commit bd611ddc23a87985b1d9caf342edd9b718580e7c
Merge: 2d905aa ac508e7
Date:   Fri Feb 27 11:24:02 2015 -0600

    Merge pull request #324 from RosettaCommons/roccomoretti/braaaiiins
    
    File-level dead code removal
    
    Remove files that aren't compiled or used by any of the standard processes (regular build, unit test, PyRosetta) This includes both .cc files and header files. Only the main library directories (basic, utility, numeric, core, protocols) have been cleaned. "External" libraries (I include ObjexxFCL in this) weren't touched. I also didn't touch the unit test directory (I want to make it easy to re-enable those tests which aren't running currently), nor the apps or devel directory (as I didn't want to penalize people who sped up compilation by turning off their devel work). -- Though if we're sunsetting the devel directory, a cleanup there may be warranted.
    
    If I deleted something you needed, feel free to add it back (remember it's still available in git's history), but: 1) make sure you put the .cc file in the appropriate .src.settings file 2) make (and enable) a unit test for the functionality
    
    No test changes expected, as the removed code shouldn't be used.

commit 2d905aad02e6abd022eff11c0ed511ac8b3d9fbe
Date:   Thu Feb 26 17:03:13 2015 -0500

    updating the site.settings.tacc.stampede for compatibility with new pointer system.  These setting have been tested on stampede and work properly as of this commit.  Thanks to Cyrus Proctor for helping me determine the correct settings

commit f81002db341b31938a5767d4c5f99afaa51e4377
Date:   Thu Feb 26 16:38:14 2015 -0500

    trying to revert my revert

commit a89befdab9019be9718a5a26f5668271ca662ba9
Merge: bc4d219 f05812e
Date:   Thu Feb 26 15:31:45 2015 -0500

    Re-merging pull request number 328
    
    Only carbohydrates test should change.

commit bc4d21982239a9655a5f1dd81ae7b501f43e1f73
Merge: 5b71444 f894898
Date:   Thu Feb 26 14:49:11 2015 -0500

    Merge pull request #340 from RosettaCommons/revert-328-JWLabonte/sugars/input
    
    Revert "Properties/VariantTypes Refactor Part IIB & CarbohydrateInfo Pro...
    
    (I didn't notice that I had changed one integration test. Oops!)

commit 5b71444e2b618a272a6421d82e19760a8bd6d067
Merge: 8ac6676 85c9417
Date:   Thu Feb 26 14:40:22 2015 -0500

    Merge pull request #328 from RosettaCommons/JWLabonte/sugars/input
    
    Properties/VariantTypes Refactor Part IIB & CarbohydrateInfo Property-Handling Refactor
    
    The purpose of this code is to ultimately allow one to generate poses with branched and/or modified carbohydrates from annotated sequences or `.GWS` files. Currently, branching and modified sugar residues can only work if loaded in from a `.pdb`.
    
    To do this, I realized I needed to go back to my unfinished refactor of the `Properties`/`VariantTypes` system just a bit, so this merge will include a mixture of changes.
    
    Please see: `source/src/core/chemical/residue_properties/README.txt` in this pull request for what I'm doing with the `Properties`/`VariantTypes`.
    
    All unit tests pass.
    Carbohydrate integration test changes are expected.

commit 8ac6676808f884a0a40b71988a0152ff195d0a45
Merge: 1e75064 d2faac3
Date:   Thu Feb 26 01:20:15 2015 -0800

    Merge pull request #313 from RosettaCommons/vmullig/genkic_sampling
    
    Create a bin transition probability-based backbone sampling method.
    
    This allows sampling based on the probability of residue i being in mainchain torsion bin X, given the mainchain torsion bin of one or both adjacent residues.
    
    
    
    Organization/Tasks:
        In database/protocol_data/generalizedKIC/bin_params/, added data files for bin transition probabilities.
        In core.3 (core/scoring/bin_transitions/) created a new BinTransitionCalculator class with methods for calculating bin transition probabilities, and a new BinTransitionData class for storing bin transition probability matrices and derived data. These classes also have methods for reading in bin transition probability data files. (Note that this has to be in core.3 because it draws on functions from the Ramachandran class, and it will be used by energy methods among other things.)
        Added a unit test for some of the core functionality of the above.
        In protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber class, added a new "randomize_backbone_by_bins" perturber.
        In protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber class, added a new "perturb_backbone_by_bins" perturber.
        Adding an integration test for GenKIC with bin-based initialization.
        Adding an integration test for GenKIC with bin-based perturbations.
        Adding a stand-alone randomize mover.
        Adding a stand-alone perturb mover.
        Adding integration tests for the stand-alone randomize mover.
        Adding integration tests for the stand-alone perturb mover.
        Documentation.
    
