Bindings for protocols::stepwise::modeler::rna namespace

Modules
		rosetta.protocols.stepwise.modeler.rna.bulge rosetta.protocols.stepwise.modeler.rna.checker rosetta.protocols.stepwise.modeler.rna.helix rosetta.protocols.stepwise.modeler.rna.o2prime rosetta.protocols.stepwise.modeler.rna.phosphate rosetta.protocols.stepwise.modeler.rna.rigid_body rosetta.protocols.stepwise.modeler.rna.sugar

Classes
		builtins.object Combine_Tags_Info Filterer_Count InternalWorkingResidueParameter Jump_point Residue_info StepWiseRNA_CombineLongLoopFilterer StepWiseRNA_CountStruct Torsion_Info output_data_struct   class Combine_Tags_Info(builtins.object)     ////////////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info,  : rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info,  : rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info) -> rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info Data descriptors defined here: combine_score side_one_tag side_two_tag   class Filterer_Count(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.stepwise.modeler.rna.Filterer_Count) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.rna.Filterer_Count,  : rosetta.protocols.stepwise.modeler.rna.Filterer_Count) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.rna.Filterer_Count,  : rosetta.protocols.stepwise.modeler.rna.Filterer_Count) -> rosetta.protocols.stepwise.modeler.rna.Filterer_Count Data descriptors defined here: chain_closable_geometry_screen filter_for_moving_res_contact filter_for_previous_clash filter_for_previous_contact score_cut_count total_count   class InternalWorkingResidueParameter(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.stepwise.modeler.rna.InternalWorkingResidueParameter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: fake_working_moving_suite possible_working_res_1 possible_working_res_2   class Jump_point(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.stepwise.modeler.rna.Jump_point) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.rna.Jump_point,  : rosetta.protocols.stepwise.modeler.rna.Jump_point) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.rna.Jump_point,  : rosetta.protocols.stepwise.modeler.rna.Jump_point) -> rosetta.protocols.stepwise.modeler.rna.Jump_point Data descriptors defined here: cut_point five_prime_atom five_prime_seq_num three_prime_atom three_prime_seq_num   class Residue_info(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.stepwise.modeler.rna.Residue_info) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.rna.Residue_info,  : rosetta.protocols.stepwise.modeler.rna.Residue_info) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.rna.Residue_info,  : rosetta.protocols.stepwise.modeler.rna.Residue_info) -> rosetta.protocols.stepwise.modeler.rna.Residue_info Data descriptors defined here: name seq_num   class StepWiseRNA_CombineLongLoopFilterer(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, combine_helical_silent_file : bool) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer,  : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. filter(...) from builtins.PyCapsule filter(rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer) -> NoneType set_filter_for_previous_clash(...) from builtins.PyCapsule set_filter_for_previous_clash(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting : float) -> NoneType set_filter_for_previous_contact(...) from builtins.PyCapsule set_filter_for_previous_contact(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting : float) -> NoneType set_max_decoys(...) from builtins.PyCapsule set_max_decoys(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting : int) -> NoneType set_output_filename(...) from builtins.PyCapsule set_output_filename(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting : str) -> NoneType set_parin_favorite_output(...) from builtins.PyCapsule set_parin_favorite_output(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting : bool) -> NoneType set_silent_files_in(...) from builtins.PyCapsule