commit 840ffd57a64d4c0dc6234a80fa031bfb7bacf1c9
Merge: 1b66840 ec33383
Date:   Wed Apr 29 11:23:38 2015 -0700

    Merge pull request #494 from RosettaCommons/vmullig/fix_atomtree_mover
    
    Removing FoldTree reordering in the parse_my_tag() function of the AtomTree mover.
    
    If the user does not want a FoldTree rooted on residue 1, he/she should not get a Foldtree rooted on residue 1.
    
    No integration test changes or unit test failures expected.

commit 1b668405f29d6b3cd90aa9f884867b6e49494061
Merge: 5095b25 b1b7402
Date:   Tue Apr 28 19:55:06 2015 -0700

    Merge pull request #492 from RosettaCommons/vmullig/minor_tweak_1
    
    Minor change to backbonegridsampler_nstruct_mode integration test.

commit 5095b252400c693ee3882ea37f133eb432846ec5
Merge: 1abe2c3 8f1fa8d
Date:   Tue Apr 28 14:03:05 2015 -0500

    Merge pull request #478 from RosettaCommons/roccomoretti/bowdlerize
    
    Remove some of the known user-facing swearing in Rosetta

commit 1abe2c34b9961f9d60e958e4ce8476be2e31705b
Date:   Mon Apr 27 19:44:00 2015 -0700

    adding xray/electron scattering factors for metal ions.

commit bb3f2ad03f93c5360b4b8e076488141cec720f7e
Merge: 0f3afb1 0aba1cf
Date:   Mon Apr 27 17:58:24 2015 -0700

    Merge pull request #474 from RosettaCommons/tlinsky/genericmc
    
    Fix uninitialized variables/segfault in GenericMonteCarloMover

commit 0f3afb1acb48f0271802e22f617b725c5bfb644a
Merge: 3b624d3 627e08c
Date:   Sat Apr 25 10:44:27 2015 -0500

    Merge pull request #477 from RosettaCommons/roccomoretti/no_scores_in_pdb
    
    Add option -out:file:no_scores_in_pdb
    
    This prevents addition of the scoretable and the extra scores at the end of Rosetta PDB output. The default is to preserve the current behavior (with the score table in output).

commit 3b624d3fbfa9f8448f542524cc30f38abb9a379a
Merge: b387389 ddfc204
Date:   Sat Apr 25 13:16:31 2015 +0200

    Merge pull request #485 from RosettaCommons/smoe/no_raw_strings_prior_to_cpp11
    
    smoe/no raw strings prior to cpp11
    
    Concerning \n across platforms see
    http://stackoverflow.com/questions/3671462/is-n-multi-character-in-c
    or  Rocco's comment :+1:
    Many thanks.

commit b38738909a0589988c0a99baacecf5d5c7ff800d
Merge: 2b13761 63d3984
Date:   Fri Apr 24 02:07:56 2015 -0700

    Merge pull request #484 from RosettaCommons/vmullig/ncaa_residue_counter
    
    Updating ResidueCountFilter.cc to work if the input pose has a different residue type set from the pose at apply time.
    
    This can happen if, for example, the parse-time pose is a centroid pose (e.g. the product of the -in:file:fasta flag) while the apply-time pose is full atom. The current hacky fix is to try first with the residue type set of the parse-time pose, then with the fa_standard residue type set.
    
    Note that mpi tests have been failing intermittently depending on which test server node runs the test.  Aside from this, no integration or unit test failures are anticipated.

commit 2b13761214ace18a200138d589dc3f51f2f6b897
Merge: bbd4a29 5bbf3f7
Date:   Thu Apr 23 16:10:23 2015 -0700

    Merge pull request #480 from RosettaCommons/vmullig/demo_fix_1
    
    Fixing a "bug" for the Rosetta 201 training session.
    
    
    
    This is intended to demo the GitHub pull request workflow for Bakerites during the Rosetta 201 lecture on Thursday. The "bug" is a typo in an output message in GeneralizedKIC that I introduced deliberately a few days ago. Fixing this should result in cosmetic integration test changes in the GeneralizedKIC tests.
    
