![]() |
Rosetta
2019.07
|
Variables | |
tuple | pose = pose_from_file("../test/data/workshops/complex.start.pdb") |
int | jump_num = 1 |
tuple | pert_mover = rigid_moves.RigidBodyPerturbMover(jump_num, 8, 3) |
tuple | randomize1 = rigid_moves.RigidBodyRandomizeMover(pose, jump_num, rigid_moves.partner_upstream) |
tuple | randomize2 = rigid_moves.RigidBodyRandomizeMover(pose, jump_num, rigid_moves.partner_downstream) |
tuple | slid = protocols.docking.DockingSlideIntoContact(jump_num) |
tuple | slide = protocols.docking.FaDockingSlideIntoContact(jump_num) |
tuple | movemap = MoveMap() |
tuple | scorefxn = create_score_function("ref2015") |
tuple | min_mover = protocols.minimization_packing.MinMover() |
tuple | switch_low = SwitchResidueTypeSetMover("centroid") |
tuple | pose_high = Pose() |
tuple | pose_low = Pose() |
tuple | scorefxn_low = create_score_function("interchain_cen") |
tuple | dock_lowres = protocols.docking.DockingLowRes(scorefxn_low, jump_num) |
tuple | output = tempfile.mkstemp() |
tuple | jd = PyJobDistributor(output, 10, scorefxn_low) |
tuple | native_pose = pose_from_file("../test/data/workshops/complex.high.pdb") |
tuple | starting_pose = Pose() |
tuple | scorefxn_high = create_score_function("ref2015.wts", "docking") |
tuple | dock_hires = protocols.docking.DockMCMProtocol() |
tuple | recover_sidechains = protocols.simple_moves.ReturnSidechainMover(pose_high) |
tuple test.Workshop7test.dock_hires = protocols.docking.DockMCMProtocol() |
tuple test.Workshop7test.dock_lowres = protocols.docking.DockingLowRes(scorefxn_low, jump_num) |
tuple test.Workshop7test.jd = PyJobDistributor(output, 10, scorefxn_low) |
int test.Workshop7test.jump_num = 1 |
tuple test.Workshop7test.min_mover = protocols.minimization_packing.MinMover() |
tuple test.Workshop7test.movemap = MoveMap() |
tuple test.Workshop7test.native_pose = pose_from_file("../test/data/workshops/complex.high.pdb") |
Referenced by analyze_base_pair_test(), HDdesignMover.apply(), calc_rms_test(), calculate_pairwise_RMSD(), StepWiseJobQueen.complete_larval_job_maturation(), main(), measure_sequence_recovery(), rebuild_test(), rna_fullatom_minimize_test(), rna_score_test(), run(), DockFragmentsMover.run(), stepwise_monte_carlo_legacy(), and swa_rna_sample().
tuple test.Workshop7test.output = tempfile.mkstemp() |
tuple test.Workshop7test.pert_mover = rigid_moves.RigidBodyPerturbMover(jump_num, 8, 3) |
tuple test.Workshop7test.pose = pose_from_file("../test/data/workshops/complex.start.pdb") |
tuple test.Workshop7test.pose_high = Pose() |
tuple test.Workshop7test.pose_low = Pose() |
tuple test.Workshop7test.randomize1 = rigid_moves.RigidBodyRandomizeMover(pose, jump_num, rigid_moves.partner_upstream) |
Referenced by add_rosetta_options_7().
tuple test.Workshop7test.randomize2 = rigid_moves.RigidBodyRandomizeMover(pose, jump_num, rigid_moves.partner_downstream) |
Referenced by add_rosetta_options_7(), and main().
tuple test.Workshop7test.recover_sidechains = protocols.simple_moves.ReturnSidechainMover(pose_high) |
Referenced by add_rosetta_options_7().
tuple test.Workshop7test.scorefxn = create_score_function("ref2015") |
Referenced by add_rosetta_options_7(), supercharge.apply(), build_full_model_test(), demo.D090_Ala_scan.calc_binding_energy(), calc_rama_scores(), calc_scores(), StepWiseJobQueen.complete_larval_job_maturation(), create_cs_rosetta_rna_scorefxn(), create_scorefxn(), cs_rosetta_rna_pdb(), densityTools(), supercharge.design_supercharge(), supercharge.design_supercharge_AvNAPSA(), do_color_by_score(), erraser2_test(), fill_designable_set(), get_stepwise_score_function(), demo.D090_Ala_scan.interface_ddG(), main(), make_fragments(), mg_modeler_test(), minimize_test(), demo.D040_Movemap.movemap(), nucleobase_probe_score_test(), o2prime_packer(), pyrosetta.toolbox.py_jobdistributor.output_scorefile(), demo.D050_Packer_task.packer_task(), demo.D020_Pose_scoring.pose_scoring(), post_rebuild_bulge_assembly(), supercharge.prepack_input_structure(), process_for_motifs(), quick_score_test(), rebuild_test(), repack_test(), resample_full_model_test(), rna_build_helix_test(), rna_design_test(), rna_sample_virtual_sugar(), rna_score_test(), ScoreBenchmark.run(), ScoreEachBenchmark.run(), ConsensusFragmentMover.run(), run_pep_prep(), demo.D070_Refinement.sample_refinement(), demo.D090_Ala_scan.scanning(), ScoreEachBenchmark.set_scorefxn(), ScoreAnalyticEtableBenchmark.setUp(), zinc1_homodimer_design.setup_scorefunctions(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), stepwise_monte_carlo_legacy(), and swa_rna_sample().
tuple test.Workshop7test.scorefxn_high = create_score_function("ref2015.wts", "docking") |
tuple test.Workshop7test.scorefxn_low = create_score_function("interchain_cen") |
tuple test.Workshop7test.slid = protocols.docking.DockingSlideIntoContact(jump_num) |
tuple test.Workshop7test.slide = protocols.docking.FaDockingSlideIntoContact(jump_num) |
tuple test.Workshop7test.starting_pose = Pose() |
Referenced by supercharge.apply(), and main().
tuple test.Workshop7test.switch_low = SwitchResidueTypeSetMover("centroid") |