -0400

    Transferring over cleaned up membrane applications from the old messy framework applications branch

commit 6265ee3635ecce85ee7c2a6e3fd98e6194a8ede5
Date:   Sat Aug 23 14:15:06 2014 -0400

    Cleaning up my pilot apps (ralford) and the pilot membrane directory in preparation for promoting applications to public apps

commit f8dcbf4b53a3baf71fc53c9efdf3da6e662f8421
Merge: f2d6674 5933dbf
Date:   Sat Aug 23 11:53:45 2014 -0600

    Merge pull request #67 from RosettaCommons/benchmark
    
    Updating benchmark scripts. Adding 'config' option. Adding 'script failed' state for regression sub-tests.

commit 356e60741127441d1bec1793cd2238d2a5591c85
Date:   Sat Aug 23 13:33:36 2014 -0400

    Adding membrane funcitonality to the existing score_jd2 application

commit f95ba9150ceb9160aecbb53a03d519912686b75e
Date:   Sat Aug 23 13:26:13 2014 -0400

    Adding a method to check the pose for an existing membrane residue at the end of a single chain. If the residue is present, it will be kept and tracked. If not, a new membrane residue will be added to the pose

commit a09bf7bba43bae062d45df3ed33713b4bcfcf959
Date:   Sat Aug 23 13:08:04 2014 -0400

    Removing legacy unit tests from initial membrane framework (along with old files)
    Reorganization of resource manager io code into protocols/membrane/io
    Reorganization of geometry (membrane utility funcitons) into protocols/membrane/geometry
    
    Just moving stuff/cleaning up the membrane code - no functional changes
    
    Unit Tests: Pass
    Integration tests: failures due to timeouts (but also fails on previous revisions)

commit 7b7a77d494b3274b517009805fe10a2741aa73b5
Date:   Sat Aug 23 11:40:31 2014 -0400

    Fixing namespacing error ins apnning topology unit test

commit ca93e249b9aa14bdad3f3ed05e3e967335e56ab6
Merge: 7274832 f2d6674
Date:   Sat Aug 23 11:01:04 2014 -0400

    Merging master 8/23/14 into branch rename_geometry

commit 72748329a1e3386481094fe3df3c6c189079bdb2
Date:   Sat Aug 23 10:59:02 2014 -0400

    Cleaning out protocols/membrane/io unit test directory - will fix later on

commit 17796e2d82b6c1bd8655123baaf636f311acfb2c
Date:   Fri Aug 22 23:48:11 2014 -0400

    Adding unit tests to the correct directories to match their structure in soruce - will most likely not compile at first

commit 82923494742d2e90d73755efc3c95e85c6429f15
Date:   Fri Aug 22 23:43:16 2014 -0400

    Fixing executables to match new namespacing criteria

commit f2d6674c85e576e15f934659c7afa6abeef8ad83
Date:   Fri Aug 22 19:17:10 2014 -0700

    SaveResfileToDiskFilter now preserved insertion codes

commit 5c01e4475db7e425078a9bb547800b248e6aed42
Date:   Fri Aug 22 19:14:20 2014 -0700

    Fixing unit test broken in my commit

commit 69174c2f9b06915e1b24060a0ced45c692a23e02
Date:   Fri Aug 22 17:45:17 2014 -0700

    Working on modifications to design_cycpeptide_MPI.cc that are needed for designing binding proteins for rigidity (Per's application).  TODO: make the new flags work.

commit 2e88c3dbc769f8925b61ed0999110e8697be5fa9
Date:   Fri Aug 22 18:14:39 2014 -0400

    corrections to header guard labels

commit 39423864d10d04e0afef74dddd05f7b82f8c81bd
Date:   Fri Aug 22 17:52:05 2014 -0400

    Fixing renaming and renamespacing of source geometry code

commit d7453eb8984db42cf7adb9ccc97d7e41cc31db81
Date:   Fri Aug 22 14:51:14 2014 -0700

    Minor changes to the cartbonded potential.
    - Adding in a backbone O-C-N-H torsional potential.
    - Many of the planar restraints are now period 1 instead of period 2.  Previously, badly clashing structures, when minimized, would cause these groups to flip.  This will no longer happen.
    - Greatly reducing some of the hydrogen torsional potential weights.  Doing so sees modest improvements in non-ideal rotamer recovery.
    - Uniformly increasing bond angle weights.  This shows a similar improvement in nonideal RR.
    