    (This is the "Martha Stewart" pull request that I'm setting up the day before so that it will be all tested and ready to go during the actual session, so that I can push the big green button there. "So put that in the oven and let it bake. Now here's one we made earlier.")

commit bbd4a297f9c02b99751ab24f32a06f07e2dd3809
Merge: 8dfd864 51f0600
Date:   Wed Apr 22 21:26:17 2015 -0700

    Merge pull request #473 from RosettaCommons/tlinsky/dssp_zero
    
    fix dssp so that it doesn't segfault on zero-length poses

commit 8dfd86473eae5ace594b6c59353cbdd1c777aa9d
Merge: 025c48f e2808c8
Date:   Wed Apr 22 17:21:27 2015 -0700

    Merge pull request #479 from RosettaCommons/vmullig/z_is_for_zibo_that_good_enough_for_me
    
    Adding Crick parameters for an alpha helix with a turn per residue of exactly 100 degrees
    
    The new Crick parameters file was generated by fitting an alpha helix with phi=-62.648, psi=-41.0, omega=180.0. No test changes expected (database-only change).

commit 025c48f99c8cda6bd75d9c44f401f26a6d52a456
Date:   Wed Apr 22 15:48:45 2015 -0700

    fixing build

commit f9ef7e42e8f95d8e7a3dd5576579792dfb27ec89
Date:   Wed Apr 22 13:38:50 2015 -0700

    Adding a few new options to crystal refinement

commit 6a9d7f904c253091f202b0c5a3fea7f50c346d20
Merge: 0b0f978 5ff90f4
Date:   Tue Apr 21 17:04:29 2015 -0700

    Merge pull request #472 from RosettaCommons/calebgeniesse/backtrace-color-reset
    
    Fix std::cerr color reset in backtrace.hh

commit 0b0f97857f0d476506bf0846ecd8495530608737
Merge: 8419cb6 369d103
Date:   Tue Apr 21 10:35:21 2015 -0700

    Merge pull request #471 from RosettaCommons/vmullig/z_is_for_zibo_that_good_enough_for_me
    
    Adjusting z1_offset parameter in helical bundle code to match Grigoryan paper's convention.
    
    This adds a correction factor so that z1_offset is measured as the offset along the global z-axis, in Angstroms, rather than as the offset along the local helix axis. This is intended to match Grigoryan and DeGrado (2011) J. Mol. Biol. 405(4):1079-1100.
    
    Tasks:
    
    --  Add correction factor.
    --  Double-check that this does, indeed, produce the correct offsets.
    --  Update documentation.
    --  Also, switch convention for inverted helices.  (They now move in the opposite direction to right-side-up helices).
    
    Expect integration test changes to z0_offset and z1_offset integration tests for the BundleGridSampler and PerturbBundle movers.

commit 8419cb653b49149b7bfb0da756421f7b8ca37fc7
Merge: c2c5d3f 80e7940
Date:   Tue Apr 21 09:30:44 2015 +0300

    Merge pull request #468 from RosettaCommons/sjf/FilterScan
    
    FilterScan will now append entries to the resfile rather than writing a ...

commit c2c5d3f851d6dfdeb30c214eb7751103a09b6f16
Merge: c876538 081cea9
Date:   Mon Apr 20 18:10:55 2015 -0700

    Merge pull request #470 from RosettaCommons/vmullig/demo_fix_1
    
    Small cosmetic change to GenKIC

commit c8765386401b9b9e7d4797ab833de2d1b723e8ea
Merge: 3a75290 310a5da
Date:   Mon Apr 20 14:06:48 2015 -0700

    Merge pull request #458 from RosettaCommons/sheffler/holes_fix
    
    RosettaHoles Fix: add atomtype mapping to remove fixed numbering assumption in rosettaholes

commit 3a75290595982bc41a2f8e1c0cc3409f5db22fca
Merge: 87b3c01 5fa817e
Date:   Mon Apr 20 09:54:38 2015 -0700

    Merge pull request #466 from RosettaCommons/tjbrunette/repeat_code
    
    fix to the remodel_repeat integration test

commit 87b3c0156148742a2649029b9c43200f680aaaad
Merge: 679b68a 6e3b82c
Date:   Sun Apr 19 18:43:24 2015 -0500

