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.