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Revisions №61105

branch: master 「№61105」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「763f7940ff4c1c57」 「№4368」
Difference from previous tested commit:  code diff
Commit date: 2020-01-17 11:57:48
linux.clang linux.gcc linux.srlz mac.clang
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels build.ninja_debug graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.PyRosetta4.MinSizeRel release.source scientific.docking.debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release gcc-9.gcc.unit util.apps

Merge pull request #4368 from RosettaCommons/jadolfbr/glycan_benchmarking2 General ===== - Fix `Or_combine` and `And_combine` functions - Fix `get_score_function` to correctly use the local options collection - Fix `set_weight_if_zero` by comparing the 0 delta instead of actual 0. - Fix `extract_asymmetric_unit` to be much more robust, using `create_subpose` as a guide but keeping the additional functionality. - Fix `RMSDMetric` to extract the asymmetric unit if the pose is symmetric and the ref/native is not. This works fine for RMSD but failed for superposition. The fixes here and with `extract_asymmetric_unit` now allow glycans poses to be properly extracted and superimposed. - Add options to allow RMSDMetrics to use a different set of residue_selectors for superposition vs RMSD. - Add a warning to `superimpose_pose` that warns when a user is trying to superimpose a symmetric pose with an asymmetric pose (even with a correct `AtomID_map`). It won't crash, but it will give you a garbage superposition. - Fix flip of HNQ for residues across a side-chain branch point Glycans ===== - Add option to force `sugar_bb` 0 (if using get_score_function) - Add ability to control `kT` properly - Add conformer probability option for root of glycan only - Allow `sugar_bb` to be set on cmd-line or through score functions without overriding to 1.0 - only set to 1.0 if it had not been set manually - Add `match_window_one` option for glycans that is used for benchmarking so that the total number of rounds is the same for various sampling techniques. Beta Scorefunction ============== - Make -beta score function work for JD3 apps - Add serialization methods to core beta energy classes that are stored in the pose