rna¶

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

class pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member¶

Bases: pybind11_object

property ID¶

property RMSD¶

property score¶

class pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser¶

Bases: Mover

The RNA de novo structure modeling protocol

apply(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the loop-rebuild protocol to the input pose

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

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

choose_best_solution_based_on_score_function(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_best_solution_based_on_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

choose_least_perturb_solution(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser) → None¶: C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::choose_least_perturb_solution() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser) → pyrosetta.rosetta.protocols.moves.Mover¶

Clone this object

C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fill_solution(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, n: int) → None¶: C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::fill_solution(class core::pose::Pose &, const unsigned long) const –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_all_solutions(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None¶: C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_all_solutions(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser) → str¶

Each derived class must specify its name. The class name.

C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_torsions(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser, n: int) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions(const unsigned long) –> class utility::vector1<double, class std::allocator<double> >

get_torsions_for_all_solutions(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t¶: C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_torsions_for_all_solutions() –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

nsol(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser) → int¶: C++: protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::nsol() –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters, : pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters) → pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters¶: C++: protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::operator=(const class protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters &) –> class protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters &

create_sliced_pose(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters, working_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::create_sliced_pose(const class core::pose::Pose &) –> class core::pose::Pose

setup(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → None¶: C++: protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &) –> void

property sliced_pose_best_alignment¶

property sliced_pose_calc_rms_res¶

property sliced_pose_full_to_sub¶

property sliced_pose_is_prepend_map¶

class pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, : pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer) → pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::operator=(const class protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer &) –> class protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer &

cluster(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster() –> void

get_best_neighboring_shift_RMSD_and_output_silent_file(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, silent_file: str) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(const std::string &) –> void

output_silent_file(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, silent_file: str) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::output_silent_file(const std::string &) –> void

recalculate_rmsd_and_output_silent_file(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, silent_file: str, stepwise_rna_pose_setup: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup, write_score_only: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(const std::string &, class std::shared_ptr<class protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup> &, const bool) –> void

set_PBP_clustering_at_chain_closure(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_PBP_clustering_at_chain_closure(const bool &) –> void

set_VDW_rep_screen_info(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_VDW_rep_screen_info(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_add_lead_zero_to_tag(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_add_lead_zero_to_tag(const double &) –> void

set_align_only_over_base_atoms(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_align_only_over_base_atoms(const bool &) –> void

set_cluster_radius(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_cluster_radius(const double &) –> void

set_distinguish_pucker(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_distinguish_pucker(const double &) –> void

set_filter_virtual_res_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_filter_virtual_res_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_full_length_loop_rmsd_clustering(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_full_length_loop_rmsd_clustering(const bool &) –> void

set_ignore_FARFAR_no_auto_bulge_parent_tag(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_parent_tag(const bool &) –> void

set_ignore_FARFAR_no_auto_bulge_tag(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_tag(const bool &) –> void

set_ignore_unmatched_virtual_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_ignore_unmatched_virtual_res(const bool &) –> void

set_keep_pose_in_memory(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_keep_pose_in_memory(const bool &) –> void

set_loop_cluster_radius(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_loop_cluster_radius(const double &) –> void

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

Filter a list of poses by score.

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

set_min_num_south_sugar_filter(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: int) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_min_num_south_sugar_filter(const unsigned long &) –> void

set_optimize_memory_usage(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_optimize_memory_usage(const bool &) –> void

set_output_pdb(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_output_pdb(const bool) –> void

set_perform_VDW_rep_screen(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_perform_VDW_rep_screen(const bool &) –> void

set_perform_filters(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_perform_filters(const bool &) –> void

set_perform_score_diff_cut(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_perform_score_diff_cut(const bool &) –> void

set_quick_alignment(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_quick_alignment(const bool &) –> void

set_rename_tags(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_rename_tags(const double &) –> void

set_score_diff_cut(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_score_diff_cut(const double &) –> void

set_skip_clustering(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_skip_clustering(const bool &) –> void

set_suite_cluster_radius(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_suite_cluster_radius(const double &) –> void

set_two_stage_clustering(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_two_stage_clustering(const bool &) –> void

set_user_input_VDW_bin_checker(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, user_input_VDW_bin_checker: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_user_input_VDW_bin_checker(const class std::shared_ptr<class protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker> &) –> void

set_verbose(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_verbose(const bool &) –> void

set_working_parameters(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_working_parameters(class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &) –> void

set_working_parameters_exist(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, working_parameters_exist: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::set_working_parameters_exist(const bool) –> void

class pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection¶

Bases: pybind11_object

cluster_pose_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list() –> void

finalize(*args, **kwargs)¶

Overloaded function.