    Updating the unit test to reflect these scorefunction changes.
    
    All nonideal integration tests will show changes.
    
    Thanks to Hahnbeom who did most of the work for this commit.

commit d1341b9ed668b408ce65f00a91dc66335e84cea1
Date:   Fri Aug 22 17:39:18 2014 -0400

    Carbohydrates: in integration test, assigned Gasteiger atom types for testing

commit db437a698fd7a0676170adc02eaf005e9f869d5e
Date:   Fri Aug 22 17:38:46 2014 -0400

    Progress.  The code now compiles, and links, but it segfaults.

commit fc1016acf5ed2ee87da186b722372c899b0a3b50
Date:   Fri Aug 22 14:08:25 2014 -0700

    potentially critical bug fix; O2prime hydroxyls were not getting reinstantiated, once virtualized!

commit 6f02ecdd7476820656ff9964ab54d8fbd1b2a7fb
Date:   Fri Aug 22 14:06:47 2014 -0700

    onelettersequence output in silentstruct -- just use what is in pose, not full_model_parameters, otherwise having a problem with extract_pdb now.

commit be29eb1e8741dbb61c7f4d4f9f26bfddfab1b372
Date:   Fri Aug 22 16:55:46 2014 -0400

    Atoms: minor tweaks

commit 6cb92415138d98e30d55062f6fb56ff9ee9e621a
Date:   Fri Aug 22 16:18:35 2014 -0400

    Ok, compiling version of the MTJD.

commit ba2a0faf9799489f1c34c2391d489f9bac45193e
Date:   Fri Aug 22 16:16:12 2014 -0400

    Atoms: expanded output for Residue, ResidueType, and chmical::Atom

commit 4eb65ce50130290e3227bb6faab1f278ad67d774
Date:   Fri Aug 22 14:13:52 2014 -0400

    Atoms: adding conformation/Atom.cc to settings file

commit e44e06df0d48d9be2cccbb40608105947dc8b19f
Date:   Fri Aug 22 13:54:50 2014 -0400

    Atoms: Residue::show() now calls conformation::Atom::show()

commit d0e3400f9a58bcaedd87b4931edceaa4df935d50
Date:   Fri Aug 22 13:44:12 2014 -0400

    Atoms: simplified output for conformation::Atom to only coordinates

commit ed262c85c47706a9596382ed3511fcc038392c4d
Date:   Fri Aug 22 13:38:50 2014 -0400

    First pass implementation of a MultiThreadedJobDistributor.
    
    There are many bells and whistles that it lacks, and this surely
    does not compile, and there aren't really any tests for it yet
    (though there's a test suite for it where I've been testing things
    like the boost::thread_specific_ptr (which requires the boost
    libraries to work) and C++11's thread_local storage class specifier).
    
    The framework is in place, though.

commit b4906dc4c6e1358b5e0453f68e4fb920cf766663
Date:   Fri Aug 22 13:38:14 2014 -0400

    Atoms: fixed chemical::Atom::show() to use private data instead of getters

commit c37294bedec78a60eb54cfcd902328f6641caf4b
Date:   Fri Aug 22 13:37:41 2014 -0400

    Fixing the C++11 #inclusion for singleton classes to fix the extras=cxx11thread build.

commit fa5abd344243c2a5fd7e2f5820e2e56b0e1abdc6
Date:   Fri Aug 22 13:36:25 2014 -0400

    Atoms: renamed chemical::Atom::print() to show()

commit 208c67e8ceb8ac581f5e70443b36cbf34d80eeb3
Date:   Fri Aug 22 13:33:34 2014 -0400

    Atoms: added show()

commit 3222134f676959fc9e039e917d9e1f34d9946111
Date:   Fri Aug 22 12:16:54 2014 -0500

    Removing unused flags from oop_create integration test
    
    Removed mm_std weights and resfile from commandline flags after cleanup
    of options system. The score function in oop_create is hard coded to
    mm_std so the commandline weights flag was being ignored.  The resfile
    can be used during a final repack in oop_create but not in this
    integration test.
    
    oop_create integration test will change in the log file because the
    options warning will no longer print.  Also, the commentted out options
    in the flags file and deletion of res file and unused constraints file
    will show changes.  The remainder of the log file should be the same
    though.

commit 8e011b57b6d60a3b08ecc04ca39b2036ed80eeb1
Date:   Fri Aug 22 13:16:32 2014 -0400

