Merge pull request #4303 from RosettaCommons/roccomoretti/drug_design_background
Grab-bag of changes from my drug design branch.
This is a selection of changes from #1036 which touch existing code (Versus adding new classes/etc.) The changes all relate to things done with drug-design, but aren't dependent on the new stuff therein. (I apologize for the grab-bag nature of the changes. I didn't necessarily want to split things out further.)
A short summary of major changes:
* Permit the MonteCarlo object to manage a pose, but use a score which isn't the pose's total score.
* Change logic in Residue::orient_onto_residue() to better handle orienting non-related types.
* Don't assume the root atom is atom 1 in core::pack::scmin::ResidueAtomTreeCollection
* Better diagnostics for CompoundFilter
* For ligand docking FinalMinimizer, add option to remove the constraints which the mover adds
* For ligand docking FinalMinimizer, fix nonsensical backbone-minimization-without-chainbreak-term
* For ligand docking HighResDocker, remove the dihedral restraints added (just like we remove the ligand tethers)
* Update automatic neighbor atom finding for MutableResidueType change
* Additional formatting options in SDF residue type input/output (still not ready for prime-time)
* Various convenience functions added.