    Put off to a future pull request:
        Figure out how to do the stats for D-amino acids, and add D-amino acids probability matrices to the database.

commit 1e750649f2de09ff079d8347677cb7736f3225bb
Merge: e8b0389 4b07df6
Date:   Wed Feb 25 19:07:33 2015 -0800

    Merge pull request #270 from RosettaCommons/calebgeniesse/mac-stack-size
    
    Increasing process and thread stack size (at runtime) on macs.

commit e8b0389a486134ee38562232699d07cd1c5c4b7f
Merge: 59015e4 8f4c838
Date:   Wed Feb 25 17:46:40 2015 -0800

    Merge pull request #333 from RosettaCommons/vmullig/bluegene_mpi_problem
    
    Vmullig/bluegene mpi problem
    
    On the Argonne "Mira" Blue Gene/Q machine, I was having a problem with the MPI version of the RosettaScripts app. Every time a slave process asked for a job, the master process would send it a nonzero job number, but the slave process would interpret it as "0".  This fixes that problem, at least with the MPIWorkPoolJobDistributor.
    
    In MPIWorkPoolJobDistributor, core::Size values were being sent and received as MPI_INTs. On little-endian systems (e.g. x86 processors), the data truncation resulted in the value being preserved for any reasonably small value, which is why, I think, no one had seen the problem anywhere else, but on big-endian systems (like Blue Gene), for a small value like a job number, only the leading zeroes were sent and received. I switched all the MPI_INTs to MPI_UNSIGNED_LONGs (which should match core::Size on most systems -- core::Size is actually of type std::size_t, which is usually unsigned long), and adjusted a few ints defined locally to be core::Sizes. This got RosettaScripts working properly in MPI mode on Blue Gene.
    
    Note that MPI_Send and MPI_Recv take a virtual pointer to the datum being sent or recieved, so there is no check that its type matches the type that MPI thinks it's sending or receiving.  Data truncation errors are easy with MPI.

commit 59015e488ece3aa56d645b3666563c15eac1f723
Merge: 9c93e1d fd35b64
Date:   Thu Feb 26 00:19:06 2015 +0200

    Merge pull request #100 from RosettaCommons/kwikwag/peptiderive-talaris
    
    A refactor of PeptideDeriver, aka Peptiderive.
    It was a pilot app. Now it's a protocol + app.
    
    **Main classes and features:**
    
      - `PeptideDeriverFilter` (`protocols/analysis`, `protocols.3`) - the essence of the protocol. Given a pose, calculates the peptidic stretch contributing more than others to the interaction energy. It also reports on and optionally models cyclizable peptides (thanks to @orlypolo ). Data is written down to the log or to a file, in one of two formats.
      - `DisulfideInserterMover` (`protocols/simple_moves`, `protocols.3`) -  a mover that given a receptor peptide pose mutates the peptides edge residues to cysteines, if needed, and enforces disulfide bonding by constrained minimization of the bond and the interaction. (again, thanks to @orlypolo )
      - `FilterReporterMover` (`protocols/moves`, `protocols.1`) -  a `FilterMover` that also calls `report()` on `apply()`
      - `PeptideDeriverOutputter` (in `PeptideDeriverFilter.hh`) - a abstract base class for handling calculation outputs from `PeptideDeriverFilter`. Since `PeptideDeriverFilter` might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. I figured I should decouple the calculation from the representation of results. Implementors of this class are responsible to implement representation of results. Subclasses are: (a) `PeptideDeriverMarkdownOutputter`, (b) `PeptideDeriverBasicOutputter` - output data from the protocol to a stream, in either a human-readable (markdown) or easily parsable (basic) format. (c) `PeptideDeriverPoseOutputter` - outputs important poses (using JD2 if possible). (d) `PeptideDeriverOutputterContainer` - delegates calls to a list of outputters; allows aggregation to allow multiple outputs from one `PeptideDeriverFilter` instance.

commit 9c93e1d3329c550a82f1235081e6824026b9ea64
Date:   Tue Feb 24 14:51:42 2015 -0500

    Fix core/kinematics/util.cc
    
    You know, it turns out that fixing an illegible function to be more legible carries risks.

commit 350bcb1f14fbb64efc3a2a56465fb33ff50b983d
Merge: 9d29e51 0c6614c
Date:   Tue Feb 24 14:20:38 2015 -0500

    Merge pull request #329 from RosettaCommons/everyday847/semirotameric_ncaas
    
    Rotamer libraries for NCAAs with a semirotameric chi

commit 9d29e51a317ff23f794d56dee982cc1e2aa6a4c7
Date:   Tue Feb 24 14:19:31 2015 -0500

    Update flags_601
    
    symmetry typo

commit 55382eb12bbfaeb811f20e27302cd7deb9105133
Merge: 4e7aaa5 d93baf7
Date:   Mon Feb 23 22:12:39 2015 -0800

    Merge pull request #335 from RosettaCommons/vmullig/bgs_parallel
    
    Minor bugfix to the BundleGridSampler.
    
