beta_sc_scan Namespace Reference

Functions
def	set_up_movemap (pose)
def	scan_chi (pose, score_fxn, mm, extension)

Variables
	score_fxn = core.scoring.get_score_function()
	name3 = sys.argv[1]
	chm = rosetta.core.chemical.ChemicalManager.get_instance()
	restype_set = chm.residue_type_set('fa_standard').get_self_ptr()
string	seq = 'X[{name3}:AcetylatedNtermProteinFull:MethylatedCtermProteinFull]'.format(name3=name3)
	pose = pyrosetta.pose_from_sequence(seq)
def	mm = set_up_movemap(pose)

Function Documentation

scan_chi()

def beta_sc_scan.scan_chi	(		pose,
			score_fxn,
			mm,
			extension
	)

References pyrosetta.tests.distributed.test_dask.format, and basic.init().

set_up_movemap()

def beta_sc_scan.set_up_movemap

(

pose

)

Set up a movemap that allows every DOF to minimize except for 
certain chis.

References natoms().

Variable Documentation

chm

beta_sc_scan.chm = rosetta.core.chemical.ChemicalManager.get_instance()

mm

def beta_sc_scan.mm = set_up_movemap(pose)

name3

beta_sc_scan.name3 = sys.argv[1]

Referenced by pyrosetta.distributed.cluster.initialization._get_residue_type_set_name3(), ZincMinimize.add_zinc_constraints(), PeptoidDesignMover.apply(), ChiMover.ChiMover(), collect_residue_types(), MPDomainAssembly.create_residue_from_resn(), doit(), lactamize.find_lactams(), MatchSet.init(), main(), make_helix(), make_pose(), trivial_alascan.mutate_residue_to_ala(), PoseWrap.PoseWrap(), register_options(), rna_sequence_recovery_metrics(), and vsasa_bunsats().

pose

beta_sc_scan.pose = pyrosetta.pose_from_sequence(seq)

restype_set

beta_sc_scan.restype_set = chm.residue_type_set('fa_standard').get_self_ptr()

Referenced by A3BHbsCreatorMover.apply(), ligand_dock_main_jd1(), main(), A3BHbsCreatorMover.make_a3b_pose(), mutate_residue(), zinc_stats::ZincStatisticGenerator.mutate_residue(), BacksideHbondFinderMover.mutate_residue(), mutate_to_ala(), apps::pilot::SampleSecondaryStructureAlignmentMover.revert_loops_to_original(), and apps::pilot::SampleSecondaryStructureAlignmentMover.set_loops_to_virt_ala().

score_fxn

beta_sc_scan.score_fxn = core.scoring.get_score_function()

seq

string beta_sc_scan.seq = 'X[{name3}:AcetylatedNtermProteinFull:MethylatedCtermProteinFull]'.format(name3=name3)

Referenced by add_symm_sf4(), add_symm_zns(), append_alanines(), MPFoldingMover.apply(), build_helix_test(), FixbbJobQueen.complete_larval_job_maturation(), composite_sequences_from_cmd_line(), delta_chi_correction_test(), double_helix_test(), dump_sequences(), each_aa_test(), helix_from_sequence(), helix_ST(), HECTAllMover.init_on_new_input(), HECTUBQMover.init_on_new_input(), initialize_base_pair(), Link.Link(), main(), make_1mer_frags(), make_coiled_coil(), make_frags(), HECTMover.make_frags(), make_helix(), make_pose(), my_main(), output_seq_with_residue_emphasis(), ConstraintConfig.parse_config_file(), pep_scan_analysis(), ConstraintConfig.pick_sequence(), Prepare(), utility::tag::XMLSchemaComplexTypeGeneratorImpl.prepare_sequence_of_subelement_sets(), utility::tag::XMLSchemaComplexTypeGeneratorImpl.prepare_subelement_single_instance_required_ordered(), print_seq_map(), protein_helix_test(), rebuild_test(), rna_assemble_test(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_thread_test(), setup_capri_data(), setup_dinucleotide_pose(), setup_double_helix_pose(), setup_one_chain_pose(), setup_two_base_pair_pose_with_chainbreak(), ConstraintConfig.show_sequence(), spec_test(), test_refold(), and tf_specificity_test().