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Revisions №57583

branch: master 「№57583」
Commited by: jkleman
GitHub commit link: 「b338d72c17e68abb」 「№298」
Difference from previous tested commit:  code diff
Commit date: 2015-02-03 11:48:36

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

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