set_silent_files_in(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting : rosetta.utility.vector1_std_string) -> NoneType   ////////////////////////////////////////////////////////////////////// set_undercount_sugar_rotamers(...) from builtins.PyCapsule set_undercount_sugar_rotamers(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting : bool) -> NoneType   class StepWiseRNA_CountStruct(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct,  : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct,  : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) -> rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct Data descriptors defined here: Near_Native_StepWiseSampler_Count base_pairing_count base_stack_count before_chain_break_grid_index_screening both_count bulge_at_chain_closure_count chain_break_grid_index_screening chain_break_screening_count chain_closable_geometry_count chain_closable_geometry_count2 chain_closable_geometry_count3 fast_full_atom_VDW_repulsion_screen fine_rmsd_count full_score_count good_angle_count good_atr_rotamer_count good_bin_rep_count good_distance_count good_rep_rotamer_count in_range_CCD_torsion non_clash_sugar output_pose_count pass_base_centroid_screen residues_contact_screen rmsd_count strict_base_pairing_count test_count_one test_count_two tot_rotamer_count total_bin   class Torsion_Info(builtins.object)     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.stepwise.modeler.rna.Torsion_Info) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: id value   class output_data_struct(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.stepwise.modeler.rna.output_data_struct) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: O3_C5_distance current_score diff_torsions loop_rmsd loop_rmsd_wrt_correct_minimized loop_rmsd_wrt_minimized rmsd rmsd_wrt_correct_minimized rmsd_wrt_minimized

Functions
		add_fade_chain_break_constraint_across_gap(...) method of builtins.PyCapsule instance add_fade_chain_break_constraint_across_gap(pose : rosetta.core.pose.Pose, five_prime_res : int, three_prime_res : int, gap_size : int) -> NoneType add_harmonic_chain_break_constraint(...) method of builtins.PyCapsule instance add_harmonic_chain_break_constraint(pose : rosetta.core.pose.Pose, five_prime_res : int) -> NoneType align_poses(...) method of builtins.PyCapsule instance align_poses(*args, **kwargs) Overloaded function.   1. align_poses(moving_pose : rosetta.core.pose.Pose, moving_tag : str, static_pose : rosetta.core.pose.Pose, static_tag : str, working_best_alignment : rosetta.utility.vector1_unsigned_long) -> NoneType   2. align_poses(moving_pose : rosetta.core.pose.Pose, moving_tag : str, static_pose : rosetta.core.pose.Pose, static_tag : str, working_best_alignment : rosetta.utility.vector1_unsigned_long, base_only : bool) -> NoneType apply_full_to_sub_mapping(...) method of builtins.PyCapsule instance apply_full_to_sub_mapping(*args, **kwargs) Overloaded function.   1. apply_full_to_sub_mapping(res_vector : rosetta.utility.vector1_unsigned_long, is_working_res : rosetta.utility.vector1_unsigned_long, full_to_sub : rosetta.std.map_unsigned_long_unsigned_long) -> rosetta.utility.vector1_unsigned_long   2. apply_full_to_sub_mapping(res_vector : rosetta.utility.vector1_unsigned_long, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> rosetta.utility.vector1_unsigned_long apply_protonated_H1_adenosine_variant_type(...) method of builtins.PyCapsule instance apply_protonated_H1_adenosine_variant_type(*args, **kwargs) Overloaded function.   