    Fixing an issue with reset mode. No test changes expected.

commit 4e7aaa570a6fcc3def67810c25ba037d79a9c139
Merge: bf32850a 975db35
Date:   Mon Feb 23 21:00:52 2015 -0800

    Merge pull request #334 from RosettaCommons/vmullig/bgs_parallel
    
    Fix the bundlegridsampler_design_nstruct_mode integration test
    
    Fixes an integration test that's currently failing to finish.

commit bf32850a04ca269bcb4ae2298da95ccbd5249289
Date:   Mon Feb 23 18:43:59 2015 -0800

    Fixing another bug with sigmoidal dielectric

commit bfd0666df9dca81064219a3b2af3d8e9d75d3bad
Date:   Mon Feb 23 10:54:40 2015 -0800

    Fixing another derivative bug with per-SC density reweighing

commit 3aef519a2c18d58804d77e34cc0877c3d9a0ee78
Merge: 573ea2d c7392f0
Date:   Mon Feb 23 01:19:13 2015 -0800

    Merge pull request #330 from RosettaCommons/vmullig/bgs_parallel
    
    Vmullig/bgs parallel
    
    
    
    This allows simple parallelization of the BundleGridSampler (without violating the one-mover-per thread/process rule, or the movers-don't-send-MPI-messages rule).
    
    --    The mover now has a "nstruct_mode" option. In nstruct_mode, one set of Crick parameters is sampled per job; otherwise, all sets are sampled every job. (This means that if a parallel job distributor is being used, different sets of Crick parameters will be sampled in different parallel trajectories.)
    --    To allow this to be used with other movers that might also have a similar sampling option, there's also an "nstruct_repeats" option. Let's say that you wanted to sample 10 different sets of Crick parameters and 10 different sets of parameters for another mover (for a total of 100 pairwise combinations). You could set nstruct_repeats to 10, which means that each set of Crick parameters is sampled 10 times, and cycle through all parameters sampled by the other mover in jobs where the Crick parameter set is sampled over and over.
    --     This is currently covered with a (conventional) integration test using the non-MPI job distributor, but I'd really like to cover this with an MPI-mode integration test, if we could add such a category.
    --      I have updated the documentation.
    
    Expected test changes:
    -- New integration test bundlegridsampler_design_nstruct_mode.
    -- Cosmetic change to bundlegridsampler and bundlegridsampler_design.

commit 573ea2dd723d8463de99aace2b2bc0cd29ef4f97
Date:   Sun Feb 22 17:36:02 2015 -0500

    Dummy commit to trigger Testing Server run

commit bed8710ad0aee658257fad9567d610c2f5fb67d9
Date:   Thu Feb 19 19:32:49 2015 -0800

    Bugfix for per-residue SC density reweighing

commit 7b74eb0f3c26d593b405b19cf8979b887fc3f0ae
Merge: fb47760 8e21501
Date:   Thu Feb 19 20:57:58 2015 -0500

    Merge pull request #306 from RosettaCommons/jkleman/mp_updates
    
    Jkleman/mp updates:
    
    = added observers to integration tests
    = renamed integration tests to mp_<app>

commit fb47760d022c3a97e1d3456a0ea0437ce97c237a
Date:   Thu Feb 19 16:10:44 2015 -0500

    Somehow my altered residue_types.txt got changed, sorry -- it was from testing the new NCAAs!

commit 131b08b7efa45490f0cc5da92ace469793def5ce
Merge: d8ff5bf 1adffff
Date:   Thu Feb 19 16:05:41 2015 -0500

    Several NCAAs that segfaulted upon read have been repaired (params, rotlibs, or both)

commit d8ff5bf18d0ea70c38cfe3a757f97569db90b969
Date:   Thu Feb 19 16:03:10 2015 -0500

    Fixes to a number of broken NCAA parameters

commit 72d3e99f805110b058ae7952eaeca7c3cb204f18
Merge: 86b9fe1 42687cb
Date:   Tue Feb 17 08:51:49 2015 -0500

    Merging fix to fixed_size_array bug

commit 86b9fe158b142b27eb165370aee2a9a588e83718
Merge: f32cc7a ffdfc87
Date:   Tue Feb 17 02:27:57 2015 -0800

    Merge pull request #304 from RosettaCommons/tlinsky/hotfix
    
    Bugfix to protocols::fldsgn::filters::HelixKinkFilter.cc -- previously, ...

commit f32cc7a02bf07e7bb400d8639257fb6f64156104
Merge: e9853c3 fdcd5ae
Date:   Tue Feb 17 02:27:08 2015 -0800

    Merge pull request #132 from RosettaCommons/tlinsky/filedata
    
    Update FileData to add an additional hook into build_pose_from_pdb_as_is...

commit e9853c37d3a5bcead66c67e3e409d2f8f4ee151e
Merge: fdf94fa efa6788
Date:   Mon Feb 16 21:42:45 2015 -0600

    Merge pull request #195 from RosettaCommons/roccomoretti/valgrind
    
    Valgrind automation scripts
    
    Add option to run unit and integration tests with the valgrind memory checker, and hook them into the benchmark system. Simply add "--valgrind" to the unit or integration test scripts to run them under valgrind (assuming you have valgrind installed). This will take a while, but should show memory issues.

commit fdf94fabf897cc9c07609227a65a2659080df7b2
Date:   Sun Feb 15 16:45:00 2015 -0800

    Adding an option to Coulomb.cc to allow the use of sigmoidal dielectric in fa_elec/fa_grpelec.
    
