Merge pull request #504 from RosettaCommons/rhiju/dimaio_uniform_rotation_sampler adding UniformRotationSampler.hh, developed by Frank Dimaio

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Merge pull request #424 from RosettaCommons/sh-maxim/DunbrackLibs Sh maxim/dunbrack libs

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A small bugfix for hybrid when mixing template-based and extended (de novo) models in a single run

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Updating a pilot app

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Merge pull request #509 from RosettaCommons/pocket-optimization Sets current_tag_ on all movers in a mover container, added pocket_relax...

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Merge pull request #507 from RosettaCommons/raywangyr/denovo_modelbuilding Raywangyr/denovo modelbuilding merging apps for de novo model building in near-atomic resolution cryoEM maps

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Merge pull request #512 from RosettaCommons/sjf/FilterScan_thresholdvector Sjf/filter scan thresholdvector

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Merge pull request #511 from RosettaCommons/wpotrzebowski/fiber_diffraction_defs Wpotrzebowski/fiber diffraction defs

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Merge pull request #506 from RosettaCommons/rhiju/angle_deriv_tol updating tolerance on angle_deriv function from 1.0e-3 to 1.0e-8. This fix does cause changes in several integration tests that carry out minimizes. In several cases, the final energy is noticeably better than before (by many Rosetta units), but in most cases changes to final energies are less than 0.1 Rosetta units.

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Merge pull request #505 from RosettaCommons/rhiju/turn_off_cmake_warning turning off -inline_functions as generic flag in cmake builds

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Fixing Rosetta build on Intel on Stampede

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Merge pull request #508 from RosettaCommons/tlinsky/named_atom_constraint Add NamedAngleConstraint

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Merge pull request #481 from RosettaCommons/justinrporter/env_release Fixes to AbinitoLoopCM. Minimal changes; no unit test differences, one integration test change that's likely a red herring.

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Merge pull request #487 from RosettaCommons/roccomoretti/no_boostserialize Remove USEBOOSTSERIALIZE code from Rosetta This was an old attempt to serialize Rosetta objects. It's no longer being maintained, and when Rosetta does get serialization it will be with a different technique. As we can always recover the code from the git history, there's no reason to keep it in master.

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Merge pull request #495 from RosettaCommons/roccomoretti/xml_dualspace_fix Fix behavior of XML FastRelax with dualspace. The XML version of FastRelax completely ignored any commandline flags about dualspace and cartesian. This was counter-intuitive for people here in the Meiler lab. Fix this such that commandline flags are honored by default. (Explicit settings in the tag override, of course.)

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Update default-torsions.txt The C-N-CA-CB and N-C-CA-CB improper torsions for CYS were being scored, but the corresponding torsions for CYD were not being scored. I confirmed with Frank that this is an error, one that I wished to fix before handling the whole disulfide patch merge--this is a simple enough bugfix that it doesn't require a pull request.

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