rna

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

class pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info, : pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info) → pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info

C++: protocols::stepwise::modeler::rna::Combine_Tags_Info::operator=(const class protocols::stepwise::modeler::rna::Combine_Tags_Info &) –> class protocols::stepwise::modeler::rna::Combine_Tags_Info &

property combine_score
property side_one_tag
property side_two_tag
class pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count, : pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count) → pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count

C++: protocols::stepwise::modeler::rna::Filterer_Count::operator=(const class protocols::stepwise::modeler::rna::Filterer_Count &) –> class protocols::stepwise::modeler::rna::Filterer_Count &

property chain_closable_geometry_screen
property filter_for_moving_res_contact
property filter_for_previous_clash
property filter_for_previous_contact
property score_cut_count
property total_count
class pyrosetta.rosetta.protocols.stepwise.modeler.rna.InternalWorkingResidueParameter

Bases: pybind11_object

property fake_working_moving_suite
property possible_working_res_1
property possible_working_res_2
class pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point, : pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point) → pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point

C++: protocols::stepwise::modeler::rna::Jump_point::operator=(const class protocols::stepwise::modeler::rna::Jump_point &) –> class protocols::stepwise::modeler::rna::Jump_point &

property cut_point
property five_prime_atom
property five_prime_seq_num
property three_prime_atom
property three_prime_seq_num
class pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info, : pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info) → pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info

C++: protocols::stepwise::modeler::rna::Residue_info::operator=(const struct protocols::stepwise::modeler::rna::Residue_info &) –> struct protocols::stepwise::modeler::rna::Residue_info &

property name
property seq_num
class pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer

Bases: pybind11_object

filter(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter() –> void

set_filter_for_previous_clash(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting: float) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_clash(const double) –> void

set_filter_for_previous_contact(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting: float) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_contact(const double) –> void

set_max_decoys(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting: int) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_max_decoys(const unsigned long &) –> void

set_output_filename(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting: str) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_output_filename(const std::string &) –> void

set_parin_favorite_output(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting: bool) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_parin_favorite_output(const bool) –> void

set_silent_files_in(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_silent_files_in(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_undercount_sugar_rotamers(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer, setting: bool) → None

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_undercount_sugar_rotamers(const bool) –> void

class pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct

Bases: pybind11_object

property Near_Native_StepWiseSampler_Count
assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct, : pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) → pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct

C++: protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::operator=(const class protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &) –> class protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &

property base_pairing_count
property base_stack_count
property before_chain_break_grid_index_screening
property both_count
property bulge_at_chain_closure_count
property chain_break_grid_index_screening
property chain_break_screening_count
property chain_closable_geometry_count
property chain_closable_geometry_count2
property chain_closable_geometry_count3
property fast_full_atom_VDW_repulsion_screen
property fine_rmsd_count
property full_score_count
property good_angle_count
property good_atr_rotamer_count
property good_bin_rep_count
property good_distance_count
property good_rep_rotamer_count
property in_range_CCD_torsion
property non_clash_sugar
property output_pose_count
property pass_base_centroid_screen
property residues_contact_screen
property rmsd_count
property strict_base_pairing_count
property test_count_one
property test_count_two
property tot_rotamer_count
property total_bin
class pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info

Bases: pybind11_object

property id
property value
pyrosetta.rosetta.protocols.stepwise.modeler.rna.add_fade_chain_break_constraint_across_gap(pose: pyrosetta.rosetta.core.pose.Pose, five_prime_res: int, three_prime_res: int, gap_size: int) → None

C++: protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.add_harmonic_chain_break_constraint(pose: pyrosetta.rosetta.core.pose.Pose, five_prime_res: int) → None

C++: protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.align_poses(*args, **kwargs)

Overloaded function.

  1. align_poses(moving_pose: pyrosetta.rosetta.core.pose.Pose, moving_tag: str, static_pose: pyrosetta.rosetta.core.pose.Pose, static_tag: str, working_best_alignment: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  2. align_poses(moving_pose: pyrosetta.rosetta.core.pose.Pose, moving_tag: str, static_pose: pyrosetta.rosetta.core.pose.Pose, static_tag: str, working_best_alignment: pyrosetta.rosetta.utility.vector1_unsigned_long, base_only: bool) -> None

C++: protocols::stepwise::modeler::rna::align_poses(class core::pose::Pose &, const std::string &, const class core::pose::Pose &, const std::string &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.apply_full_to_sub_mapping(*args, **kwargs)

Overloaded function.