    Atom: moving operator<< from Residue.cc to Atom.cc

commit 82b648c67c82ce73947c92b415afb1db6abe8d84
Date:   Fri Aug 22 13:15:18 2014 -0400

    Atom: adding conformation/Atom.cc

commit a1ea33c68ae71579c1011887e732e7352f914fc8
Date:   Fri Aug 22 13:11:52 2014 -0400

    Atoms: more clean-up/Doxygen

commit 48b32a42b069f2b77a08d46df325ffa0e836a69e
Date:   Fri Aug 22 12:56:15 2014 -0400

    Atoms: cleaned up files and improved Doxygen

commit 53dc2349b1ede38abdef7b8684e6704ee90e9260
Merge: d337bd1 47d559c
Date:   Fri Aug 22 11:37:58 2014 -0500

    Merge pull request #65 from RosettaCommons/roccomoretti/option_cleanup
    
    Option System Cleanup
    
    Reorganize options_rosetta.py to be a bit more ... organized. It's now ordered: major option groups (in, out, run, jd2, score, packing) first, then other general option groups in alphabetical order, then application-specific option groups in alphabetical order, and then personal/pilot option groups in alphabetical order. (Classification was done by best guess, and is not an official pronouncement. Feel free to reorganize. Also, alphabetical ordering is not absolute - logical regroupings can be permitted.) Some formatting cleanup (tabs, not spaces, despite being a .py file) was also done.
    
    Additionally, approximately 200 options which were never referenced on the C++ level were commented out. Use of these options will now result in an error when you try to run a protocol with them. (Thanks to Luki for help with the clang AST parser, which was used to ferret out unreferenced options.)
    
    Finally, a new option "-run:show_unused_options" was added. When set, at the end of the run a list of options which were user set but never actually referenced by the program will be printed out. The flag is unneeded for JD2 protocols, which will automatically print out the list of user-set-but-unused options at the end of a successful run with at least one output structure. (Thanks to Doug for suggesting this feature.)
    
    No unit test changes, but a large number of integration test changes. These are due either to removed options being removed from the flag file for integration tests, or from the new default-on-in-jd2 behavior of the show_unused_options feature, which touched a large number of tests. (A fair number of non-JD2 integration tests also have user-set-but-unused-options, but are silent in this change.)

commit cb1c6e8f41963b0611c92fd63a0a60d5d48d88c6
Date:   Fri Aug 22 18:10:05 2014 +0300

    Added to CutChainMover a functions that finds a chainbreak between input residues

commit affc756f0ce973e1e9bd6945095da3b9065d8f46
Date:   Fri Aug 22 18:04:33 2014 +0300

    Commiting Splice before making changes to the way the cut point is chosen in the loop before llc
    Right now I am getting segfaults when the source loop is the same length as the template loop

commit 5923841431c581ab0b4120ea5c7deaebd465d289
Date:   Thu Aug 21 23:52:01 2014 -0700

    Update KicSandbox to reflect recent changes to loop_modeling.

commit 99d3d13cb0ab1909b6db7375449f9ea7543fe987
Date:   Thu Aug 21 23:37:48 2014 -0700

    Add a TotalScoreFeatures features reporter.
    
    This is an alternative to the StructureScoresFeatures feature reporter.
    StructureScoreFeatures is more thorough, in a sense, because it outputs
    scores for each individual term.  But this thoroughness comes with
    several major disadvantages:
    
    1. It makes it hard to get at the total score.  First, you have to
       figure out that the total score is score type 311 (which for me
       required scrolling through 311 rows in a MySQL gui).  Then you have
       to trust that no new score types ever get added, or you have to do a
       join.  All this just to get the total score.
    
    2. It can waste a lot of space.  StructureScoresFeatures requires each
       batch to fill in the score types table.  Since it's not uncommon for
       jobs in our lab to end up creating >25000 batches, the score_types
       tables can get gigantic.  And it doesn't really have any useful
       information.
    