    It is turned on with the flag -elec_sigmoidal_die, and there are three parameters that control its behavior:
       -elec_sigmoidal_die_D0 : the dielectric at short range
       -elec_sigmoidal_die_D : the dielectric at long range
       -elec_sigmoidal_die_S : the transition between the two (higher is faster fade)

commit 7467bad7aa2e4d474bd8e8e72c824ed987518c90
Merge: d86661d df5b3db
Date:   Sun Feb 15 15:43:25 2015 -0600

    Merge pull request #323 from RosettaCommons/bazzoli/ppi-weights
    
    Added weight file PPI_discrimination.wts.

commit d86661ddd01642a876b8734446aaf6a3c3e9b497
Merge: 1aaae1f bdf4af8
Date:   Fri Feb 13 17:11:51 2015 -0700

    Merge pull request #318 from RosettaCommons/rfalford12/delete_extra_memb_etable
    
    Removing duplicated non compiling membrane etable from core/scoring/etable

commit 1aaae1f4b0d75a4294f240854f83bc476498dd97
Date:   Fri Feb 13 12:31:07 2015 -0800

    Fixing a bug that was causing the clang integration test crashes for hybridization and dens_refine_symm

commit 067120141649aa4861b09a0ab9e7a31775c35831
Merge: 82bfc7d 7b43233
Date:   Thu Feb 12 07:29:08 2015 -0700

    Merge pull request #312 from RosettaCommons/rfalford12/rosettamp_updates
    
    Updates to RosettaMP Framework
    
    (1) General membrane Symmetry
    = Created SymmetricAddMembraneMover: A subclass of AddMembraneMover that invokes the membrane framework for symmetric poses in protocols/membrane/symmetry
    = Added unit test, SymmetricAddMembraneMoverTest, for this Mover
    
    (2) Membrane symmetric docking protocol
    = Created MPSymDockMover: General membrane symmetric protein docking mover (previously in a pilot app) in protocols/symmetric_docking/membrane
    = membrane_symdocking: Now directly calls MPSymDockMover, located in the protocols library
    
    (3) RosettaScripts Support:
    = Added full RosettaScripts support for MPDockingMover, MPDockingSetupMover, SymmetricAddMembraneMover, MPSymDockMover, and SetMembranePositionMover
    
    (4) AddMembraneMover:
     = Default membrane position always gets set by SetMembranePositionMover at the end of the AddMembraneMover apply() method
    = Added an interface, allowing the user to set the initial center/normal (which actually get set this time!)
    = Added better error checking when reading in center and normal xyz Vectors from the command line
    = Added new unit tests to check for a user defined or custom set membrane position
    
    (4) MPHbond Flag:
    = Removed hbond flag from both score function fingerprint tests: membrane_fa_scorefxn and menv_smooth_sfxn. Behavior remains the same, as this energy term is now automatically turned on when the membrane framework is invoked
    
    Test Changes:
    -----------------
    Unit: All Pass
    Integration: Expected Changes
      - Symmetric docking has a new set of tracers for each Mover (Symmetric Add & MPSymDock)
      - Default SetMembrane prevents -0 from occurring - no numerical difference
    
    Score Regression: Expected Changes
      - Default SetMembrane prevents -0 from occurring - no numerical difference

commit 82bfc7d4e102ecd32751e47bc33387829e8520b6
Date:   Wed Feb 11 16:22:06 2015 -0800

    Adding functionality for per-residue reweighing of sidechain density.  Specified by setting the option SCALE_SIDECHAIN_DENSITY_WEIGHTS in the scorefile or Set scale_sc_dens_byres in the xml.  Fixing broken build.

commit 8c617884f6c14766708315e1e0a970654648a112
Date:   Wed Feb 11 13:34:28 2015 -0800

    Fixing clang build

commit 2ff1686c8f8b1a023c44902938fcf65447af4032
Date:   Wed Feb 11 11:14:04 2015 -0800

    Updating FastDensEnergy to make use of the new minimization interface.  Density integration test changes expected.  Also modifying a few files that failed to build on my Mac (llvm-gcc-4.2).

commit adb90f2624093a0485db909f06138467653e0af5
Merge: c8ef3ef b677e92
Date:   Wed Feb 11 09:49:03 2015 -0600

    Merge pull request #314 from RosettaCommons/roccomoretti/fixedsizearray_asserts
    
    Fix issue with gcc 4.8 release_debug compile and fixedsizearray.
    
    Changes debug_assert() to assert() in utility::fixedsizearray1::operator[]

commit c8ef3efbb0fe87e93f412dfed7648af933cd8d23
Date:   Tue Feb 10 13:04:25 2015 -0800

    Bugfix for fold-and-dock.  Previously, an asymmetric repack was called on the pose before relax, now this is symmetry aware.

commit ab77b55fa2d2dbdaaf13d003d37d5e4eef93ba16
Merge: 28a9050 3c9e2a4
Date:   Tue Feb 10 08:02:49 2015 -0800

    Merge pull request #311 from RosettaCommons/phbradley/scc_excn_fix
    
    Phbradley/scc excn fix: fix an issue in the constructor of the SurfaceComplementarity exception class that could cause segfaults when exceptions are thrown.

commit 28a90508fb69a8b557b84994006758137a9f551f
Merge: 65baa24 14ad6e7
Date:   Tue Feb 10 10:46:50 2015 -0500