  1. apply_full_to_sub_mapping(res_vector: pyrosetta.rosetta.utility.vector1_unsigned_long, is_working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, full_to_sub: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

  1. apply_full_to_sub_mapping(res_vector: pyrosetta.rosetta.utility.vector1_unsigned_long, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.stepwise.modeler.rna.apply_protonated_H1_adenosine_variant_type(*args, **kwargs)

Overloaded function.

  1. apply_protonated_H1_adenosine_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) -> None

  2. apply_protonated_H1_adenosine_variant_type(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int, apply_check: bool) -> None

C++: protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(class core::pose::Pose &, const unsigned long &, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.apply_sub_to_full_mapping(working_res_vector: pyrosetta.rosetta.utility.vector1_unsigned_long, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::rna::apply_sub_to_full_mapping(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.stepwise.modeler.rna.atom_square_deviation(rsd_1: pyrosetta.rosetta.core.conformation.Residue, rsd_2: pyrosetta.rosetta.core.conformation.Residue, atomno_1: int, atomno_2: int, verbose: bool) → float

C++: protocols::stepwise::modeler::rna::atom_square_deviation(const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long &, const unsigned long &, bool) –> double

pyrosetta.rosetta.protocols.stepwise.modeler.rna.base_atoms_square_deviation(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, moving_res_1: int, moving_res_2: int, atom_count: int, sum_sd: float, verbose: bool, ignore_virtual_atom: bool) → None

C++: protocols::stepwise::modeler::rna::base_atoms_square_deviation(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long &, const unsigned long &, unsigned long &, double &, bool, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.check_for_messed_up_structure(pose: pyrosetta.rosetta.core.pose.Pose, tag: str) → bool

C++: protocols::stepwise::modeler::rna::check_for_messed_up_structure(const class core::pose::Pose &, const std::string &) –> bool

pyrosetta.rosetta.protocols.stepwise.modeler.rna.check_instantiated_O2Prime_hydrogen(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::check_instantiated_O2Prime_hydrogen(const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.check_is_working_res(full_seq_num: int, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → bool

C++: protocols::stepwise::modeler::rna::check_is_working_res(const unsigned long, const class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &) –> bool

pyrosetta.rosetta.protocols.stepwise.modeler.rna.check_validity_and_get_working_res(full_seq_num: int, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → int

C++: protocols::stepwise::modeler::rna::check_validity_and_get_working_res(const unsigned long, const class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &) –> unsigned long

pyrosetta.rosetta.protocols.stepwise.modeler.rna.choose_random_if_unspecified_nucleotide(newrestype: str) → None

C++: protocols::stepwise::modeler::rna::choose_random_if_unspecified_nucleotide(char &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.choose_randomly_from_allowed_at_position(pose: pyrosetta.rosetta.core.pose.Pose, ii: int) → str

C++: protocols::stepwise::modeler::rna::choose_randomly_from_allowed_at_position(const class core::pose::Pose &, const unsigned long) –> std::string

pyrosetta.rosetta.protocols.stepwise.modeler.rna.copy_all_o2prime_torsions(mod_pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::copy_all_o2prime_torsions(class core::pose::Pose &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.copy_dofs_sort_criterion(residue_info_1: pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info, residue_info_2: pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info) → bool

C++: protocols::stepwise::modeler::rna::copy_dofs_sort_criterion(struct protocols::stepwise::modeler::rna::Residue_info, struct protocols::stepwise::modeler::rna::Residue_info) –> bool

pyrosetta.rosetta.protocols.stepwise.modeler.rna.create_full_to_input_res_map(input_res_vector: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long

C++: protocols::stepwise::modeler::rna::create_full_to_input_res_map(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >

pyrosetta.rosetta.protocols.stepwise.modeler.rna.create_rotamer_string(*args, **kwargs)

Overloaded function.

  1. create_rotamer_string(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int, is_prepend: bool) -> str

C++: protocols::stepwise::modeler::rna::create_rotamer_string(const class core::pose::Pose &, const unsigned long, const bool) –> std::string

  1. create_rotamer_string(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int, reference_res: int) -> str

C++: protocols::stepwise::modeler::rna::create_rotamer_string(const class core::pose::Pose &, const unsigned long, const unsigned long) –> std::string

pyrosetta.rosetta.protocols.stepwise.modeler.rna.create_standard_o2prime_pack_task(*args, **kwargs)

Overloaded function.