finalize(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection) -> None
finalize(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, do_clustering: bool) -> None

C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::finalize(const bool) –> void

initialize_modeler_scorefxn(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::initialize_modeler_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction> &) –> void

pose_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::pose_list() –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

pose_selection_by_full_score(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, current_pose: pyrosetta.rosetta.core.pose.Pose, tag: str) → float¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::pose_selection_by_full_score(class core::pose::Pose &, const std::string &) –> double

set_PBP_clustering_at_chain_closure(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_PBP_clustering_at_chain_closure(const bool &) –> void

set_cluster_rmsd(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, setting: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_cluster_rmsd(const double &) –> void

set_count_data(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, setting: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_count_data(class protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &) –> void

set_distinguish_pucker(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_distinguish_pucker(const bool &) –> void

set_num_pose_kept(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, num_pose_kept: int) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_num_pose_kept(const unsigned long &) –> void

set_pose_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_pose_list(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

update_pose_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection, tag: str, current_pose: pyrosetta.rosetta.core.pose.Pose, current_score: float) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::update_pose_list(const std::string &, const class core::pose::Pose &, const double &) –> void

class pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, : pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup) → pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::operator=(const class protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup &) –> class protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup) → str¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_align_to_native(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_align_to_native(const bool) –> void

set_apply_virtual_res_variant_at_dinucleotide(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_apply_virtual_res_variant_at_dinucleotide(const bool) –> void

set_bulge_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, bulge_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_bulge_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_copy_DOF(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_copy_DOF(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_input_tags(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_input_tags(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_virtual_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, native_virtual_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_native_virtual_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_output_pdb(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_output_pdb(const bool) –> void

set_silent_files_in(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_silent_files_in(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_use_phenix_geo(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_use_phenix_geo(const bool) –> void

set_verbose(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_verbose(const bool) –> void

set_virtual_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, virtual_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_virtual_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

setup_full_model_info(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_full_model_info(class core::pose::Pose &) const –> void

setup_native_pose(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(class core::pose::Pose &) –> void

setup_vdw_cached_rep_screen_info(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_vdw_cached_rep_screen_info(class core::pose::Pose &) const –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

update_fold_tree_at_virtual_sugars(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars(class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup¶

Bases: pybind11_object

apply(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::apply() –> void

force_fold_tree(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_fold_tree(const class core::kinematics::FoldTree &) –> void

set_add_virt_res_as_root(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_add_virt_res_as_root(const bool) –> void

set_alignment_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_alignment_res(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_allow_chain_boundary_jump_partner_right_at_fixed_BP(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_allow_chain_boundary_jump_partner_right_at_fixed_BP(const bool) –> void

set_allow_fixed_res_at_moving_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_allow_fixed_res_at_moving_res(const bool) –> void

set_assert_jump_point_in_fixed_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_assert_jump_point_in_fixed_res(const bool) –> void

set_calc_rms_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_calc_rms_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_cutpoint_closed_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_cutpoint_closed_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_filter_user_alignment_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_filter_user_alignment_res(const bool) –> void

set_fixed_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, fixed_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_floating_base(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_floating_base(const bool) –> void

set_floating_base_anchor_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: int) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_floating_base_anchor_res(const unsigned long) –> void

set_force_anti_chi_res_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_anti_chi_res_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_force_internal(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_internal(const bool) –> void

set_force_north_sugar_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_north_sugar_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_force_south_sugar_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_south_sugar_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_force_syn_chi_res_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_syn_chi_res_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_force_user_defined_jumps(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_user_defined_jumps(const bool) –> void

set_global_sample_res_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_global_sample_res_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_input_tags(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_input_tags(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_jump_point_pair_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, jump_point_pairs_string: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_native_alignment_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, native_alignment: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_native_alignment_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_output_extra_RMSDs(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_output_extra_RMSDs(const bool) –> void

set_protonated_H1_adenosine_list(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_protonated_H1_adenosine_list(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_rebuild_bulge_mode(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_rebuild_bulge_mode(const bool) –> void

set_sample_both_sugar_base_rotamer(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_sample_both_sugar_base_rotamer(const bool) –> void

set_silent_files_in(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_silent_files_in(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_simple_append_map(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_simple_append_map(const bool) –> void

set_skip_complicated_stuff(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, setting: bool) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_skip_complicated_stuff(const bool) –> void

set_terminal_res(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, terminal_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_terminal_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

