Merge pull request #401 from RosettaCommons/vmullig/fix_sc
Adding fluorine to the sc_radii for the shape complementarity calculator
Trivial database change. No test changes expected.
(Also, fixed the PyRosetta tests that TJ accidentally broke while I was at it. @tjbrunette, when you get a chance, please check protocols/simple_filters/RepeatParameterFilter.hh line 47 -- there was a function prototype here with no function defined for it that I commented out.)
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Merge pull request #395 from RosettaCommons/PyRosetta
Updating PyRosetta build scripts so it works on Yosemite. Also fixing PyRosetta release archive names so tar will not get confuse on some shell's.
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Merge pull request #386 from RosettaCommons/vmullig/genkic_sampling
Vmullig/genkic sampling
This adds support for D/L-proline sub-bins to the BinTransitionData object, and updates the ABBA.bin_params file accordingly.
Tasks:
Update ABBA.bin_params
Add support for D/L-proline sub-bins to the BinTransitionData object.
Update documentation.
No test changes expected.
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Fixing pyrosetta & other broken builds. Removing per-residue sequence shift controls since they were only working previously for one mode, which has since been removed. Restoring old global sequence shift control which had been previously disabled.
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A number of updates for hybridize (RosettaCM).
New features:
- if template="extended" is specified, this will trigger ab initio sampling in stage 1. This may be combined with template structures to allow fragment harvesting.
- add an option 'max_contig_insertion' that sepecifies the max length continuous segment that will be inserted in stage 2. This allows more model diversity when fulllength inputs are provided. Default of -1 maintains current behavior.
- add an option 'csts_from_frags' that generates dihedral constraints from fragments that may be used in minimization during stages 2 and 3; useful for CS fragments. Adds a new constraint type, CircularSplineFunc.
Smaller changes/bugfixes
- turning on align_templates_stage2 by default
- removing the ramping of constraint energies in stage 2
- tweaking of probabilities of moves in cartesian hybridize
- changing the logic for determining allowed insertions, no flooding the screen in warnings if no insertions allowed
- cenrot is now turned on by an XML switch (the flag is still needed to enable loading of the rot library)
- template realignment and ligand placement are no longer mutually exclusive
- changing the hbond weight to 1.0 (was 2.0) in score4_smooth and score4_smooth_cart, based on extensive testing
Removing duplicated/unused code:
- Removing the separate HybridizeSetup mode of initialization since functions were copy/pasted directly from HybridizeProtocol and the versions had already gone out of sync
- For the same reason, removing separate parsing of the individual stage 1 & 2 movers since code had gone out of synch, moving some added functionality from
- removing DomainAssembly mode
- removing a few other unused modes
Additionally, making a small bugfix to silent file reading (should not be encountered in normal silent files; but may allow recovery of structs from corrupted ones).
Finally, some updates to pilot apps.
** hybridize and mr_protocols integration test changes expected.
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