  1. create_standard_o2prime_pack_task(pose: pyrosetta.rosetta.core.pose.Pose, O2prime_pack_seq_num: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.core.pack.task.PackerTask

  2. create_standard_o2prime_pack_task(pose: pyrosetta.rosetta.core.pose.Pose, O2prime_pack_seq_num: pyrosetta.rosetta.utility.vector1_unsigned_long, pack_virtual_o2prime_hydrogen: bool) -> pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::stepwise::modeler::rna::create_standard_o2prime_pack_task(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> class std::shared_ptr<class core::pack::task::PackerTask>

pyrosetta.rosetta.protocols.stepwise.modeler.rna.create_tag(prestring: str, i: int) → str

C++: protocols::stepwise::modeler::rna::create_tag(const std::string &, const unsigned long) –> std::string

pyrosetta.rosetta.protocols.stepwise.modeler.rna.create_torsion_value_string(torsion_value: float) → str

C++: protocols::stepwise::modeler::rna::create_torsion_value_string(const double &) –> std::string

pyrosetta.rosetta.protocols.stepwise.modeler.rna.ensure_valid_full_seq_num(full_seq_num: int, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → None

C++: protocols::stepwise::modeler::rna::ensure_valid_full_seq_num(const unsigned long, const class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.figure_out_moving_rna_chain_breaks(pose: pyrosetta.rosetta.core.pose.Pose, moving_partition_res: pyrosetta.rosetta.utility.vector1_unsigned_long, rna_cutpoints_closed: pyrosetta.rosetta.utility.vector1_unsigned_long, rna_five_prime_chain_breaks: pyrosetta.rosetta.utility.vector1_unsigned_long, rna_three_prime_chain_breaks: pyrosetta.rosetta.utility.vector1_unsigned_long, rna_chain_break_gap_sizes: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::stepwise::modeler::rna::figure_out_moving_rna_chain_breaks(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.freeze_sugar_torsions(mm: pyrosetta.rosetta.core.kinematics.MoveMap, total_residue: int) → None

C++: protocols::stepwise::modeler::rna::freeze_sugar_torsions(class core::kinematics::MoveMap &, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.get_anchor_res(rebuild_res: int, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::stepwise::modeler::rna::get_anchor_res(const unsigned long, const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.stepwise.modeler.rna.get_binary_rna_silent_struct_safe(const_pose: pyrosetta.rosetta.core.pose.Pose, tag: str, silent_file: str) → pyrosetta.rosetta.core.io.silent.BinarySilentStruct

C++: protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(const class core::pose::Pose &, const std::string &, const std::string &) –> class core::io::silent::BinarySilentStruct

pyrosetta.rosetta.protocols.stepwise.modeler.rna.get_binary_rna_silent_struct_safe_wrapper(const_pose: pyrosetta.rosetta.core.pose.Pose, tag: str, silent_file: str, write_score_only: bool) → pyrosetta.rosetta.core.io.silent.BinarySilentStruct

C++: protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe_wrapper(const class core::pose::Pose &, const std::string &, const std::string &, const bool) –> class core::io::silent::BinarySilentStruct

pyrosetta.rosetta.protocols.stepwise.modeler.rna.get_modeler_scorefxn(scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::stepwise::modeler::rna::get_modeler_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> class std::shared_ptr<class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.stepwise.modeler.rna.get_partition_definition_floating_base(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::stepwise::modeler::rna::get_partition_definition_floating_base(const class core::pose::Pose &, const unsigned long &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.stepwise.modeler.rna.get_possible_O3prime_C5prime_distance_range(gap_size_: int, min_dist: float, max_dist: float) → None

C++: protocols::stepwise::modeler::rna::get_possible_O3prime_C5prime_distance_range(const unsigned long, double &, double &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.get_surrounding_O2prime_hydrogen(*args, **kwargs)

Overloaded function.

  1. get_surrounding_O2prime_hydrogen(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.utility.vector1_unsigned_long

  2. get_surrounding_O2prime_hydrogen(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: pyrosetta.rosetta.utility.vector1_unsigned_long, verbose: bool) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.stepwise.modeler.rna.is_residues_in_contact(*args, **kwargs)

Overloaded function.