    Merge pull request #465 from RosettaCommons/justinrporter/env_release
    
    Error reporting for RigidChunkCM & SlidingWindowLoopClosure. Performance and integration test changes are being shown for other branches as well--will revert if they persist.

commit 679b68a21fc3ffcca0a1a20a9a8adfe52c4d6aee
Date:   Sun Apr 19 09:33:25 2015 +0300

    reverting change in FragmentPicker.cc which caused integration test break

commit df6e44d84174a47b9ddeedb51c10a35559637348
Merge: afcffb4 31cb00a
Date:   Fri Apr 17 15:11:59 2015 -0400

    Merging in build-setting change that avoids a warning from
    g++4.9 in ObjexxFCL::DynamicIndexRange that just makes no sense

commit afcffb4eb3adc24eaaef148e390e8260c7159d96
Date:   Fri Apr 17 15:06:29 2015 -0400

    Saving a modification to basic.settings to avoid an error out
    of ObjexFCL::DynamicIndexRange that just makes no sense and
    that only shows up in g++4.9

commit 1c0f4089cbc4f4ebc921e7660d9c8c3fba2607b5
Merge: aae51e5 d672518
Date:   Tue Mar 31 10:17:49 2015 -0700

    Merge pull request #423 from RosettaCommons/tlinsky/tlinsky/remodelloop_sealfoldtree
    
    Add "seal_foldtree" option to RemodelLoopMover

commit aae51e5adfd62ab775e51ee2b1718244e7442c5d
Merge: f7cf37f 6430228
Date:   Tue Mar 31 11:05:41 2015 +0200

    Merge pull request #421 from RosettaCommons/smoe/find_python_modules_also_as_symlink
    
    Excluding MacOS X from readlink PyRosetta setup.sh

commit f7cf37f8b590e4df4c8f5b59915162b5bfe3e256
Merge: 6aa1e22 1e71e09
Date:   Mon Mar 30 19:35:00 2015 -0700

    Merge pull request #425 from RosettaCommons/vmullig/genkic_sampling
    
    Vmullig/genkic sampling
    
    Small change to GenKIC output requested by Gaurav. This might cause some cosmetic integration test changes to one of the GenKIC integration tests.

commit 6aa1e2295dcf61d237675435235e5ccb3239ea25
Date:   Mon Mar 30 18:44:39 2015 -0700

    A few more options to hybrid
    - bugfix for starting from extended chain
    - change add_non_init_chunks to integer parameter indicating the mean number of off-template chunks to steal (Poisson distribution)
    - max_contig_insertion is now applied in stage 1 in addition to stage 2

commit 50d8c93daa00fbfc73f6658bb61a166af049767f
Merge: 8f13df1 a442743
Date:   Mon Mar 30 12:34:10 2015 -0700

    Merge pull request #405 from RosettaCommons/tlinsky/disulfidize
    
    Improvements to disulfidize mover

commit 8f13df1821e0eab6a4953ef05acf8f4ab07d9c2a
Merge: 77ccc95 33e058b
Date:   Mon Mar 30 02:27:04 2015 -0700

    Merge pull request #422 from RosettaCommons/tlinsky/remodelrevert
    
    Revert change to remodel that caused problems for repeat proteins

commit 77ccc95fa250d61d9a1ed30a6ee3462540d94062
Merge: 34f1e31 029337b
Date:   Sun Mar 29 12:33:13 2015 -0700

    Merge pull request #368 from RosettaCommons/rhiju/stepwise_benchmark
    
    integrating stepwise_benchmark

commit 34f1e311842178aed03cf63d44b43d54cce23fdd
Date:   Sat Mar 28 13:56:10 2015 -0400

    Typo fix--null commit to test performance tests

commit 57e281b0bfa3551cd932afef424c8e21f3c660d9
Merge: 5de348c 1156452
Date:   Sat Mar 28 13:55:04 2015 -0400

    Updating performance benchmarks to hopefully achieve stability at last

commit 5de348c48f3da7e5503cf676559615546b5853aa
Merge: afa8f0b ff6efcf
Date:   Fri Mar 27 17:48:40 2015 -0700

