Another set of updates for RosettaCM.
- updated logic for fragment placement in stage 1
- updated domain parsing logic in realign_domains
- fixing bug in realign_domains where templates would accumulate drift over time (thanks Rocco!)
- better handing of realignment of ligand-containing poses
- removing more unused or redundant options
- small changes to smoothing kernel for fragment-derived constraints
- removing extraneous output accidently checked in in the previous commit
Hybridize and mr_protocols integration test changes expected.
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Merge pull request #408 from RosettaCommons/rfalford12/add_var_thk
Add thickness/steepness setters to MembraneInfo - Allow the user to adjust the membrane hydrophobic thickness and transition steepness, symmetrically about the center along the normal axis. This can be done programmatically and via the command line. Additionally, the thickness used by the PyMOL viewer is now linked to MembraneInfo (can also be changed separately)
No test changes expected
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Updating Xcode project.pbxproj.template so that core.1 properly links to basic and Xcode compile now works. Because I'm only changing this one file, and it only affects Xcode and no other builds, I am pushing to master without pull request or test servers
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Merge pull request #400 from RosettaCommons/JWLabonte/sugars/ring_conformers
Code clean-up and refactoring of the `RingConformerSet`-related code.
NEWS:
This merge should allow one to use the `RingConformationMover` on NCAAs with aliphatic, saturated rings, provided the `.params` files are set up properly.
This merge also allows one to specify the lowest and low-energy conformers in the topology files for residues with rings, if this information is known. The `RingConformationMover` will by default only select ideal ring conformers from among this set.
no unit test changes
carbohydrates and rings integration test changes expected
In addition, this merge makes the following improvements to the ring conformer system:
* `RingConformationMover` should now work with RosettaScripts.
* All static const `RingConformer` data that a `RingConformerSet` uses is accessed via the singleton `RingConformerManager`, so everything should now be thread-safe.
* An option flag `-sample_high_energy_conformers` allows the `RingConformationMover` to do exactly that.
* Unit tests for ring-related things are more robust.
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