  1. is_residues_in_contact(res_ONE: int, pose_ONE: pyrosetta.rosetta.core.pose.Pose, res_TWO: int, pose_TWO: pyrosetta.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: pyrosetta.rosetta.core.pose.Pose, res_TWO: int, pose_TWO: pyrosetta.rosetta.core.pose.Pose, atom_atom_overlap_dist_cutoff: float, num_atom_contacts_cutoff: int, verbose: bool) -> bool

C++: protocols::stepwise::modeler::rna::is_residues_in_contact(const unsigned long &, const class core::pose::Pose &, const unsigned long &, const class core::pose::Pose &, const double, const unsigned long, const bool) –> bool

pyrosetta.rosetta.protocols.stepwise.modeler.rna.is_virtual_base(rsd: pyrosetta.rosetta.core.conformation.Residue) → bool

C++: protocols::stepwise::modeler::rna::is_virtual_base(const class core::conformation::Residue &) –> bool

pyrosetta.rosetta.protocols.stepwise.modeler.rna.just_rna(res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::rna::just_rna(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.stepwise.modeler.rna.minimize_with_constraints(pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, options: pyrosetta.rosetta.core.optimization.MinimizerOptions) → None

C++: protocols::stepwise::modeler::rna::minimize_with_constraints(class core::pose::Pose &, const class core::kinematics::MoveMap &, const class std::shared_ptr<class core::scoring::ScoreFunction> &, const class core::optimization::MinimizerOptions &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.mutate_res_if_allowed(*args, **kwargs)

Overloaded function.

  1. mutate_res_if_allowed(pose: pyrosetta.rosetta.core.pose.Pose, mutate_res: int) -> bool

  2. mutate_res_if_allowed(pose: pyrosetta.rosetta.core.pose.Pose, mutate_res: int, mutation_frequency: float) -> bool

C++: protocols::stepwise::modeler::rna::mutate_res_if_allowed(class core::pose::Pose &, const unsigned long, const double) –> bool

pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime_trials(*args, **kwargs)

Overloaded function.

  1. o2prime_trials(pose: pyrosetta.rosetta.core.pose.Pose, packer_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

  2. o2prime_trials(pose: pyrosetta.rosetta.core.pose.Pose, packer_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pack_virtual_o2prime_hydrogen: bool) -> None

C++: protocols::stepwise::modeler::rna::o2prime_trials(class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction> &, const bool) –> void

  1. o2prime_trials(pose: pyrosetta.rosetta.core.pose.Pose, packer_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, O2prime_seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  2. o2prime_trials(pose: pyrosetta.rosetta.core.pose.Pose, packer_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, O2prime_seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long, pack_virtual_o2prime_hydrogen: bool) -> None

C++: protocols::stepwise::modeler::rna::o2prime_trials(class core::pose::Pose &, const class std::shared_ptr<const class core::scoring::ScoreFunction> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data(*args, **kwargs)

Overloaded function.

  1. output_data(silent_file: str, tag: str, write_score_only: bool, pose: pyrosetta.rosetta.core.pose.Pose, native_poseCOP: pyrosetta.rosetta.core.pose.Pose, working_parameters_: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> None

  2. output_data(silent_file: str, tag: str, write_score_only: bool, pose: pyrosetta.rosetta.core.pose.Pose, native_poseCOP: pyrosetta.rosetta.core.pose.Pose, working_parameters_: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, NAT_rmsd: bool) -> None

C++: protocols::stepwise::modeler::rna::output_data(const std::string &, const std::string &, const bool, const class core::pose::Pose &, class std::shared_ptr<const class core::pose::Pose>, class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>, const bool) –> void

  1. output_data(silent_file_data: pyrosetta.rosetta.core.io.silent.SilentFileData, silent_file: str, tag: str, write_score_only: bool, pose: pyrosetta.rosetta.core.pose.Pose, native_poseCOP: pyrosetta.rosetta.core.pose.Pose, working_parameters_: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> None

  2. output_data(silent_file_data: pyrosetta.rosetta.core.io.silent.SilentFileData, silent_file: str, tag: str, write_score_only: bool, pose: pyrosetta.rosetta.core.pose.Pose, native_poseCOP: pyrosetta.rosetta.core.pose.Pose, working_parameters_: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, NAT_rmsd: bool) -> None

C++: protocols::stepwise::modeler::rna::output_data(class core::io::silent::SilentFileData &, const std::string &, const std::string &, const bool, const class core::pose::Pose &, class std::shared_ptr<const class core::pose::Pose>, class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>, const bool) –> void

class pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct

Bases: pybind11_object

property O3_C5_distance
property current_score
property diff_torsions
property loop_rmsd
property loop_rmsd_wrt_correct_minimized
property loop_rmsd_wrt_minimized
property rmsd
property rmsd_wrt_correct_minimized
property rmsd_wrt_minimized
pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_res_map(my_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, max_seq_num: int) → None

C++: protocols::stepwise::modeler::rna::output_res_map(const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_seq_num_list(*args, **kwargs)

Overloaded function.