    Merge PyRosetta build fixes.

commit afa8f0b615f78ebd6c87f9ec2625fe7e60d383b2
Date:   Fri Mar 27 17:25:40 2015 -0700

    Fix PyRosetta build

commit d3d1dbb805c57098aa4ea0af67297713fac2d087
Date:   Fri Mar 27 14:54:07 2015 -0700

    Missed a file in my previous commit

commit 14bce6aa1f4b2187007be97a0506f71ff00b5abe
Date:   Fri Mar 27 14:48:12 2015 -0700

    Another set of updates for RosettaCM.
    - updated logic for fragment placement in stage 1
    - updated domain parsing logic in realign_domains
    - fixing bug in realign_domains where templates would accumulate drift over time (thanks Rocco!)
    - better handing of realignment of ligand-containing poses
    - removing more unused or redundant options
    - small changes to smoothing kernel for fragment-derived constraints
    - removing extraneous output accidently checked in in the previous commit
    
    Hybridize and mr_protocols integration test changes expected.

commit aa5247d80cd6f601b4cb5bc9329b6fdd4366acfe
Merge: 0e9cd5a 27c6086
Date:   Thu Mar 26 20:11:37 2015 -0700

    Merge pull request #418 from RosettaCommons/tlinsky/jd2_format
    
    Make jd2 follow its typical %04d format in MultiplePoseMover tags

commit 0e9cd5ac094853f1ed650c83dbeb33f8c0d1106a
Merge: 847d777 2ac2297
Date:   Thu Mar 26 17:25:12 2015 -0700

    Merge pull request #417 from RosettaCommons/tlinsky/multiplepose
    
    Prepare MultiplePoseMover for overriding.

commit 847d777e5980d988f0ce298a6532f11aaa0333d4
Merge: e0894f5 ff26b50
Date:   Thu Mar 26 08:52:05 2015 -0400

    Merge pull request #416 from RosettaCommons/rfalford12/add_ddG_script
    
    Add PyRosetta script for membrane protein ddG Predictions

commit e0894f519515dcd5dd9f85758c834feb7db1ef7c
Date:   Wed Mar 25 13:34:29 2015 -0400

    Reverting 57732

commit edcf63b47b40856f3356ac6472871330c1d281fd
Date:   Wed Mar 25 13:33:53 2015 -0400

    Reverting 57736

commit 9e2dd10d41f1df77e4b640ef4463efc4be5bc8dd
Date:   Wed Mar 25 13:33:34 2015 -0400

    Reverting 57737

commit 9b655a83d65f2932daf2260dc227b3f8f4c130f2
Merge: f6d177a d77db74
Date:   Wed Mar 25 09:19:09 2015 -0400

    Merge pull request #408 from RosettaCommons/rfalford12/add_var_thk
    
    Add thickness/steepness setters to MembraneInfo - Allow the user to adjust the membrane hydrophobic thickness and transition steepness, symmetrically about the center along the normal axis. This can be done programmatically and via the command line. Additionally, the thickness used by the PyMOL viewer is now linked to MembraneInfo (can also be changed separately)
    
    No test changes expected

commit f6d177a956bdb5d624c7275054e5a3e7fe03dfa2
Date:   Wed Mar 25 01:17:24 2015 -0400

    Update FastRelax.cc
    
    I am doomed to forever break master when I quickly fix bugs online. Curses.

commit 80704780adfad85b98960f398b0eccf094f2094d
Date:   Wed Mar 25 01:01:38 2015 -0400

    Embarrassing error turned nrchi_min on by default

commit dbd801b32fee2c626a08c3fd05b818bd32e70f2a
Date:   Tue Mar 24 18:56:06 2015 -0700

    Updating Xcode project.pbxproj.template so that core.1 properly links to basic and Xcode compile now works.  Because I'm only changing this one file, and it only affects Xcode and no other builds, I am pushing to master without pull request or test servers

commit 8ad359fff21c4fc0824a0068a575e23f6f5162c0
Merge: 0cd8b27 ee24a06
Date:   Tue Mar 24 17:38:41 2015 -0400

    Merge pull request #400 from RosettaCommons/JWLabonte/sugars/ring_conformers
    
    Code clean-up and refactoring of the `RingConformerSet`-related code.
    
