Merge pull request #292 from RosettaCommons/justinrporter/env_devel Multiple small bug fixes to the broker (see commits 9854a39, 13d49bd, and 09033a4). No broken integration tests outside the usual failures or unit tests outside of the Windows pyrosetta build, which seems to be broken for everybody at the moment (and it wouldn't really make sense for what I've done to break it...).

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Fix issues with reading waters from silent files Thanks to Per for pointing it out.

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Merge pull request #293 from RosettaCommons/revert-280-jkleman/mp_updates Revert "Jkleman/mp updates" reverting merge for now until I figure out what's going on with the windows.PyRosetta build.

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Merge pull request #281 from RosettaCommons/phbradley/tiny_hbscale_bugfix tiny hbond-scale bugfix: the per-atom hbond scale factors were applied to the derivatives but not to the function values for the chi score.

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Merge pull request #280 from RosettaCommons/jkleman/mp_updates = 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

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warnings as errors correction

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Merge pull request #291 from RosettaCommons/sjf/InterfaceAngle reducing verbosity

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Merge pull request #288 from RosettaCommons/sjf/InterfaceAngle Sjf/interface angle Compute the angle between a small molecule and a predetermined vector. This is very ad hoc; not sure it will be of general use...

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In integration tests, ignore lines about updating an outdated Dunbrack binary.

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Merge pull request #263 from RosettaCommons/justinrporter/env_release Commiting fixes to Broker framework, small updates to syntax, renaming claiming mover to client mover, NullMover is now a MovemapMover (it doesn't do anything with the movemap it gets). Integration test changes for a) broken tests and b) unstable performance tests. Otherwise clean.

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Fix PyRosetta MPIJobDistributor.

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Merge pull request #287 from RosettaCommons/vmullig/fix_metal_issues Fixed a bug in automatic metal setup when patches are applied. (The name order was incorrect.) No integration or unit test changes expected. Since this is a very minor change, I will merge immediately.

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Merge pull request #90 from RosettaCommons/everyday847/everyday847/disulfides Adding support for disulfides including homocysteine and D-homocysteine

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Fix DockingTest:test_DockingProtocolFunctions Change the UTracer results for this test. The difference is a small change in the fa_dun term in one instance (and resulting change in total score). This is easily explained by the Dunbrack binary issues we've seen recently.

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Merge pull request #277 from RosettaCommons/roccomoretti/rotlib_cmp Add Dunbrack binary validation tests We've had issues with changes to the codebase which alter the contents of the Dunbrack-library-as-read-from-ASCII versus the Dunbrack-library-as-read- from-a-previous-version's-binary. There's a version number in core/pack/dunbrack/RotamerLibrary.cc which is supposed to control for this, but people don't always realize that their changes require a version number bump. This commit adds unit and integration tests which attempt to compare the ASCII and binary versions of the Dunbrack library, and see if they're different. Note that this integration test is looking at a single version, rather than a version comparison. The test is also not foolproof, as there is a delta in the real number comparisons, but hopefully it should catch the major changes. New unit tests and integration tests - they shouldn't (cross fingers) be failing, due to the previous commit which bumped the version number and forced binary regeneration.

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Bump version number on Dunbrack binary. There's been a number of changes which have changed the contents of the ASCII-loaded Dumbrack library versus what's loaded from a binary generated by a previous version. These should have come along with a version number increase for the binary, but weren't always. This commit number increase should reset any remaining old binaries, and going forward we can hopefully keep on top of increments. (A separate commit will introduce a unit/integration test for changes.) Known changes which changed the binary: 2015-01-13 - resolution fix for rotlibs (prob <= 1e-6, not prob == 0) 57550 (test) c7ce5fe8d820cb13 (merge) f8ce0ac3bc65c8 (change) 2014-12-01 - Fixing an error in SingleResidueDunbrackLibrary::rotno_2_rotwell 57471 (test) 5b0686ce58de4832 (merge & change) * There may be others as well, which weren't noticed. Possible integration test changes on the server as old Dunbrack binaries are flushed.

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