    The simplest and most intuitive way to store scores is to have a table
    that maps structure ids to scores.  That's what the TotalScoreFeatures
    feature reporter does.

commit 5933dbfda7e4b2755bb8f6e1862c1bb2eaabc64b
Date:   Thu Aug 21 23:03:31 2014 -0400

    Removing priority of _S_script_failed_ over _S_failed_. Fixing score test example.

commit d7402cec24dbf795141060a57e8abe3698364140
Date:   Thu Aug 21 18:12:29 2014 -0700

    Andrew's recent changes to Ramachandran (changing the behaviour of the random_phipsi_from_rama() function) broke randomization of D-amino acid phi/psi angles.  This is really my fault -- I should have added a unit test for this.  I've restored this functionality.

commit 34164d1a19baa66105a2c04c96ae64424fd7300b
Date:   Thu Aug 21 20:09:32 2014 -0400

    Triggering server run

commit 43f68c37ca61088550aa6a893b36b70fbacdd7fb
Date:   Thu Aug 21 16:47:42 2014 -0700

    improvements to FULL_MODEL_PARAMETERS output to silent structs. Do not output if the full_model_parameters looks like what you would just get with default values from the pose. Get rid of full_sequence_ stored in silent structs, since it is now held in full_model_parameters_. In default setting of WORKING_RES from a pose, set to all residues...

commit 9d30ed28984e4d5fd62cd70d9fee957e81513002
Date:   Thu Aug 21 15:26:46 2014 -0700

    major bug potentially -- in RNA base centroid screening was only looking at immediate moving_res and previous -- inefficient resampling of internal DOFs. Caught with GAGUA pentaloop benchmark case.

commit 631e26837bb7c2c61252ec3bafc6c1581fbe6fe7
Date:   Thu Aug 21 18:07:16 2014 -0400

    Adding updated resource manager hooks for membrane classes

commit bf7782d9dc3f1b2197f8ae9127280d7477f9e453
Date:   Thu Aug 21 18:04:24 2014 -0400

    Removing old resource manager hooks from core/init.cc

commit 20c13f3324916cd27b03b2a13dffc69c68f55a6f
Date:   Thu Aug 21 18:02:43 2014 -0400

    Refactoring namespaces in protocols/membrane/io

commit d762d51b134fa2a5cfbb1174091612a987f6330e
Date:   Thu Aug 21 17:57:24 2014 -0400

    Fixing namespaces in protocols/membrane/geometry code

commit bb94fbcfcade762472a798777135c9e56f7e45b4
Date:   Thu Aug 21 17:49:03 2014 -0400

    Reindexing code to use geometry and io classes at the protocols level - should show up well in xcode for src refactoring

commit 6a5c4ef214238b52e59fdc001bb4a50253a7ec7d
Date:   Thu Aug 21 17:45:17 2014 -0400

    Removing core/membrane directories and moving geometry and io to new homes at the protocol level

commit d337bd15d7bab899684cb47db07f9f12399bce42
Date:   Thu Aug 21 12:49:29 2014 -0700

    Bugfix for derivatives of RG with symmetric systems.  hybridization integration test changes expected.

commit e937f0870e274f5f98a12c5b2c644be3a4ecdfcb
Date:   Thu Aug 21 12:44:30 2014 -0700

    Fixing assert in LoopMover_CCD

commit c023a2db369fcd4c8ad867fbcffee58fe9c41f23
Date:   Thu Aug 21 12:38:05 2014 -0700

    update to pilot app

commit 77b6fec61cea930cf92d471e7f791114094230aa
Date:   Thu Aug 21 14:42:23 2014 -0400

    Updating score test example and breaking dummy test for debugging

commit 104d18487fc3edec7587c511e3b9aac52e700824
Date:   Thu Aug 21 10:28:40 2014 -0700

    update to other_pose output to silent files -- now tagging those lines with OTHER: instead of SCORE: to allow more convenient grepping of one SCORE line per model.

commit 96a825c7e61e228b28ee7eb95dbdc111039b79b2
Date:   Thu Aug 21 11:25:52 2014 -0500

    add BasicProtocolMover as stop-gap between now and broker implementation

commit 47d559ce05fa2727ac679fbe8bf70151a9987dc3
Date:   Thu Aug 21 09:38:52 2014 -0500

    Make sure -run:nodelay is touched even in debug mode.

commit 59d226b979ee1d9c4e788c13fad7539bbf4cb39c
Date:   Thu Aug 21 15:38:57 2014 +0300

    A version of Splice that works

commit 69a4d1864b219ca0f2fa7e3c105c0dea5a7c7aaf
Date:   Thu Aug 21 01:07:38 2014 -0400

    Updating benchmark scripts. Giving _S_script_failed_ higher priority over _S_failed_.

commit 95c79649b12ada0f47a9c90b36c87cf86f52fdb5
Date:   Wed Aug 20 20:59:17 2014 -0700

    fix to full_model_parameters setting to take in chain, if defined by pose. caught by failure of BinarySilentTests unit test.

