Merge pull request #127 from RosettaCommons/dougrenfrew/fix_app_exception_itest
Fix the app_integration_handeling itest by adding a return -1 to couple_moves
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Merge pull request #124 from RosettaCommons/dougrenfrew/fix_splice_itest_case
Removing duplicate splice integration test for case-insensitive file systems
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Merge pull request #126 from RosettaCommons/revert-125-revert-113-calebgeniesse/graphics_build
Revert "Revert "Fixing graphics build through small changes in protocols...
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Merge pull request #125 from RosettaCommons/revert-113-calebgeniesse/graphics_build
Revert "Fixing graphics build through small changes in protocols/viewer"
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Merge pull request #116 from RosettaCommons/nollikai/coupled_moves
Adding coupled_moves application and integration test
coupled_moves is a simple design application that runs a constant temperature Monte Carlo simulation using the CoupledMover, a new mover that performs coupled side-chain / backbone moves as well as coupled ligand rigid-body rotation, translation and rotamer optimization.
All sequences that are accepted during the simulation are recorded and are output in a fasta file at the end of the simulation. This application is useful for predicting the set of tolerated sequences for a given design problem and makes it very easy to incorporate backbone flexibility into design.
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Fixing a bug I'd introduced into the Tracer system which required
core::init to complete in order for Tracers to get written to. That
is, the Tracers asserted that their visibility had been computed
before their output could be flushed. If, however, core::init hasn't
yet been called, or if core::init threw an exception, then the
visibility would not have been calculated. Now the assertion is that
either the visibility has been calculated or core::init has not
yet been called. This should fix the failing app_exception_handling
integration tests for the release_debug mode build.
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Merge pull request #118 from RosettaCommons/vmullig/mastermerge
Updates to GenKIC
This merge primarily updates GeneralizedKIC with a new pre_selection_mover option that allows an arbitrary mover to be applied to all candidate closures prior to picking one. (This would allow, for example, a user to run the packer and a side-chain minimizer prior to choosing a low-energy solution with the fullatom scorefunction.)
Other tweaks in this include:
-- Updating beta-3-amino acids with the METALBINDING property
-- Updates to the set_phi, set_psi, and set_omega functions in core::pose::Pose to correctly associate these with the appropriate backbone dihedral angles in beta-3-amino acids. (Also, added a theta() and set_theta() function for the additional beta-amino acid dihedral angle).
-- A typo fix in a D-proline variant type.
-- Tweaks to the MolecularSurfaceCalculator to allow it to be used with metalloproteins (currently by ignoring metals, though actual support for metals can be added in the future). It was crashing when it encountered a metal, before, so ignoring metals is an improvement.
Current test failures:
--PyRosetta tests (failing for everything right now until the owning pointer issues are resolved).
--cxx11thread build (already failing).
--Some numerical instability in some integration tests (all of which are showing similar numerical instability in previous tests; none of which seem to be related to my changes).
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Updated all Splice integration tests. Changes include adding the default ignore list to all command files and limiting the residues that are designed to reduce the run time
Splice mover is also updated. "add_dihedral_constraints" was changed to solve problem with n-ter tails.
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