  1. output_seq_num_list(tag: str, seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  2. output_seq_num_list(tag: str, seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream) -> None

  3. output_seq_num_list(tag: str, seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream, spacing: int) -> None

C++: protocols::stepwise::modeler::rna::output_seq_num_list(const std::string &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, std::ostream &, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_title_text(*args, **kwargs)

Overloaded function.

  1. output_title_text(title: str) -> None

  2. output_title_text(title: str, outstream: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::stepwise::modeler::rna::output_title_text(const std::string &, std::ostream &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate_base_phosphate_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, moving_res_num: int, ignore_virtual_atom: bool) → float

C++: protocols::stepwise::modeler::rna::phosphate_base_phosphate_rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long &, const bool) –> double

pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate_base_phosphate_square_deviation(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, moving_res_1: int, moving_res_2: int, atom_count: int, sum_sd: float, verbose: bool, ignore_virtual_atom: bool) → None

C++: protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long &, const unsigned long &, unsigned long &, double &, bool, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate_square_deviation(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, moving_res_1: int, moving_res_2: int, atom_count: int, sum_sd: float, verbose: bool, ignore_virtual_atom: bool) → None

C++: protocols::stepwise::modeler::rna::phosphate_square_deviation(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long &, const unsigned long &, unsigned long &, double &, bool, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.print_base_state(*args, **kwargs)

Overloaded function.

  1. print_base_state(tag: str, base_state: int) -> None

  2. print_base_state(tag: str, base_state: int, outstream: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::stepwise::modeler::rna::print_base_state(const std::string &, const unsigned long, std::ostream &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.print_sugar_pucker_state(*args, **kwargs)

Overloaded function.

  1. print_sugar_pucker_state(tag: str, pucker_state: int) -> None

  2. print_sugar_pucker_state(tag: str, pucker_state: int, outstream: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::stepwise::modeler::rna::print_sugar_pucker_state(const std::string &, const unsigned long, std::ostream &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.print_torsion_info(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int, rna_torsion_number: int, type: str) → None

C++: protocols::stepwise::modeler::rna::print_torsion_info(const class core::pose::Pose &, const unsigned long, const unsigned long, const std::string &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.remove_all_variant_types(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::remove_all_variant_types(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.remove_all_virtual_phosphates(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::remove_all_virtual_phosphates(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.remove_chain_break_variants(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint: int) → None

C++: protocols::stepwise::modeler::rna::remove_chain_break_variants(class core::pose::Pose &, const unsigned long &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.remove_file(file_name: str) → None

C++: protocols::stepwise::modeler::rna::remove_file(const std::string &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.remove_virtual_O2Prime_hydrogen(pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::stepwise::modeler::rna::remove_virtual_O2Prime_hydrogen(class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.stepwise.modeler.rna.rescale_scorefxn(starting_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, scaling_factor: float) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::stepwise::modeler::rna::rescale_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &, const double) –> class std::shared_ptr<class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.stepwise.modeler.rna.rmsd_over_residue_list(*args, **kwargs)

Overloaded function.

  1. rmsd_over_residue_list(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, residue_list: pyrosetta.rosetta.utility.vector1_unsigned_long, full_to_sub: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, is_prepend_map: pyrosetta.rosetta.std.map_unsigned_long_bool, verbose: bool) -> float

  2. rmsd_over_residue_list(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, residue_list: pyrosetta.rosetta.utility.vector1_unsigned_long, full_to_sub: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, is_prepend_map: pyrosetta.rosetta.std.map_unsigned_long_bool, verbose: bool, ignore_virtual_atom: bool) -> float

C++: protocols::stepwise::modeler::rna::rmsd_over_residue_list(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class std::map<unsigned long, bool, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, bool> > > &, const bool, const bool) –> double

  1. rmsd_over_residue_list(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, working_parameters_: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> float

  2. rmsd_over_residue_list(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, working_parameters_: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, ignore_virtual_atom: bool) -> float

C++: protocols::stepwise::modeler::rna::rmsd_over_residue_list(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>, const bool) –> double

pyrosetta.rosetta.protocols.stepwise.modeler.rna.set_CCD_torsions_to_zero(pose: pyrosetta.rosetta.core.pose.Pose, five_prime_res: int) → None

C++: protocols::stepwise::modeler::rna::set_CCD_torsions_to_zero(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.setup_chain_break_variants(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint: int) → None

C++: protocols::stepwise::modeler::rna::setup_chain_break_variants(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.setup_suite_atom_id_map(*args, **kwargs)

Overloaded function.