1. apply_protonated_H1_adenosine_variant_type(pose : rosetta.core.pose.Pose, seq_num : int) -> NoneType   2. apply_protonated_H1_adenosine_variant_type(pose : rosetta.core.pose.Pose, seq_num : int, apply_check : bool) -> NoneType apply_sub_to_full_mapping(...) method of builtins.PyCapsule instance apply_sub_to_full_mapping(working_res_vector : rosetta.utility.vector1_unsigned_long, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> rosetta.utility.vector1_unsigned_long atom_square_deviation(...) method of builtins.PyCapsule instance atom_square_deviation(rsd_1 : rosetta.core.conformation.Residue, rsd_2 : rosetta.core.conformation.Residue, atomno_1 : int, atomno_2 : int, verbose : bool) -> float base_atoms_square_deviation(...) method of builtins.PyCapsule instance base_atoms_square_deviation(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, moving_res_1 : int, moving_res_2 : int, atom_count : int, sum_sd : float, verbose : bool, ignore_virtual_atom : bool) -> NoneType check_for_messed_up_structure(...) method of builtins.PyCapsule instance check_for_messed_up_structure(pose : rosetta.core.pose.Pose, tag : str) -> bool check_instantiated_O2Prime_hydrogen(...) method of builtins.PyCapsule instance check_instantiated_O2Prime_hydrogen(pose : rosetta.core.pose.Pose) -> NoneType check_is_working_res(...) method of builtins.PyCapsule instance check_is_working_res(full_seq_num : int, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> bool check_validity_and_get_working_res(...) method of builtins.PyCapsule instance check_validity_and_get_working_res(full_seq_num : int, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> int choose_random_if_unspecified_nucleotide(...) method of builtins.PyCapsule instance choose_random_if_unspecified_nucleotide(newrestype : str) -> NoneType copy_all_o2prime_torsions(...) method of builtins.PyCapsule instance copy_all_o2prime_torsions(mod_pose : rosetta.core.pose.Pose, template_pose : rosetta.core.pose.Pose) -> NoneType copy_dofs_sort_criterion(...) method of builtins.PyCapsule instance copy_dofs_sort_criterion(residue_info_1 : rosetta.protocols.stepwise.modeler.rna.Residue_info, residue_info_2 : rosetta.protocols.stepwise.modeler.rna.Residue_info) -> bool create_full_to_input_res_map(...) method of builtins.PyCapsule instance create_full_to_input_res_map(input_res_vector : rosetta.utility.vector1_unsigned_long) -> rosetta.std.map_unsigned_long_unsigned_long create_rotamer_string(...) method of builtins.PyCapsule instance create_rotamer_string(*args, **kwargs) Overloaded function.   1. create_rotamer_string(pose : rosetta.core.pose.Pose, moving_res : int, is_prepend : bool) -> str   2. create_rotamer_string(pose : rosetta.core.pose.Pose, moving_res : int, reference_res : int) -> str create_standard_o2prime_pack_task(...) method of builtins.PyCapsule instance create_standard_o2prime_pack_task(*args, **kwargs) Overloaded function.   1. create_standard_o2prime_pack_task(pose : rosetta.core.pose.Pose, O2prime_pack_seq_num : rosetta.utility.vector1_unsigned_long) -> rosetta.core.pack.task.PackerTask   2. create_standard_o2prime_pack_task(pose : rosetta.core.pose.Pose, O2prime_pack_seq_num : rosetta.utility.vector1_unsigned_long, pack_virtual_o2prime_hydrogen : bool) -> rosetta.core.pack.task.PackerTask create_tag(...) method of builtins.PyCapsule instance create_tag(prestring : str, i : int) -> str create_torsion_value_string(...) method of builtins.PyCapsule instance create_torsion_value_string(torsion_value : float) -> str ensure_valid_full_seq_num(...) method of builtins.PyCapsule instance ensure_valid_full_seq_num(full_seq_num : int, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType figure_out_moving_rna_chain_breaks(...) method of builtins.PyCapsule instance figure_out_moving_rna_chain_breaks(pose : rosetta.core.pose.Pose, moving_partition_res : rosetta.utility.vector1_unsigned_long, rna_cutpoints_closed : rosetta.utility.vector1_unsigned_long, rna_five_prime_chain_breaks : rosetta.utility.vector1_unsigned_long, rna_three_prime_chain_breaks : rosetta.utility.vector1_unsigned_long, rna_chain_break_gap_sizes : rosetta.utility.vector1_unsigned_long) -> NoneType file_exists(...) method of builtins.PyCapsule instance file_exists(file_name : str) -> bool freeze_sugar_torsions(...) method of builtins.PyCapsule instance freeze_sugar_torsions(mm : rosetta.core.kinematics.MoveMap, total_residue : int) -> NoneType get_anchor_res(...) method of builtins.PyCapsule instance get_anchor_res(rebuild_res : int, pose : rosetta.core.pose.Pose) -> int get_binary_rna_silent_struct_safe(...) method of builtins.PyCapsule instance get_binary_rna_silent_struct_safe(const_pose : rosetta.core.pose.Pose, tag : str, silent_file : str) -> rosetta.core.io.silent.BinarySilentStruct get_binary_rna_silent_struct_safe_wrapper(...) method of builtins.PyCapsule instance get_binary_rna_silent_struct_safe_wrapper(const_pose : rosetta.core.pose.Pose, tag : str, silent_file : str, write_score_only : bool) -> rosetta.core.io.silent.BinarySilentStruct get_max_seq_num_from_res_map(...) method of builtins.PyCapsule instance get_max_seq_num_from_res_map(my_map : rosetta.std.map_unsigned_long_unsigned_long) -> int get_modeler_scorefxn(...) method of builtins.PyCapsule instance get_modeler_scorefxn(scorefxn_ : rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction get_one_letter_name(...) method of builtins.PyCapsule instance get_one_letter_name(three_letter_name : str) -> str get_partition_definition_floating_base(...) method of builtins.PyCapsule instance get_partition_definition_floating_base(pose : rosetta.core.pose.Pose, moving_res : int) -> rosetta.utility.vector1_bool get_possible_O3prime_C5prime_distance_range(...) method of builtins.PyCapsule instance get_possible_O3prime_C5prime_distance_range(gap_size_ : int, min_dist : float, max_dist : float) -> NoneType get_surrounding_O2prime_hydrogen(...) method of builtins.PyCapsule instance get_surrounding_O2prime_hydrogen(*args, **kwargs) Overloaded function.   1. get_surrounding_O2prime_hydrogen(pose : rosetta.core.pose.Pose, moving_res : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long   2. get_surrounding_O2prime_hydrogen(pose : rosetta.core.pose.Pose, moving_res : rosetta.utility.vector1_unsigned_long, verbose : bool) -> rosetta.utility.vector1_unsigned_long get_three_letter_name(...) method of builtins.PyCapsule instance get_three_letter_name(one_letter_name : str) -> str is_residues_in_contact(...) method of builtins.PyCapsule instance is_residues_in_contact(*args, **kwargs) Overloaded function.   1. is_residues_in_contact(res_ONE : int, pose_ONE : rosetta.core.pose.Pose, res_TWO : int, pose_TWO : rosetta.core.pose.Pose, atom_atom_overlap_dist_cutoff : float, num_atom_contacts_cutoff : int) -> bool   2. is_residues_in_contact(res_ONE : int, pose_ONE : rosetta.core.pose.Pose, res_TWO : int, pose_TWO : rosetta.core.pose.Pose, atom_atom_overlap_dist_cutoff : float, num_atom_contacts_cutoff : int, verbose : bool) -> bool is_virtual_base(...) method of builtins.PyCapsule instance is_virtual_base(rsd : rosetta.core.conformation.Residue) -> bool just_modeling_RNA(...) method of builtins.PyCapsule instance just_modeling_RNA(sequence : str) -> bool just_rna(...) method of builtins.PyCapsule instance just_rna(res_list : rosetta.utility.vector1_unsigned_long, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long minimize_with_constraints(...) method of builtins.PyCapsule instance minimize_with_constraints(pose : rosetta.core.pose.Pose, mm : rosetta.core.kinematics.MoveMap, scorefxn : rosetta.core.scoring.ScoreFunction, options : rosetta.core.optimization.MinimizerOptions) -> NoneType mutate_res_if_allowed(...) method of builtins.PyCapsule instance mutate_res_if_allowed(*args, **kwargs) Overloaded function.   1. mutate_res_if_allowed(pose : rosetta.core.pose.Pose, mutate_res : int) -> bool   2. mutate_res_if_allowed(pose : rosetta.core.pose.Pose, mutate_res : int, mutation_frequency : float) -> bool o2prime_trials(...) method of builtins.PyCapsule instance o2prime_trials(*args, **kwargs) Overloaded function.   1. o2prime_trials(pose : rosetta.core.pose.Pose, packer_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   2. o2prime_trials(pose : rosetta.core.pose.Pose, packer_scorefxn : rosetta.core.scoring.ScoreFunction, pack_virtual_o2prime_hydrogen : bool) -> NoneType   3. o2prime_trials(pose : rosetta.core.pose.Pose, packer_scorefxn : rosetta.core.scoring.ScoreFunction, O2prime_seq_num_list : rosetta.utility.vector1_unsigned_long) -> NoneType   4. o2prime_trials(pose : rosetta.core.pose.Pose, packer_scorefxn : rosetta.core.scoring.ScoreFunction, O2prime_seq_num_list : rosetta.utility.vector1_unsigned_long, pack_virtual_o2prime_hydrogen : bool) -> NoneType output_data(...) method of builtins.PyCapsule instance output_data(*args, **kwargs) Overloaded function.   