    Merge pull request #309 from RosettaCommons/rfalford12/revert_anchor_point_change
    
    Adding back a feature that allows the user to specify the 'anchor residue' for the membrane residue in AddMembraneMover and on the RosettaScripts commandline. Also included a unit test for this feature in the AddMembraneMover unit test

commit 65baa2496bf2b18809bdd621f4dc6ead62f7c4a5
Merge: ecefd76 94aa104
Date:   Mon Feb 9 18:51:34 2015 -0800

    Merge pull request #305 from RosettaCommons/kylebarlow/alascan
    
    Alanine (and generalized ddG) scanning features reporter
    
    The DdGFeatures reporter provides an alternate way to output ddG values through the features framework. This reporter can calculate ddG of binding for multimeric proteins, as well as ddG of mutation for monomeric and multimeric complexes. Options also exist to control repacking and relaxation, allowing for a no-repacking and no-relaxation alanine scanning-style method.

commit ecefd765432d7fded4d9741ab1becb580014a866
Date:   Mon Feb 9 13:24:23 2015 -0500

    Final unused variable error

commit ce17dde299dc28a86c148e0adeea2808db157496
Date:   Mon Feb 9 11:04:02 2015 -0500

    Fixed gcc only warning

commit 3fe7f99628535cad499196f02d23bf6ca68ecf35
Date:   Mon Feb 9 09:21:53 2015 -0500

    including backtrace in Rot

commit 9d27821f9b1c0a869775e33a12e17977beede0f6
Date:   Mon Feb 9 09:21:27 2015 -0500

    debug_assert issues in Semi

commit 7954b1afb3dff2193dce2baff352297fa4d05143
Date:   Mon Feb 9 09:14:04 2015 -0500

    Oh my god recover_rotamers_in_order was a bad idea I had. What a fool!

commit 76c13f90b3cbfe94ef418f74cc7ab234093e17af
Date:   Mon Feb 9 09:11:05 2015 -0500

    I think this should resolve everything. I think there was a merge issue I didn't anticipate

commit 68429e94cff0098cf48692aec2c0d4abfbf4a59e
Date:   Mon Feb 9 08:48:26 2015 -0500

    Fixing more mistakes in merge

commit b67896b0f7307dc94d6375af5ee6b6917458aca5
Date:   Mon Feb 9 08:20:53 2015 -0500

    fixing group_elec issue?

commit 890fd84254eee4776a98d7162dcdd3de18c0da57
Merge: d43dacc f2d9fd5
Date:   Mon Feb 9 07:28:50 2015 -0500

    Completed merge of general backbone rotamer libraries.
    So basically, now we can make rotamer libraries of up to five backbone dihedrals. (That many should be rarely necessary, and I would suggest going pretty sparse on the bins if you need four or five, seeing as a 10 degree bin rotlib for beta-3-arginine, for example, is quite large.) But this way we can have a much better representation of non-alpha-AA rotamers, so that's pretty nice. Moreover, this makes it possible to use talaris to score beta amino acids properly (instead of highly approximately) which is very nice for the Mulligan Army.
    
    Some integration tests are expected for long enough trajectories. ALF and I have confirmed that they are just floating point issues and thus can be disregarded.

commit d43dacc6e96854130c716becbb5618e856574903
Date:   Wed Jan 28 13:09:03 2015 -0500

    Cleaned up code

commit 55139988ad8d6ea1b2b59b1eebe618e00b7dfe9d
Date:   Mon Jan 26 11:45:55 2015 -0500

    Removing cout statements that had been used for chidevpen debugging; now I can examine remaining test failures

commit 58e1cdf6557bad52d53f6a7fb98b7272359d6b3f
Date:   Fri Jan 23 14:13:56 2015 -0500

    Sigh. I need to figure out whether an error of 1e-9 in chidevpensum is machine precision

commit b7364531a53241c89f5f1d091480f4c981728063
Date:   Thu Jan 22 18:30:33 2015 -0500

    Merge with Rocco's changes. This will definitely change integration tests because I am dumping a lot of scoring output to help track down differences

commit eda963d34441d6d5259f40b46bacfa07c9070ddb
Merge: 1d581b8 b14a1f5
Date:   Thu Jan 22 14:08:10 2015 -0500

    Merging in master

commit 1d581b85600c1570ec74449ad0823334bf5b80ab
Date:   Thu Jan 22 13:59:40 2015 -0500

    indentation

commit edbeb1955b192d0c6ab57037fef3560ac2d8404f
Date:   Thu Jan 22 13:28:54 2015 -0500

    Testing source of deviations--extra tracer output on testing server
    New database version number

commit ca5ff53536bb01487f3d70ac22ecc3a17ca8b023
Date:   Wed Jan 21 15:26:53 2015 -0500

    Fixed that nasty probability issue!

commit f26b5bd0448f0464ea6f94c4d6d600f165caff34
Date:   Wed Jan 21 09:38:18 2015 -0500

    whoops

commit 733232c413de904ad07ae9f5f823ca4fbfe80213
Date:   Wed Jan 21 08:28:09 2015 -0500

    Cleaned up one broken integration test... many more to go.

