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

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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

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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.

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Fixing clang build

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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).

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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[]

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

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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.

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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

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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.

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Final unused variable error

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Fixed gcc only warning

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including backtrace in Rot

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Fixing more mistakes in merge

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fixing group_elec issue?

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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.

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