test.Workshop7test Namespace Reference

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)

Variable Documentation

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(), my_main(), rebuild_test(), rna_fullatom_minimize_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(), my_main(), 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(), 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(), swa_rna_sample(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_from_reproduce(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_minimizer_nstruct(), and pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_packer_nstruct_multi_decoy_ids().

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")