commit fad2f3d1283ad6501a6f60f5a461e5096e7976da
Date:   Tue Jan 20 17:06:43 2015 -0500

    Standardizing residue types to minimize changes

commit 7486830f98d75dd788468179cf5c324e8fcdfbe0
Date:   Tue Jan 20 16:23:22 2015 -0500

    fixing two broken release builds

commit 946a79eb45018139e846a0c502f45cbf9951cfcd
Date:   Tue Jan 20 14:09:49 2015 -0500

    Oddly won't push

commit 7563da72ba404b5df844f593522a24496e960e08
Date:   Tue Jan 20 13:15:20 2015 -0500

    Finished templating rework. Now faster input/output. scoring is consistent, too.

commit ab6ca6839dfed2bb76662e6554bc6047c566e1c2
Date:   Sun Jan 18 17:07:43 2015 -0500

    Fixed unused variable

commit 38188ffecf06b5cf4dc539e3595f966adebcb08a
Date:   Sun Jan 18 16:52:27 2015 -0500

    Okay, so I changed everything around to a templated solution so that I can allocate everything on the stack. Massive changes expected.

commit 23052339da57c1b307529a819d43670af718a244
Date:   Wed Jan 14 18:47:45 2015 -0500

    Checking, now that the binary hash is updated, that the integration tests work out better

commit 1e004c264975c859d22d9c259a0313b71065cbe2
Merge: f9366a1 c7ce5fe
Date:   Tue Jan 13 13:34:43 2015 -0500

    Merging in master post resolution fix

commit f9366a12eba9163b3c49f2177f664c932feb00e1
Date:   Tue Jan 13 13:06:05 2015 -0500

    Some code cleanup, consistency with MakeRotLib app

commit 001a199db4f5ba63d095c921f12ab120aa4306ad
Date:   Mon Jan 12 16:02:32 2015 -0500

    Binary format change noted

commit 7522203918f57871e39e0bbd5d885c32214db361
Merge: bd3f8ce ddd0ca5
Date:   Mon Jan 12 15:09:29 2015 -0500

    Making 1e-6 changes to the make_rot_lib_general branch

commit bd3f8ce687cb06ca9d5d98a68c135c83cc5ce3ac
Date:   Wed Dec 31 22:28:37 2014 -0500

    Okay, so that was wrong.

commit 8976251ea7530615b15190568794403abd94ca13
Date:   Wed Dec 31 20:12:13 2014 -0500

    Adding omega dependence (possibly restoring omega dependence?) to some of the scoreterm components.

commit 5054e99d18dd9cea106d5cae7e61d00b4ae2bfbb
Date:   Tue Dec 30 20:33:06 2014 -0500

    Shot in the dark fixes

commit c546d11b1f4762b9ec9a695599b7d50625170148
Date:   Mon Dec 29 22:25:24 2014 -0500

    Fixed some final rotamer probabilities; is this what we needed?!

commit 1c217a4ea31a00b5b74a2078d303210f4b9061fa
Date:   Mon Dec 29 21:18:08 2014 -0500

    Factoring out functions to generate array indices
    NEWS: [DETAILED DESCRIPTION OF CHANGE]
    You often want a single index to refer to a rotamer. You assemble it by
    bb_bin[1]*N_PHIPSI_BINS + bb_bin[2]+1
    or
    bb_bin[2]*N_PHIPSI_BINS*N_PHIPSIBINS + bb_bin[2]*N_PHIPSI_BINS + bb_bin[3]+1
    and you do something similar, choosing between two bin numbers, with interpolation

commit b08de0a5ab812b21a95d1338c02ff0792627bd4b
Date:   Mon Dec 29 16:10:48 2014 -0500

    Unused variable

commit 43037733bf0af1a58d31555796e830efbe7a8cc7
Date:   Mon Dec 29 13:33:49 2014 -0500

    Fixing nrchi deriv issue, perhaps

commit cd3ba71fd6bd84dc893c5887f6151099c1c3e2b8
Date:   Sun Dec 28 23:39:38 2014 -0500

    Excessive output and a fence-post error

commit 294c4462f7a90cebe9b3319a321249a03da3a5f2
Date:   Sun Dec 28 22:44:20 2014 -0500

    Fixed a unit test issue and an issue with get_bb_bins that caused a separate unit test issue

commit 052a0e4a86933755b3c2a99cd8d4f20e9a186ee9
Date:   Sun Dec 28 20:08:24 2014 -0500

    Fixing deriv calcs for chi

commit c01966fbd45cd829cca9ec8bd801eefae2dee11b
Date:   Sun Dec 28 10:51:18 2014 -0500

    Fixed NaN issue by flooring rotamer_probability correctly

commit 846c8dd253d1ed322412a12691ce454947c65297
Date:   Sun Dec 28 01:46:40 2014 -0500

    Fixed issue with generating no proton rotamers!

commit 2a350db6bb476cf6c0b6be7d04bc5bd42f540ce1
Date:   Sat Dec 27 14:18:40 2014 -0500

    Unused variable due to spline change

commit c00b91037381188faef0d5a2eac63dbd3dcdae8d
Date:   Sat Dec 27 14:09:20 2014 -0500

