rna

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

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

Bases: pybind11_builtins.pybind11_object

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

Bases: pyrosetta.rosetta.protocols.moves.Mover

The RNA de novo structure modeling protocol

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser, moving_suite: int, chainbreak_suite: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser, arg0: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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, other: 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.

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_std_allocator_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

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
2. 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(class std::basic_ostream<char> &) 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.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

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

Bases: pybind11_builtins.pybind11_object

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, silent_files_in: pyrosetta.rosetta.utility.vector1_std_string) -> None
2. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, silent_file_in: str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) -> None
4. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer, arg0: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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: pyrosetta.rosetta.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_PoseSetup

Bases: pyrosetta.rosetta.protocols.moves.Mover

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> None
2. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup, arg0: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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_std_allocator_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

name() → str

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
2. 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(class std::basic_ostream<char> &) 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.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

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_builtins.pybind11_object

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, moving_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, full_sequence: str, input_res: pyrosetta.rosetta.utility.vector1_unsigned_long, input_res2: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_closed: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup, arg0: pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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 class std::basic_string<char> &, 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 class std::basic_string<char> &) –> 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(class std::basic_string<char> &, class std::basic_string<char> &, const unsigned long &, const bool &, const class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &, const class std::basic_string<char> &) –> 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 class std::basic_string<char> &, const class std::basic_string<char> &) –> 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.

1. output_bool_list(tag: str, bool_list: pyrosetta.rosetta.utility.vector1_bool) -> None
2. output_bool_list(tag: str, bool_list: pyrosetta.rosetta.utility.vector1_bool, outstream: pyrosetta.rosetta.std.ostream) -> None
3. 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 class std::basic_string<char> &, const class utility::vector1<bool, class std::allocator<bool> > &, class std::basic_ostream<char> &, const unsigned long) –> void

4. output_bool_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
5. output_bool_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream) -> None
6. 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 class std::basic_string<char> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::basic_ostream<char> &, const unsigned long) –> void

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

Overloaded function.

1. output_fold_tree_info(fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, pose_name: str) -> None
2. 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 class std::basic_string<char> &, class std::basic_ostream<char> &) –> void

3. output_fold_tree_info(pose: pyrosetta.rosetta.core.pose.Pose, pose_name: str) -> None
4. 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 &, class std::basic_string<char>, class std::basic_ostream<char> &) –> void

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

Overloaded function.

1. output_is_prepend_map(tag: str, my_map: pyrosetta.rosetta.std.map_unsigned_long_bool, max_seq_num: int) -> None
2. 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
3. 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 class std::basic_string<char> &, 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, class std::basic_ostream<char> &, const unsigned long) –> void

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

Overloaded function.

1. output_pair_size(pair_size: Tuple[int, int]) -> None
2. 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> &, class std::basic_ostream<char> &) –> void

3. output_pair_size(pair_size_vector: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, output_string: str) -> None
4. 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
5. 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 class std::basic_string<char> &, class std::basic_ostream<char> &, const unsigned long) –> void

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

Overloaded function.

1. output_size_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
2. output_size_list(tag: str, size_list: pyrosetta.rosetta.utility.vector1_unsigned_long, outstream: pyrosetta.rosetta.std.ostream) -> None
3. 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 class std::basic_string<char> &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::basic_ostream<char> &, 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 class std::basic_string<char> &) –> std::string

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

Overloaded function.

1. print_WorkingParameters_info(WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str) -> None
2. print_WorkingParameters_info(WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str, outstream: pyrosetta.rosetta.std.ostream) -> None
3. 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 class std::basic_string<char> &, class std::basic_ostream<char> &, const bool) –> void

4. print_WorkingParameters_info(const_WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str) -> None
5. print_WorkingParameters_info(const_WP: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, WP_name: str, outstream: pyrosetta.rosetta.std.ostream) -> None
6. 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 class std::basic_string<char> &, class std::basic_ostream<char> &, 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.

1. setup_bulge_jump_point(pose: pyrosetta.rosetta.core.pose.Pose, moving_base: int, reference_base: int) -> int
2. 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.

1. setup_pose_setup_class(working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup
2. 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.

1. setup_rna_working_parameters() -> protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
2. 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