1. output_data(silent_file : str, tag : str, write_score_only : bool, pose : rosetta.core.pose.Pose, native_poseCOP : rosetta.core.pose.Pose, working_parameters_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType   2. output_data(silent_file : str, tag : str, write_score_only : bool, pose : rosetta.core.pose.Pose, native_poseCOP : rosetta.core.pose.Pose, working_parameters_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, NAT_rmsd : bool) -> NoneType   3. output_data(silent_file_data : rosetta.core.io.silent.SilentFileData, silent_file : str, tag : str, write_score_only : bool, pose : rosetta.core.pose.Pose, native_poseCOP : rosetta.core.pose.Pose, working_parameters_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType   4. output_data(silent_file_data : rosetta.core.io.silent.SilentFileData, silent_file : str, tag : str, write_score_only : bool, pose : rosetta.core.pose.Pose, native_poseCOP : rosetta.core.pose.Pose, working_parameters_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, NAT_rmsd : bool) -> NoneType output_res_map(...) method of builtins.PyCapsule instance output_res_map(my_map : rosetta.std.map_unsigned_long_unsigned_long, max_seq_num : int) -> NoneType output_residue_struct(...) method of builtins.PyCapsule instance output_residue_struct(residue : rosetta.protocols.stepwise.modeler.rna.Residue_info) -> NoneType phosphate_base_phosphate_rmsd(...) method of builtins.PyCapsule instance phosphate_base_phosphate_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, moving_res_num : int, ignore_virtual_atom : bool) -> float phosphate_base_phosphate_square_deviation(...) method of builtins.PyCapsule instance phosphate_base_phosphate_square_deviation(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, moving_res_1 : int, moving_res_2 : int, atom_count : int, sum_sd : float, verbose : bool, ignore_virtual_atom : bool) -> NoneType phosphate_square_deviation(...) method of builtins.PyCapsule instance phosphate_square_deviation(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, moving_res_1 : int, moving_res_2 : int, atom_count : int, sum_sd : float, verbose : bool, ignore_virtual_atom : bool) -> NoneType print_torsion_info(...) method of builtins.PyCapsule instance print_torsion_info(pose : rosetta.core.pose.Pose, seq_num : int, rna_torsion_number : int, type : str) -> NoneType remove_all_variant_types(...) method of builtins.PyCapsule instance remove_all_variant_types(pose : rosetta.core.pose.Pose) -> NoneType remove_all_virtual_phosphates(...) method of builtins.PyCapsule instance remove_all_virtual_phosphates(pose : rosetta.core.pose.Pose) -> NoneType remove_chain_break_variants(...) method of builtins.PyCapsule instance remove_chain_break_variants(pose : rosetta.core.pose.Pose, cutpoint : int) -> NoneType remove_file(...) method of builtins.PyCapsule instance remove_file(file_name : str) -> NoneType remove_virtual_O2Prime_hydrogen(...) method of builtins.PyCapsule instance remove_virtual_O2Prime_hydrogen(pose : rosetta.core.pose.Pose) -> bool rescale_scorefxn(...) method of builtins.PyCapsule instance rescale_scorefxn(starting_scorefxn : rosetta.core.scoring.ScoreFunction, scaling_factor : float) -> rosetta.core.scoring.ScoreFunction rmsd_over_residue_list(...) method of builtins.PyCapsule instance rmsd_over_residue_list(*args, **kwargs) Overloaded function.   