  1. setup_suite_atom_id_map(rsd_1: pyrosetta.rosetta.core.conformation.Residue, rsd_2: pyrosetta.rosetta.core.conformation.Residue, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> None

  2. setup_suite_atom_id_map(rsd_1: pyrosetta.rosetta.core.conformation.Residue, rsd_2: pyrosetta.rosetta.core.conformation.Residue, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only: bool) -> None

C++: protocols::stepwise::modeler::rna::setup_suite_atom_id_map(const class core::conformation::Residue &, const class core::conformation::Residue &, class core::id::AtomID_Map<class core::id::AtomID> &, const bool) –> void

  1. setup_suite_atom_id_map(rsd_1: pyrosetta.rosetta.core.conformation.Residue, rsd_2: pyrosetta.rosetta.core.conformation.Residue, res_num_1: int, res_num_2: int, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> None

  2. setup_suite_atom_id_map(rsd_1: pyrosetta.rosetta.core.conformation.Residue, rsd_2: pyrosetta.rosetta.core.conformation.Residue, res_num_1: int, res_num_2: int, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only: bool) -> None

C++: protocols::stepwise::modeler::rna::setup_suite_atom_id_map(const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long, class core::id::AtomID_Map<class core::id::AtomID> &, const bool) –> void

  1. setup_suite_atom_id_map(pose_1: pyrosetta.rosetta.core.pose.Pose, pose_2: pyrosetta.rosetta.core.pose.Pose, base_res: int, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> None

  2. setup_suite_atom_id_map(pose_1: pyrosetta.rosetta.core.pose.Pose, pose_2: pyrosetta.rosetta.core.pose.Pose, base_res: int, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only: bool) -> None

C++: protocols::stepwise::modeler::rna::setup_suite_atom_id_map(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, class core::id::AtomID_Map<class core::id::AtomID> &, const bool) –> void

  1. setup_suite_atom_id_map(pose_1: pyrosetta.rosetta.core.pose.Pose, pose_2: pyrosetta.rosetta.core.pose.Pose, base_res_1: int, base_res_2: int, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> None

  2. setup_suite_atom_id_map(pose_1: pyrosetta.rosetta.core.pose.Pose, pose_2: pyrosetta.rosetta.core.pose.Pose, base_res_1: int, base_res_2: int, atom_ID_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, base_only: bool) -> None

C++: protocols::stepwise::modeler::rna::setup_suite_atom_id_map(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long, class core::id::AtomID_Map<class core::id::AtomID> &, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.show_scorefxn_weight_lines(scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, title: str) → None

C++: protocols::stepwise::modeler::rna::show_scorefxn_weight_lines(const class std::shared_ptr<class core::scoring::ScoreFunction> &, const std::string &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.sort_seq_num_list(seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::stepwise::modeler::rna::sort_seq_num_list(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.string_to_int(input_string: str) → int

C++: protocols::stepwise::modeler::rna::string_to_int(const std::string &) –> unsigned long

pyrosetta.rosetta.protocols.stepwise.modeler.rna.string_to_real(input_string: str) → float

C++: protocols::stepwise::modeler::rna::string_to_real(const std::string &) –> double

pyrosetta.rosetta.protocols.stepwise.modeler.rna.suite_rmsd(*args, **kwargs)

Overloaded function.

  1. suite_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, seq_num: int, prepend_res: bool) -> float

  2. suite_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, seq_num: int, prepend_res: bool, ignore_virtual_atom: bool) -> float

C++: protocols::stepwise::modeler::rna::suite_rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long &, const bool, const bool) –> double

pyrosetta.rosetta.protocols.stepwise.modeler.rna.suite_square_deviation(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.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) → None

C++: protocols::stepwise::modeler::rna::suite_square_deviation(const class core::pose::Pose &, const class core::pose::Pose &, const bool &, const unsigned long &, const unsigned long &, unsigned long &, double &, bool, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.rna.tokenize(str: str, delimiters: str) → pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::stepwise::modeler::rna::tokenize(const std::string &, const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >