Merge pull request #298 from RosettaCommons/revert-293-revert-280-jkleman/mp_updates
Revert "Revert "Jkleman/mp updates""
Merging in the stuff from an earlier reverted commit:
= corrected MPDocking weights from incorrect weights and added smooth terms and weights: mpframework_docking_<fa/cen>_2014.wts; these should be used from now on
= changed instances from using OP as args to &
= AddMembraneMover:
* switched SSize for membrane residue to regular Size
* spanfile is not a required input any more: if flag -membrane_new:setup:spans_from_structure <bool> is passed, it calculates the topology from the structure => this requires the structure to be transformed into membrane coordinates
* reading in MEMs got better: AddMembraneMover will automatically detect MEMs without a flag; flag can be used if multiple MEMs are present
* one of the constructors can now also use the anchor residue as input, default is 1 throughout
= SpanningTopology:
* adjusted method fill_from_structure so that it can be used from outside the class
= compute_structure_based_membrane_position:
* renamed to compute_structure_based_embedding
* overloaded functions to also take SpanningTopology as input: this is more useful for Symmetry or computing embedding for parts of the pose where the topology isn't necessarily for the whole pose
= protocols/membrane/geometry/util
* added split_topology_by_jump method and unit test for it
= span_from_PDB:
* changed default thickness from 12.5A to 15A
= core/pose/util.hh
* added function nres_protein that counts protein-only residues in the pose
= MEM / EMB params files:
* made all of them consistent to match the fa MEM params file, numbers didn't change except thickness is now consistently 15A for both low-res and high-res
* order of atoms in EMB changed, but this shouldn't affect any calculations
= MPDockingMover:
* reorganized code to be able to add stuff easier
* constructor now takes a jump number for docking
* added option to read in scorefunctions for both low-res and high-res steps
= FlipMover:
* added and unit tested: flips a pose element in the membrane, given a jump number
Unit tests: pass
Integration test changes: Tracers for Membrane framework are fine.
Integration.release_debug changes: Known numerical instabilities