    Replacing std::pow invocations on integers with an optimized pow for positive integers from Knuth. Hard-coding 2 and 3 because they will be vastly most common.

commit 79ad528c98d4f978b739473b1ada94a3d1ece4d9
Date:   Sat Dec 27 00:10:58 2014 -0500

    Fixed unit test references for make_rot_lib

commit d59d4b968c6efd93f713940f25d5db51e5ceb0c8
Date:   Fri Dec 26 23:34:53 2014 -0500

    Switching back to tricubic splines for testing to confirm that there exists a math bug in polycubic splines

commit e4bb9f9b16450beac2f5836b9df69867bc7e01f8
Date:   Thu Dec 25 01:08:43 2014 -0500

    Neutral psi issue was holding us back!

commit 0916c52962695be37f4b0f05b23b0ccb3ac73ca0
Date:   Wed Dec 24 21:54:28 2014 -0500

    another d_multiplier unused

commit e8fddc6211fad7e7a2b4250c452c16080e2b475d
Date:   Wed Dec 24 21:52:04 2014 -0500

    Unused variable fixed

commit a51fa08ce7790fe149770b145ed701c40b83c351
Date:   Wed Dec 24 21:38:31 2014 -0500

    Managed not to successfully add MakeRotLib.cc/.hh back to the repo for unit tests

commit 83f1c3c321184807aa2c6bad82d546e609962329
Date:   Wed Dec 24 21:20:29 2014 -0500

    Ah! The issue was in the angles version of polylinear interpolation.

commit d1132782ad124759ae1be770e3e958aa11a0d93d
Date:   Wed Dec 24 03:26:04 2014 -0500

    Vector of const rotamers caused linux build failures

commit be44ba34cd8a542c220ccb026313ea7ea6d40353
Date:   Wed Dec 24 01:40:11 2014 -0500

    copy constructor issue

commit de77da1ec34755ee91c7724bffe5bbe270b47c69
Date:   Wed Dec 24 01:01:16 2014 -0500

    minor changes

commit ca57921ed1bfd5aea59797f9ba557a55cb9350dc
Date:   Wed Dec 24 00:58:15 2014 -0500

    marking a method const for the linux builds

commit 8881393a37c1b5afa279c04bd6c0639c3fda6130
Date:   Wed Dec 24 00:39:35 2014 -0500

    Fixed stuff for cxx11 build

commit c1fb97d932f4ab8a28f8c603215fa9e3b44d3b51
Date:   Tue Dec 23 23:21:10 2014 -0500

    static bug with N_PHIPSI_BINS

commit 43bef84d2f2bc487b0db39ee0bf92ff3c1ea075a
Date:   Tue Dec 23 22:56:40 2014 -0500

    Some code whitespace standardization all over, but mostly just fixing a stupid compile error.

commit 7d41f5621fd6e32ae8a965f77ec192c916fdbc1c
Date:   Tue Dec 23 01:28:49 2014 -0500

    Minor tweaks to revert changes I never really meant to make

commit b00d7e73c13940e046d13ca8f6f5d4d809c5b2fa
Date:   Mon Dec 22 21:53:12 2014 -0500

    Think integration tests should be stable now, checking for diffs

commit c56ba0351692acd7fd137bd54fd52f4c43c5c8e8
Merge: 1ae8a6c 492e35b
Date:   Mon Dec 22 11:50:44 2014 -0500

    Merged in master just to stay up to date

commit 1ae8a6c589fad3a63075bce0509880873324a427
Date:   Mon Dec 22 11:49:20 2014 -0500

    Additional fixes for integration test changes

commit 834ef20bee34efa02121f615eea1db544ef290a8
Merge: 7f20015 3ebfb12
Date:   Wed Dec 17 19:59:29 2014 -0500

    Merge from remote apparently needed

commit 7f20015d8ff03578e5b4df309f6696126ac40c34
Date:   Wed Dec 17 19:57:02 2014 -0500

    Tracking down bugs in binary file i/o

commit 28bc34bb8623ef6be105dba7022549ea6f5228f7
Date:   Thu Dec 4 10:56:51 2014 -0500

    Build works, still need to touch up MathNTensor etc.

commit e08ddba340ff4deb4cf462458c2b3880b70274f6
Date:   Sun Nov 30 18:41:08 2014 -0500

    It builds! Now to slowly remove any other references to specific bb angles and to validate the new MathNTensor and PolycubicSpline numerically

commit bf2a39f3b3baf23b2082dcfed7fca13ebd1f8a3f
Date:   Sun Nov 30 14:39:50 2014 -0500

    fixes

commit c57dd199d1f66ef791636860016b9d4bcaaf6db9
Merge: 6568f34 52a8fc5
Date:   Sun Nov 30 14:27:03 2014 -0500

    minor merge

commit 6568f34e0e6812b1e15879f51048c6b14772ebbc
Date:   Sun Nov 30 14:24:55 2014 -0500

    Adding polycubic spline and mathntensor

commit 93952ad23ff8e6512a191c25f5dbd6499ef42f08
Date:   Sun Nov 30 13:57:08 2014 -0500