    NEWS:
    This merge should allow one to use the `RingConformationMover` on NCAAs with aliphatic, saturated rings, provided the `.params` files are set up properly.
    This merge also allows one to specify the lowest and low-energy conformers in the topology files for residues with rings, if this information is known. The `RingConformationMover` will by default only select ideal ring conformers from among this set.
    
    no unit test changes
    carbohydrates and rings integration test changes expected
    In addition, this merge makes the following improvements to the ring conformer system:
    * `RingConformationMover` should now work with RosettaScripts.
    * All static const `RingConformer` data that a `RingConformerSet` uses is accessed via the singleton `RingConformerManager`, so everything should now be thread-safe.
    * An option flag `-sample_high_energy_conformers` allows the `RingConformationMover` to do exactly that.
    * Unit tests for ring-related things are more robust.

commit 0cd8b276db0192b61cef9e5a27488dad84bafaa3
Merge: 1bb4f7c 0bf9fd0
Date:   Tue Mar 24 14:46:39 2015 -0600

    Merge pull request #412 from RosettaCommons/benchmark
    
    Adding scientific test templates

commit 1bb4f7c39b77c8b2a90420f98dc4459dbbc25d35
Merge: b284df5 dcb23f5
Date:   Tue Mar 24 15:27:59 2015 -0400

    Merge pull request #393 from RosettaCommons/everyday847/nrchi_minimization
    
    Non-rotameric chi minimization, the utterly trivial option to select all the non-rotameric chis in a protein and minimize them after every repack, is now implemented. Default to off because of course it is! Won't work for NCAAs, but that's okay--once I've made enough NCAA densities style rotlibs to make it worthwhile to actually use the SEMIROTAMERIC_NCAA property enough, I'll use it here too...

commit b284df5ab1c997dbd9a4f6d00a9c16e3b4cdacd8
Merge: 8b3852e a024e5b
Date:   Tue Mar 24 15:14:37 2015 -0400

    Merge pull request #410 from RosettaCommons/aleaverfay/dfpmin_memory_alignment
    
    This commit addresses the memory access pattern for DFPMin.  It produces many (real) integration test changes on my machine (though not on the testing server), but the change is small enough that I am confident the changes do not reflect a bug.
    
    ...
    
    Changing dfpmin's access pattern to the HESSIN matrix to better align with memory.
    
    This change is small, and though it looks like it ought to produce no integration test changes, it does.  Why?  I suspect that it's due to code that previously prevented vectorization now suddenly allowing it. Vectorized arithmetic produces subtle numeric differences.
    
    Updating the Hessian accounted for a large amount of the running time in relax when run on some of Stampede's machines.
    
    Thanks to Cyrus Proctor at TACC for finding this issue!

commit 8b3852e1e37887d586c786c6299324dcedb64ae5
Date:   Tue Mar 24 13:05:18 2015 -0400

    Disabling the antibody_graft integration test

commit c1978efc524b508c89417af6183af96b169f1455
Merge: b1611f2 ee5af9b
Date:   Tue Mar 24 10:50:50 2015 -0400

    Merging code duplication elimination efforts from everyday847/everyday847/simian
    The pull request documents the specifics:
    1) A refactored agglomerative hierarchical clustering system in numeric
    2) rsigma_dot gets its data from the database now, instead of 3 separate, identical 866 line regions of the code
    3) ChiralMover relies on data from the database (CHIRAL_EQUIVALENT in params files) rather than big std::maps
    4) NCBB design apps rely on common main loop, statistics functions, and perturbation foldtree functions
    5) Ditto the NCBB dock-design pilot apps/protocols, but the main loops are still separated (sampling differences)
    
    Integration tests are limited to log output changes (a couple tracer name changes, basically)

commit b1611f254aaa7b7db5474d9328e7dbd03badcb57
Merge: 5fbcfe3 9812d37
Date:   Mon Mar 23 19:13:14 2015 -0500

