Fixing bug in the RotamericSingleResidueDunbrackLibrary code's use of bicubic interpolation on the Shannon entropy. There had been a typo in an index--essentially, interpolation was performed using the values from bins (0,0), (0,1), (1,1), and (1,1). (The derivatives were all from the correct bins.)

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Merge pull request #191 from RosettaCommons/roccomoretti/SnugDock_fixes Fix uninitialized values in VDW_Energy, SnugDock. Should help stabilize SnugDock integration test.

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Update a pilot app

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Merge pull request #177 from RosettaCommons/rfalford12/reorganized_memb_energy_functions Updating organization and documentation of the membrane energy functions (low res and high res) and any weights sets associated with membrane framework applications These changes apply to the following weights files: = mpframework centroid, fa, and fa smooth = mpframework docking = mpframework symdocking = mpframework pH mode I also added descriptions for the 'old' membrane energy functions (same science, just not framework supported): = membrane_parameters and membrane_penalties patch files = membrane_highres energy functions = score_membrane (lowres energy function) Test Status: Unit Tests: All Pass Integration Tests: membrane_relax - printing name of the new weights files Score Tests: All - printing names of the new weights files Thanks Julia for the great suggestions!

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Fix uninitilized variable in LoopMoverGroup. Should help stabilize the KIC_with_fragments integration test.

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Merge pull request #188 from RosettaCommons/tlinsky/hotfix core::graph::Graph now uses a Tracer object instead of std::cout for outputting messages

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Added an app to suggest target residues for PocketGrid based on Robetta ddg output

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Change motif_score_filter integration test to remove timing information.

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Ask not for whom the bell tolls ... You can't catch SIGKILL, so don't bother trying. (This silences a Valgrind complaint.)

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Fix uninitialized variables in RotamerLibraryScratchSpace. These are used uninitialized in the inverse_rotamer_remodel integration test, leading to release-mode instability.

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Fixed erros in DARC GPU code for compilation with OpenlCL build.

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In Splice mover I added a tolerance tag which controls the sensitivity of the bond distance filter

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Attempt to fix dock_with_hotspot_place_simultaneously integration test PlaceSimultaneouslyMover::pair_sets_with_positions() was deleting the iterator it was iterating over. This is causing an intermittant crash on the test server Mac in release mode. Thanks to Sergey who provided the stack trace which allowed me to track this down.

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Small bugfix for crystal refinement of protein-DNA complexes

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Updating the HA chirality pseudo-torsion to match rosetta ideal. Integration changes expected in tests using cart_bonded.

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Merge pull request #184 from RosettaCommons/rpache/skip_initial_loop_build Adding option -loops:skip_initial_loop_build to the refactored KIC code. This option allows to run refactored KIC and FragmentKIC in both centroid and fullatom mode, but without building the loop from scratch first. This can be useful for broad sampling of the given loop in the vicinity of its native conformation or for backbone ensemble generation, where using fullatom refinement only would lead to ensembles of too low conformational diversity.

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