commit 3d2d8548277ab59e737217efcd4921115f4ea913
Merge: 55bf3fd 6b68bc4
Date:   Wed Aug 20 17:21:28 2014 -0700

    merge from remote to stepwise_benchmark

commit 55bf3fd27eda82c3fab94f900580e3db2f62e70a
Date:   Wed Aug 20 17:20:34 2014 -0700

    adding a uucg_refit_hack1 potential to database for uucg RNA tests.

commit 3936e63d7620459b4936adfe58a687f5d39d741f
Date:   Wed Aug 20 17:45:03 2014 -0400

    Reducing maximum log size for sub-tests to 1MB

commit 6250e92cc1c2af36e2ca1550505f1c517584b66d
Date:   Wed Aug 20 15:48:49 2014 -0500

    Keep old inaccessed_user_options and new unused_options separate

commit f5ae6983732dfc03bc1cec55a72ee8fb072261cf
Date:   Wed Aug 20 14:57:33 2014 -0500

    Remove unneeded -in/out:file:fullatom magic

commit 41335204e245ed99cb1f19f395ebf1ac8cd34f4b
Date:   Wed Aug 20 14:56:47 2014 -0500

    Differentiate option group options
    
    These shouldn't be output for unused options.

commit 5e973e1100aa3b27cedf15bca43b985dff8a80bb
Merge: 1f28485 944115c
Date:   Wed Aug 20 13:25:31 2014 -0400

    Merging master into aleaverfay/multithreaded_jd2

commit 1f284859364ad993e1eb0a06e48f406246c35876
Date:   Wed Aug 20 13:23:54 2014 -0400

    Major refactoring of JobDistributor::go_main to break up this 400 line function
    which is quite challenging to read and understand.

commit 04c88d8e61fd05bb75bf57f2c3b6f77d49626459
Date:   Wed Aug 20 11:12:15 2014 -0500

    Add -show_unused_options flag
    
    This will dump set-but-unaccessed options at the end of the run.
    The functionality will also run at the end of successful JD2 runs.

commit 944115c091102e1bcc3ffa5875f11e0edf5debb9
Merge: 29ced55 e4effc5
Date:   Tue Aug 19 18:36:09 2014 +0300

     deleted a tracer in SSMotifFinderFilter

commit e4effc5cecfb1620a13d09de4db8383908c27be2
Date:   Wed Aug 20 13:56:40 2014 +0300

    some documentation in Splice, lest we forget... no test changes expected.

commit 240c100420d85de87ae0a28e8494de8fedc0a2cb
Date:   Wed Aug 20 00:57:02 2014 -0400

    Dummy commit to trigger tests run

commit a53bc9e9b6c9ecc45965d148887d8df7df4f6d08
Date:   Wed Aug 20 00:03:57 2014 -0400

    Updating benchmark integration scrip to use _S_script_failed_ state on tests that did not run. Temporary breaking HOW_TO_MAKE_TESTS test so it fail each time.

commit 2ff90c29b79805c006485e3841a098f5e05a662b
Date:   Tue Aug 19 14:59:31 2014 -0700

    fixing error for unused variable

commit 129219784e299269086e44122c0fdfdfba74b0eb
Merge: 40d212b dca1ba8
Date:   Tue Aug 19 18:53:23 2014 +0300

       Updated the follwoing integration tests:
        1. splice_out_generic
        2. splice_out
        3. splice_in_genric
        4. splice_in
        5. splice_seq_const
    These ofcourse will fail compared to previous commits
        In Splice.cc:
        1.Add Carbonyl coordiante constraints
        2. Changed the current segment behvaiour so it reads the current segment from the XML rather than the pdb
        3. In SpliceSegments the occurrence data for H3 loops with no occurrence data is filled in by Rosetta (previously this caused a segmentation fault)
        4. In SequenceProfile I added getter and setter functions for accessing the occurrence_data array
        5. In SeqprofCons I added tracer lines to check correctness of occurrence_data array

commit 40d212b823091026ccfbe147c905a3ed451edf59
Merge: c833d13 4dddd40
Date:   Tue Aug 19 18:52:15 2014 +0300

    esolved conflicts between Splice.cc on local branch and remote branch
    
    Conflicts:
    	source/src/devel/splice/Splice.cc

commit 29ced5551f91bb8104618e164337b67f39a71374
Date:   Tue Aug 19 18:36:09 2014 +0300

     deleted a tracer in SSMotifFinderFilter