    Merge pull request #413 from RosettaCommons/bazzoli/shobuns
    
    Added 'return -1' statement to catch-block in app minimize_ppi

commit 5fbcfe331d3cd28da37a7471d0d0e8af21f47d72
Merge: 3c637b9 842ae9d
Date:   Mon Mar 23 18:30:34 2015 -0500

    Merge pull request #411 from RosettaCommons/bazzoli/shobuns
    
    Moved return statement inside try-block in app minimize_ppi

commit 3c637b95ee98562a7d3fb323afbe5181a77c4890
Merge: ca8b73a 1464b21
Date:   Mon Mar 23 12:44:58 2015 -0700

    Merge pull request #398 from RosettaCommons/tlinsky/remodel_mover_option_fix
    
    Checking for the pymol mover option should use .user() rather than .acti...

commit ca8b73ad2a49549838dbf771510fdce88011ed15
Merge: 99cf196 1392d98
Date:   Mon Mar 23 12:44:39 2015 -0700

    Merge pull request #390 from RosettaCommons/tlinsky/multiple_output_tags
    
    MultipleOutputWrapper now follows the jd2 convention of using a zero-pad...

commit 99cf1964acd4c1cb2fe92a9229b821766bb07c63
Merge: 1f15295 440f98f
Date:   Mon Mar 23 12:26:35 2015 -0700

    Merge pull request #409 from RosettaCommons/hahnbeom/patchs
    
    fixing broken unit tests with cart_bonded updates

commit 1f1529561652af48346e6aa6d7ea3ec03d6453ba
Merge: 89f648c 8d1ce30
Date:   Mon Mar 23 11:42:33 2015 -0400

    Merge pull request #399 from RosettaCommons/jkleman/jkleman/mp_updates
    
    MP updates:
    * rewrote and extensively tested SpanningTopology constructor from PDB
      * it is vastly improved and recognizes spans better
      * I tested on 34 previously broken cases, except a handful they work now
      * small problems that still occur are due to Dssp recognizing loops instead of
        secondary structure elements
      * a difference now is that spans that might not completely span the membrane
        might be recognized as "TMspans"
      * also, loop residues (except up to 3 residue loops bridging spans) are
        now excluded from the spans (and there seem to be quite a couple in the
    		structures that I looked at)
      * this impacts the spanfile_from_pdb app!!!
    * added unit tests for this constructor
    * added unit test for average_antiparallel_embeddings in MembraneGeometryUtil

commit 89f648c31eca26791e306f172c46ebf144410770
Merge: fc23868 8fec97e
Date:   Sun Mar 22 17:14:49 2015 -0400

    Merge pull request #407 from RosettaCommons/rfalford12/update_pHmode
    
    Update pH Energy Function for Membranes
    Adding electrostatic term (fa_elec) with a weight of 0.875 to the membrane pH enabled full atom energy function - needed for pH mode pyrosetta demo. No test changes expected.

commit fc238681b0c35920cecb343d63bb5c8dc43fcdba
Date:   Sun Mar 22 13:00:12 2015 -0700

    Adding some DNA lengths and angles to cartbonded database, as they are incorrectly generated in some cases.

commit 20cd547dad381cc59455ad012c9294e0afc9386b
Date:   Sun Mar 22 12:54:56 2015 -0700

    A few updates to hybridize protocol.
    Adding a few new parsable options to hybridize, allowing control of the fraction of fragment versus template insertions.  Ading some code to cart bonded energy for better handling of non-protein residues.

commit e7867c4ef535a21d8e246b19c2f37b7041de319d
Date:   Sun Mar 22 10:40:46 2015 -0500

    Fix some -Werror issues with clang 3.4.2 on linux

commit f7812b46af679a092e5757ce3fbc2250567e3bac
Merge: 2f1bf47 0ca1bd0
Date:   Sat Mar 21 01:26:55 2015 -0700

    Merge pull request #404 from RosettaCommons/tlinsky/buildfix
    
    fix the mac builds

commit 2f1bf47bf70e3d94960654b68f5e8e0d6007493e
Merge: 00371f6 583291e
Date:   Fri Mar 20 17:25:17 2015 -0700

