Updating a pilot app

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Fixing PyRosetta namespace build. Fixing issues with PyRosetta git releases.

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Fixing broken build.

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Fixing ScaleMapIntensities (which I had accidently broken in a previous commit). Separating map rescaling and resolution filtering (since these operations might want to be applied individually).

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Adding a new pilot app which makes energy-based corrections to the dunbrack library. Fixing tabs in a couple files.

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Fixing an error in SingleResidueDunbrackLibrary::rotno_2_rotwell

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Merge pull request #192 from RosettaCommons/vmullig/parametric vmullig/parametric This creates a new PerturbBundle mover, which permits sampling of Crick parameter space during a design or structure prediction protocol. Done: Created the PerturbBundle mover Created the PerturbBundleHelix mover that's called by the PerturbBundle mover. Moved utility functions from MakeBundleHelix.cc to util.cc to permit re-use by PerturbBundle.cc. Fixed a serious mistake in the MakeBundle mover that was resulting in improper placement of secondary structure elements. Added a symmetry_copies option to the MakeBundle mover to allow creation of partial bundles or beta-barrels. Implemented the PerturbBundle mover's parse_my_tags() and apply() functions. Tweaked the helical_bundle and helical_bundle_nonideal integration tests. (Changes expected.) Added additional unit tests to confirm proper copying of Paramters and ParamtersSet objects when Conformations or Poses are copied, cloned, or assigned (operator=). Added slightly more verbose output (including a summary of the perturbed Crick parameters). Added an integration test for the PerturbBundle mover. Fixed the case in which a helix copies a DOF from another helix, where the DOF is never perturbed. (Or, at least, added a suitable error message.) This merge also brings in the following changes: Added sidechain-conjugation variants of D-asp/asn, D-glu/gln, and D-lys as params files in the database. Tweaked some params files.

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Merge pull request #193 from RosettaCommons/justinrporter/env_release Update the RigidChunkCM to maintain a sensible representation of the mapping between the template pose and the simulation pose. Fix numerous bugs, implement more thorough unit testing. No unit tests broken, no integration test changes expected.

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Merge pull request #201 from RosettaCommons/fleishman_lab/Atomtree_fix Fleishman lab/atomtree fix

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fixed a typo in pocket_suggest_targets integration test

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merge of master into JK-lab

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Fixing release.binary. Adding previously omitted build files. Thanks to Oriel for catching this out!

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updating the comment section for splice template pdb ../database/protocol_data/splice/antibodies/template_pdbs/2G75.ppk.pdb. Nothing more.

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Merge pull request #189 from RosettaCommons/kylebarlow/general_dev Fixing more abs -> std:abs errors currently preventing compilation on Ubuntu 14.10 with clang and Ninja Some of these are also based off a branch Rhiju started which got merged in already by @dougrenfrew.

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Merge pull request #185 from RosettaCommons/sevya/antibody_symmetry Sevya/antibody symmetry

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Merge pull request #194 from RosettaCommons/rfalford12/fix_dock_mem_ppk_test Fixing names of scorefiles in docking membrane prepack protocol

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