1. rmsd_over_residue_list(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, residue_list : rosetta.utility.vector1_unsigned_long, full_to_sub : rosetta.std.map_unsigned_long_unsigned_long, is_prepend_map : rosetta.std.map_unsigned_long_bool, verbose : bool) -> float   2. rmsd_over_residue_list(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, residue_list : rosetta.utility.vector1_unsigned_long, full_to_sub : rosetta.std.map_unsigned_long_unsigned_long, is_prepend_map : rosetta.std.map_unsigned_long_bool, verbose : bool, ignore_virtual_atom : bool) -> float   3. rmsd_over_residue_list(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, working_parameters_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> float   4. rmsd_over_residue_list(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, working_parameters_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, ignore_virtual_atom : bool) -> float set_CCD_torsions_to_zero(...) method of builtins.PyCapsule instance set_CCD_torsions_to_zero(pose : rosetta.core.pose.Pose, five_prime_res : int) -> NoneType setup_chain_break_variants(...) method of builtins.PyCapsule instance setup_chain_break_variants(pose : rosetta.core.pose.Pose, cutpoint : int) -> NoneType setup_suite_atom_id_map(...) method of builtins.PyCapsule instance setup_suite_atom_id_map(*args, **kwargs) Overloaded function.   1. setup_suite_atom_id_map(rsd_1 : rosetta.core.conformation.Residue, rsd_2 : rosetta.core.conformation.Residue, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   2. setup_suite_atom_id_map(rsd_1 : rosetta.core.conformation.Residue, rsd_2 : rosetta.core.conformation.Residue, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only : bool) -> NoneType   3. setup_suite_atom_id_map(rsd_1 : rosetta.core.conformation.Residue, rsd_2 : rosetta.core.conformation.Residue, res_num_1 : int, res_num_2 : int, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   4. setup_suite_atom_id_map(rsd_1 : rosetta.core.conformation.Residue, rsd_2 : rosetta.core.conformation.Residue, res_num_1 : int, res_num_2 : int, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only : bool) -> NoneType   5. setup_suite_atom_id_map(pose_1 : rosetta.core.pose.Pose, pose_2 : rosetta.core.pose.Pose, base_res : int, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   6. setup_suite_atom_id_map(pose_1 : rosetta.core.pose.Pose, pose_2 : rosetta.core.pose.Pose, base_res : int, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only : bool) -> NoneType   7. setup_suite_atom_id_map(pose_1 : rosetta.core.pose.Pose, pose_2 : rosetta.core.pose.Pose, base_res_1 : int, base_res_2 : int, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   8. setup_suite_atom_id_map(pose_1 : rosetta.core.pose.Pose, pose_2 : rosetta.core.pose.Pose, base_res_1 : int, base_res_2 : int, atom_ID_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only : bool) -> NoneType show_scorefxn_weight_lines(...) method of builtins.PyCapsule instance show_scorefxn_weight_lines(scorefxn : rosetta.core.scoring.ScoreFunction, title : str) -> NoneType sort_seq_num_list(...) method of builtins.PyCapsule instance sort_seq_num_list(seq_num_list : rosetta.utility.vector1_unsigned_long) -> NoneType string_to_int(...) method of builtins.PyCapsule instance string_to_int(input_string : str) -> int string_to_real(...) method of builtins.PyCapsule instance string_to_real(input_string : str) -> float suite_rmsd(...) method of builtins.PyCapsule instance suite_rmsd(*args, **kwargs) Overloaded function.   1. suite_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, seq_num : int, prepend_res : bool) -> float   2. suite_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, seq_num : int, prepend_res : bool, ignore_virtual_atom : bool) -> float suite_square_deviation(...) method of builtins.PyCapsule instance suite_square_deviation(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, prepend_res : bool, moving_res_1 : int, moving_res_2 : int, atom_count : int, sum_sd : float, verbose : bool, ignore_virtual_atom : bool) -> NoneType tokenize(...) method of builtins.PyCapsule instance tokenize(str : str, delimiters : str) -> rosetta.utility.vector1_std_string virtualize_free_rna_moieties(...) method of builtins.PyCapsule instance virtualize_free_rna_moieties(pose : rosetta.core.pose.Pose) -> NoneType