    Merge pull request #406 from RosettaCommons/hahnbeom/patchs
    
    scorefunction test fingerprint update to accommodate the change in cart_...

commit 00371f6e111b7791ebb644fc98bb16784cc6565f
Merge: 8f091b4 de8266f
Date:   Fri Mar 20 14:06:54 2015 -0700

    Merge pull request #397 from RosettaCommons/hahnbeom/patchs
    
    Optimizing ideal angles related to PRO closure in cart_bonded term

commit 8f091b40dad36a28a52af36dae4e3b9ab19ccef9
Date:   Fri Mar 20 04:31:16 2015 -0700

    Finish comprehensive unit tests for DisulfidizeMover

commit 62c10b4afd6dd8131fb87939755edf027afe1aba
Date:   Fri Mar 20 02:27:11 2015 -0700

    Add test structure to disulfidize unit test

commit 2c888109fa65b548a885cb53497abf899fbf266b
Date:   Thu Mar 19 20:49:15 2015 -0700

    Add DisulfidizeMover for incorporation of disulfides into poses

commit 7a5dca72b85ef166a6f34eecb7fdbf25dfbac1b1
Merge: 5c86db2 5a53e0e
Date:   Fri Mar 20 11:06:42 2015 +0100

    Merge pull request #388 from RosettaCommons/smoe/find_python_modules_also_as_symlink
    
    Introducing readlink to SetPyRosettaEnvironment

commit 5c86db22947db6802ceb77e722cc9776cf2cd8b4
Merge: 027551d 156ae36
Date:   Thu Mar 19 23:34:17 2015 -0700

    Merge pull request #401 from RosettaCommons/vmullig/fix_sc
    
    Adding fluorine to the sc_radii for the shape complementarity calculator
    
    Trivial database change. No test changes expected.
    (Also, fixed the PyRosetta tests that TJ accidentally broke while I was at it.  @tjbrunette, when you get a chance, please check protocols/simple_filters/RepeatParameterFilter.hh line 47 -- there was a function prototype here with no function defined for it that I commented out.)

commit 027551d1c968d9252766794e261968966929c6ff
Merge: b211257 e244db1
Date:   Thu Mar 19 14:51:43 2015 -0700

    Merge pull request #396 from RosettaCommons/tjbrunette/repeat_filter
    
    added handedness to RepeatParameterFilter & cleaned up the code

commit b2112579a953b4686278016f692936777a63dba2
Merge: fc83c9f 74373a4
Date:   Thu Mar 19 10:18:24 2015 -0500

    Merge pull request #391 from RosettaCommons/bazzoli/shobuns
    
    Calculator and pilot app for buried unsatisfied polars under the SHO solvation model

commit fc83c9f3ba979d04a28b70dd5fefadc9338d8038
Merge: 0bb66f8 36116fd
Date:   Wed Mar 18 23:22:36 2015 -0600

    Merge pull request #395 from RosettaCommons/PyRosetta
    
    Updating PyRosetta build scripts so it works on Yosemite. Also fixing PyRosetta release archive names so tar will not get confuse on some shell's.

commit 0bb66f829f170aadf214a6e5e6bb077cdb3c53f1
Date:   Wed Mar 18 13:24:52 2015 -0700

    Fixing uninitialized read in hybridize (thanks Rocco for finding this)

commit dcc7e91ada56ed4477bb61b60ed81e3a1b8bfc6f
Date:   Wed Mar 18 11:47:46 2015 -0500

    Fix cc file inclusion in contactMap application.
    
    Bug fix on behalf of @schaarj (Joerg Schaarschmidt)

commit f24653e0d365d4380a0f11a90ca2ad80de3668ad
Date:   Tue Mar 17 20:45:48 2015 -0400

    Update RotamerLibrary.cc

commit cf8aa610775aa175694a472b0fd7fc01f2ddb39a
Merge: bb3f92b 9881b52
Date:   Tue Mar 17 16:24:33 2015 -0700

    Merge pull request #386 from RosettaCommons/vmullig/genkic_sampling
    
    Vmullig/genkic sampling
    
    
    
    This adds support for D/L-proline sub-bins to the BinTransitionData object, and updates the ABBA.bin_params file accordingly.
    