working_parameters(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup) → protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters¶: C++: protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::working_parameters() –> class std::shared_ptr<class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.apply_chi_cst(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::stepwise::legacy::modeler::rna::apply_chi_cst(class core::pose::Pose &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.check_can_append(seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long) → bool¶: C++: protocols::stepwise::legacy::modeler::rna::check_can_append(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.check_can_prepend(seq_num_list: pyrosetta.rosetta.utility.vector1_unsigned_long) → bool¶: C++: protocols::stepwise::legacy::modeler::rna::check_can_prepend(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.create_scorefxn() → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::stepwise::legacy::modeler::rna::create_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.ensure_directory_for_out_silent_file_exists() → None¶: C++: protocols::stepwise::legacy::modeler::rna::ensure_directory_for_out_silent_file_exists() –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.full_length_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_sequence: str, verbose: bool, ignore_virtual_atom: bool) → float¶: C++: protocols::stepwise::legacy::modeler::rna::full_length_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 std::string &, const bool, const bool) –> double

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.get_fixed_res(nres: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::stepwise::legacy::modeler::rna::get_fixed_res(const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.get_input_res(nres: int, pose_num: str) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::stepwise::legacy::modeler::rna::get_input_res(const unsigned long, const std::string &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.get_silent_file_tags() → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::stepwise::legacy::modeler::rna::get_silent_file_tags() –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.get_tag_and_silent_file_for_struct(swa_silent_file: str, out_tag: str, n: int, multiple_shots: bool, silent_file: str) → bool¶: C++: protocols::stepwise::legacy::modeler::rna::get_tag_and_silent_file_for_struct(std::string &, std::string &, const unsigned long &, const bool &, const std::string &) –> bool

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.get_tag_from_pdb_filename(pdb_filename: str) → str¶: C++: protocols::stepwise::legacy::modeler::rna::get_tag_from_pdb_filename(const std::string &) –> std::string

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.get_working_directory() → str¶: C++: protocols::stepwise::legacy::modeler::rna::get_working_directory() –> std::string

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.import_pose_from_silent_file(import_pose: pyrosetta.rosetta.core.pose.Pose, silent_file: str, input_tag: str) → None¶: C++: protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(class core::pose::Pose &, const std::string &, const std::string &) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.is_nonempty_input_silent_file(input_silent_file: str, exit_key_string: str) → bool¶: C++: protocols::stepwise::legacy::modeler::rna::is_nonempty_input_silent_file(const std::string &, const std::string &) –> bool

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.is_same_sugar_pucker(current_pose: pyrosetta.rosetta.core.pose.Pose, cluster_center_pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) → bool¶: C++: protocols::stepwise::legacy::modeler::rna::is_same_sugar_pucker(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long) –> bool

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.output_bool_list(*args, **kwargs)¶

Overloaded function.

output_bool_list(tag: str, bool_list: pyrosetta.rosetta.utility.vector1_bool) -> None
output_bool_list(tag: str, bool_list: pyrosetta.rosetta.utility.vector1_bool, outstream: pyrosetta.rosetta.std.ostream) -> None
output_bool_list(tag: str, bool_list: pyrosetta.rosetta.utility.vector1_bool, outstream: pyrosetta.rosetta.std.ostream, spacing: int) -> None

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

output_bool_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
output_bool_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream) -> None
output_bool_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream, spacing: int) -> None

C++: protocols::stepwise::legacy::modeler::rna::output_bool_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.legacy.modeler.rna.output_fold_tree_info(*args, **kwargs)¶

Overloaded function.

output_fold_tree_info(fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, pose_name: str) -> None
output_fold_tree_info(fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, pose_name: str, outstream: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(const class core::kinematics::FoldTree &, const std::string &, std::ostream &) –> void

output_fold_tree_info(pose: pyrosetta.rosetta.core.pose.Pose, pose_name: str) -> None
output_fold_tree_info(pose: pyrosetta.rosetta.core.pose.Pose, pose_name: str, outstream: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(const class core::pose::Pose &, std::string, std::ostream &) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.output_is_prepend_map(*args, **kwargs)¶

Overloaded function.

output_is_prepend_map(tag: str, my_map: pyrosetta.rosetta.std.map_unsigned_long_bool, max_seq_num: int) -> None
output_is_prepend_map(tag: str, my_map: pyrosetta.rosetta.std.map_unsigned_long_bool, max_seq_num: int, outstream: pyrosetta.rosetta.std.ostream) -> None
output_is_prepend_map(tag: str, my_map: pyrosetta.rosetta.std.map_unsigned_long_bool, max_seq_num: int, outstream: pyrosetta.rosetta.std.ostream, tag_spacing: int) -> None

