Merge pull request #2781 from RosettaCommons/jadolfbr/dih_cst_generator
Main
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Add a `DihedralConstraintGenerator` class using @tlinsky 's wonderful `ConstraintGenerator` framework. One instance works on a single dihedral angle type (aka Phi OR Psi). Use multiple generator to add constraints for multiple angles. Mainly works with BB dihedrals, by setting phi,psi,omega (`dihedral` option). Works with glycan backbones as well up to omega2.
Additionally, you can set arbitrary dihedrals by defining the 4 atom names and 4 residues you want. (`dihedral_atoms` and `dihedral_residues` options).
The StandardDeviation for the `CircularHarmonic` Func is set to a default of 16 degrees, which was found by taking the mean SD Within a particular CDR cluster and averaging all of those means together. The 16 degrees represents a good default that allows some movement, as well as useful lever-arm effects, but typically not huge changes to the overall structure of the loops.
Other
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- Updates to code_templates to remove the THREAD_LOCAL keywords.
- Update rosetta_scripts_jd3 to allow printing of BOTH a RosettaScript template and a JobDefinition template if used without `-job_definition` option
Tests
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Includes a comprehensive Unit test for the `DihedralConstraintGenerator` testing the setting of particular dihedrals, custom dihedrals, and parsing custom dihedral angles from a RosettaScript.