    Tasks:
    
        Update ABBA.bin_params
        Add support for D/L-proline sub-bins to the BinTransitionData object.
        Update documentation.
    
    No test changes expected.

commit bb3f92b6929051e68b13226ce813fb8b0960cb40
Merge: 01e21e1 349c6c0
Date:   Tue Mar 17 11:54:24 2015 -0700

    Merge pull request #392 from RosettaCommons/calebgeniesse/stepwise-test-observers
    
    updating 'observers' of SWA/SWM integration tests

commit 01e21e1a72cfcbeb2234acbeda43ce0355b6bbc4
Merge: 91f99ce e3fb833
Date:   Tue Mar 17 09:31:52 2015 -0500

    Merge pull request #387 from RosettaCommons/roccomoretti/cluster_filter
    
    Reenable -cluster:input_score_filter option in cluster application

commit 91f99ce23eccecffc05e19d936057064c254735d
Date:   Mon Mar 16 17:05:08 2015 -0700

    Fixing pyrosetta & other broken builds.  Removing per-residue sequence shift controls since they were only working previously for one mode, which has since been removed.  Restoring old global sequence shift control which had been previously disabled.

commit ea098777b1d372d7232ef42dfa0a905ea16efa57
Merge: 49ef504 8cdd3c6
Date:   Mon Mar 16 13:05:28 2015 -0700

    Merge pull request #376 from RosettaCommons/calebgeniesse/rna_bulge
    
    fixing another bug in calculation of rna_bulge score

commit 49ef504bebd8e41ed04ff3c8951ee3c65e879563
Date:   Mon Mar 16 11:41:36 2015 -0700

    A number of updates for hybridize (RosettaCM).
    New features:
     - if template="extended" is specified, this will trigger ab initio sampling in stage 1.  This may be combined with template structures to allow fragment harvesting.
     - add an option 'max_contig_insertion' that sepecifies the max length continuous segment that will be inserted in stage 2.  This allows more model diversity when fulllength inputs are provided.  Default of -1 maintains current behavior.
     - add an option 'csts_from_frags' that generates dihedral constraints from fragments that may be used in minimization during stages 2 and 3; useful for CS fragments.  Adds a new constraint type, CircularSplineFunc.
    
    Smaller changes/bugfixes
     - turning on align_templates_stage2 by default
     - removing the ramping of constraint energies in stage 2
     - tweaking of probabilities of moves in cartesian hybridize
     - changing the logic for determining allowed insertions, no flooding the screen in warnings if no insertions allowed
     - cenrot is now turned on by an XML switch (the flag is still needed to enable loading of the rot library)
     - template realignment and ligand placement are no longer mutually exclusive
     - changing the hbond weight to 1.0 (was 2.0) in score4_smooth and score4_smooth_cart, based on extensive testing
    
    Removing duplicated/unused code:
     - Removing the separate HybridizeSetup mode of initialization since functions were copy/pasted directly from HybridizeProtocol and the versions had already gone out of sync
     - For the same reason, removing separate parsing of the individual stage 1 & 2 movers since code had gone out of synch, moving some added functionality from
     - removing DomainAssembly mode
     - removing a few other unused modes
    
    Additionally, making a small bugfix to silent file reading (should not be encountered in normal silent files; but may allow recovery of structs from corrupted ones).
    
    Finally, some updates to pilot apps.
    
     ** hybridize and mr_protocols integration test changes expected.

commit 6c9dc67aa2823b1987a5ce22c794fa515384da41
Merge: efc0810 1f1325d
Date:   Sun Mar 15 21:35:08 2015 -0700

    Merge pull request #385 from RosettaCommons/tlinsky/remodelfix
    
    Fix apparent bug in RemodelMover where the PymolMover was always attache...

commit efc0810fb6ecef0aed7fd50a9655065fa0577112
Merge: 033713c 04cebd5
Date:   Sun Mar 15 21:34:15 2015 -0700

    Merge pull request #375 from RosettaCommons/tlinsky/remodelmover_accumulator
    
    Remodel mover now returns without further computation if accumulator is ...