    Trying to write up PolycubicSpline and MathNTensor classes for use in arbitrary bb rotamer libraries

commit 79cb23d21383e2bc53e4cfb754fdaf7b5153a222
Date:   Thu Nov 27 21:22:57 2014 -0500

    Almost all integration tests are running; hellish fence post errors are dead

commit d691503eb17215119ef78bdd85e79d2081ee3747
Date:   Mon Nov 24 22:23:39 2014 -0500

    Fixed warnings

commit 4386120e6ec33105878206f52e563967b108f8c3
Date:   Mon Nov 24 16:26:18 2014 -0500

    Fixed unused parameter

commit 187aa0025e33b081c5272ec0a2f3e8828a2ee7d7
Date:   Mon Nov 24 15:53:13 2014 -0500

    Adding multilinear interpolation and an alternate frame for tricubic interpolation

commit 85f47a73aea17c3adb4e814a22ea5d37ea607b2c
Merge: 327611c 03fda7c
Date:   Mon Nov 24 13:25:30 2014 -0500

    Merging master to local branch, only typographical changes

commit 327611ca936c428d5487ce6f9dd15bcc8d0b53df
Date:   Mon Nov 24 13:21:43 2014 -0500

    Enough changes that it builds!

commit 17ee61490d2bbfc166086fe410de5ac8c5859272
Date:   Mon Nov 24 13:11:52 2014 -0500

    Fixes for make_rot_lib atom tree stuff with dipeptoid patch

commit e89626371bdc236b0e9a9ae033ab7ed391579938
Date:   Mon Nov 24 10:17:14 2014 -0500

    Edits in progress to flatten bb-indexing
    There are a lot of multidimensional arrays indexed by ( phi, psi[ , ... ] ). This is an issue for arbitrary backbones.
    I am flattening these cases to be indexed by
    ind = phi + N_PHIPSI_BINS * psi
    which generalizes straightforwardly to
    ind = sum( bb[ i ] * N_PHIPSI_BINS ^ (i - 1) )

commit 0f1313ff6d64253150fdf47c0f20cae2a29dd52e
Merge: ff02de8 0214289
Date:   Thu Nov 20 16:57:09 2014 -0500

    Merging master

commit ff02de8673f38cf546d435098c4c396dddc1e1b4
Date:   Thu Nov 20 16:30:00 2014 -0500

    Removed tracer output from MakeRotLib

commit fa5344148b0359313d2896af7864c02980b1bae2
Merge: 0fe99a1 482ce97
Date:   Thu Nov 20 13:42:16 2014 -0500

    pulling master

commit 0fe99a160c9ae6522b98cfb29b715e964a5b11ce
Date:   Fri Nov 14 18:44:04 2014 -0500

    Reverting crazytown commit to test merge

commit 130d67960e1136e102fba6ee09540cdd0c22b80e
Date:   Fri Nov 14 18:29:59 2014 -0500

    I will revert this commit if Rocco agrees to merge and stuff.

commit bf6af40cd8ed1fda2dcd8e8909bcf0f2e8a06b3d
Date:   Fri Nov 14 15:05:24 2014 -0500

    formating changes to MakeRotLibMover

commit 29ce0abf3807a88d2426af6232fc567871da5f0a
Merge: baeff79 6788978c
Date:   Fri Nov 14 12:37:36 2014 -0500

    Merging in master

commit baeff7967f2f650311a7873e74bbca702e8bebaf
Date:   Fri Nov 14 12:21:16 2014 -0500

    generalization of make rot lib works except for omega issue

commit d7386dba74979abffb97c64e8f571206f85401e3
Date:   Thu Oct 30 14:10:26 2014 -0400

    A lot of changes make the MakeRotLib app compatible with a new input format and with multiple BB angles
    NOTE: tracer output still modified; commented out much of it. All new tracer output (temporary) should have amw in it.

commit cfa44040fdd4000bc0eb03302045781404849145
Merge: bfdc192 f385e32
Date:   Thu Sep 25 16:20:24 2014 -0400

    restoring MakeRotLib.cc

commit bfdc19262511e65b6c1417958cdce2217266e79c
Date:   Wed Sep 24 14:45:25 2014 -0400

    Trying to fix... everything

commit a50a81c50a87f1b1d44a1c6493ec3d3d8ef88b27
Date:   Thu Sep 4 09:43:40 2014 -0400

    Fixing build for generalized MakeRotLib

commit 51922fc47c892a33a6b80db0bb0fb20622116e72
Date:   Wed Sep 3 22:22:20 2014 -0400

    Adding three NCAAs, one of which tests the MakeRotLib changes
    NEWS:
    Three new NCAAs to be used in design.
    
    BCS is benzylcysteine
    BZP is benzophenone, a common photocrosslinker
    SAL is somewhat misleadingly (but literature-consistently) named; it is a 3-amino-benzoic acid derivative. (Imagine a gamma amino acid forced to be totally planar.) Its highly noncanonical backbone (inexpressible by patches) but ability to be incorporated into peptide chains quite easily necessitates a gross expansion of how we find rotamer libraries.

commit 53406b1cb5c0cca80b5646aa82f0e236fe4806ff
Date:   Wed Sep 3 21:50:10 2014 -0400

    Generalizing MakeRotLib's understanding of backbone torsions