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

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.output_pair_size(*args, **kwargs)¶

Overloaded function.

output_pair_size(pair_size: Tuple[int, int]) -> None
output_pair_size(pair_size: Tuple[int, int], outstream: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::stepwise::legacy::modeler::rna::output_pair_size(const struct std::pair<unsigned long, unsigned long> &, std::ostream &) –> void

output_pair_size(pair_size_vector: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, output_string: str) -> None
output_pair_size(pair_size_vector: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, output_string: str, outstream: pyrosetta.rosetta.std.ostream) -> None
output_pair_size(pair_size_vector: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, output_string: str, outstream: pyrosetta.rosetta.std.ostream, spacing: int) -> None

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

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.output_size_list(*args, **kwargs)¶

Overloaded function.

output_size_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
output_size_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream) -> None
output_size_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream, spacing: int) -> None

C++: protocols::stepwise::legacy::modeler::rna::output_size_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.legacy.modeler.rna.path_basename(full_path: str) → str¶: C++: protocols::stepwise::legacy::modeler::rna::path_basename(const std::string &) –> std::string

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.print_WorkingParameters_info(*args, **kwargs)¶

Overloaded function.

print_WorkingParameters_info(WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str) -> None
print_WorkingParameters_info(WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str, outstream: pyrosetta.rosetta.std.ostream) -> None
print_WorkingParameters_info(WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str, outstream: pyrosetta.rosetta.std.ostream, is_simple_full_length_WP: bool) -> None

C++: protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info(const class std::shared_ptr<class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &, const std::string &, std::ostream &, const bool) –> void

print_WorkingParameters_info(const_WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str) -> None
print_WorkingParameters_info(const_WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str, outstream: pyrosetta.rosetta.std.ostream) -> None
print_WorkingParameters_info(const_WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str, outstream: pyrosetta.rosetta.std.ostream, is_simple_full_length_WP: bool) -> None

C++: protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info(const class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &, const std::string &, std::ostream &, const bool) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.print_backbone_torsions(pose: pyrosetta.rosetta.core.pose.Pose, five_prime_chainbreak: int) → None¶: C++: protocols::stepwise::legacy::modeler::rna::print_backbone_torsions(const class core::pose::Pose &, unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.remove_chain_break_jump_point(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int, reference_res: int) → None¶: C++: protocols::stepwise::legacy::modeler::rna::remove_chain_break_jump_point(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.set_nucleotide_to_A_form(pose: pyrosetta.rosetta.core.pose.Pose, seq_num: int) → None¶: C++: protocols::stepwise::legacy::modeler::rna::set_nucleotide_to_A_form(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.setup_bulge_jump_point(*args, **kwargs)¶

Overloaded function.

setup_bulge_jump_point(pose: pyrosetta.rosetta.core.pose.Pose, moving_base: int, reference_base: int) -> int
setup_bulge_jump_point(pose: pyrosetta.rosetta.core.pose.Pose, moving_base: int, reference_base: int, verbose: bool) -> int

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

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.setup_chain_break_jump_point(pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int, reference_res: int) → int¶: C++: protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point(class core::pose::Pose &, const unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.setup_copy_DOF_input(stepwise_rna_pose_setup: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup) → None¶: C++: protocols::stepwise::legacy::modeler::rna::setup_copy_DOF_input(class std::shared_ptr<class protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup> &) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.setup_pose_setup_class(*args, **kwargs)¶

Overloaded function.

setup_pose_setup_class(working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup
setup_pose_setup_class(working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, copy_DOF: bool) -> pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup

C++: protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class(class std::shared_ptr<class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &, const bool) –> class std::shared_ptr<class protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup>

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.setup_rna_working_parameters(*args, **kwargs)¶

Overloaded function.

setup_rna_working_parameters() -> protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
setup_rna_working_parameters(check_for_previously_closed_cutpoint_with_input_pose: bool) -> protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters

C++: protocols::stepwise::legacy::modeler::rna::setup_rna_working_parameters(bool) –> class std::shared_ptr<class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.setup_simple_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::stepwise::legacy::modeler::rna::setup_simple_fold_tree(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.setup_simple_full_length_rna_working_parameters() → protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters¶: C++: protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters() –> class std::shared_ptr<class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>

pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.sort_pair_list(pair_list: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None¶: C++: protocols::stepwise::legacy::modeler::rna::sort_pair_list(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >) –> void