Merge pull request #605 from RosettaCommons/rfalford12/mp_foldtree_checks_and_new_utils
Updates to the RosettaMP Framework: FoldTrees, Tilt Angles & More
Membrane Utilities Classes:
Code: src/protocols/membrane/util.(hh/cc)
Unit Test: test/protocols/membrane/MembraneUtil.cxxtest.hh
Clean ups & Reorganization
= Merge methods in protocols/membrane/geometry/util.* and protocols/membrane/metrics.*
into a single util file in protocols/membrane
= Added significant documentation to all methods
= Consolidated unit tests MembraneMetrics + MembraneGeometryUtil into a single MembraneUtil
unit test suite
New Methods
= Added two methods for general IO: reading in a center / normal from the RosettaScripts
and command line interfaces. Aims to reduce code duplication.
= New methods for calculating the tilt angle between a TM helix and the membrane normal
= Methods for calculating
= More sophisticated method for calculating the axis of the helix
= FoldTree methods - check whether a membrane is fixed or moveable relative to the protein
TransformIntoMembraneMover Updates:
Location: src/protocols/membrane/TransformIntoMembraneMover.(hh/cc)
Unit Test: test/protocols/membrane/TransformIntoMembraneMover.cxxtest.hh
= New constructors for different types of transformations: user specified protein embeddings and membrane positions
= Checks for correct membrane foldtree setup
= Added test to TransformIntoMembraneMover that checks the angle between the protein embedding normal and membrane normal is zero after transformation
Test Changes:
Integration - mp_dock_setup, mp_transform, mp_find_interface - cosmetic tracer changes
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Merge pull request #633 from RosettaCommons/rfalford12/add_mprelax_sfxn_constructor
Add constructor to specify scoring function in MPRelax
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Added new constructor to MPRelax that takes a ScoreFunction. The ScoreFunction is also now a private member of the class to accommodate. Currently intended for use in PyRosetta so not hooked in anywhere
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Merge pull request #632 from RosettaCommons/JWLabonte/sugars/docking
Minimizer: Carbohydrate virtual atoms now ignored by the minimizer
This merge will fix a frequent bug that occurred when the minimizer tried to move virtual atoms present in carbohydrate Residues. No body will care except for me.
Also included are personal pilot app. changes and a minor tweak to some pose metric output to use tracers instead of cout. This tweak results in 11 integration tests differences that are output-only. All unit tests pass.
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Merge pull request #634 from RosettaCommons/vmullig/fix_fithelixparams
Fixing a small mistake in FitSimpleHelix.cc
Atom names were being taken from the wrong residue. Merging without testing, since this is a very minor change that should only affect one pilot app.
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Merge pull request #617 from RosettaCommons/vmullig/multirepeat_bundle
Adding a ring closure term for proline-like noncanonicals.
The pro_close term seems to do some proline-specific things, so we need a ring closure term for proline-like noncanonicals (e.g. cis-ACPC, trans-ACHC).
- Add ncaa_ring_closure scoring term.
- Set up simple harmonic potentials holding two virtuals overtop two real atoms. (The idea is that we enforce ring closure with good bond angles and bond lengths by setting up the residue with virtuals attached to the real atoms in the bond to be closed, with each virtual overlapping the atom that is not its parent: A--x y--B. By enforcing that x be overtop B and y be overtop A, we get the bond angles and bond lengths for free.)
- Set up atom derivatives for the harmonic potentials.
- Use the virtual shadow code for determining which atoms to apply the potential to.
- Update the cyclic beta-amino acid params files:
- cis-ACPC
- cis-ACHC
- Unit tests.
- Documentation.
This pull request also:
- Fixes a serious bug in the way in which shadow atom records were being set up when creating variant ResidueTypes.
- Adds a flag, "-score:no_pro_close_ring_closure", that disables the ring closure part of the pro_close score term, allowing this term to ONLY do what it does for the i-1 residue's torsions. This allows ring_close to be used with pro_close, with ring_close handling closure of the proline ring and pro_close handling mainchain torsions of the i-1 residue.
- Add a test in the pro_close unit tests for pro_close with the above flag.
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Merge pull request #616 from RosettaCommons/sergey/optimization
Upgrading default optimization settings to use Core2 instruction set and optimize code for ‘generic’ CPU.
Setting Mac Clang build to use mtune=native (since we already using native instruction due to march=native there is no harm of tuning code to native CPU as well).
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