rna

Bindings for protocols::stepwise::sampler::rna namespace

class pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser

Bases: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized

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__(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, init_pose: pyrosetta.rosetta.core.pose.Pose, moving_suite: int, chainbreak_suite: int) → 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(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose: pyrosetta.rosetta.core.pose.Pose, id: int) -> None

Apply the i-th rotamer to pose

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

assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, : pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) → pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized

C++: protocols::stepwise::sampler::StepWiseSamplerSized::operator=(const class protocols::stepwise::sampler::StepWiseSamplerSized &) –> class protocols::stepwise::sampler::StepWiseSamplerSized &

calculate_jacobians(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) → bool

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::calculate_jacobians() const –> bool

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>

fast_forward(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) → None

C++: protocols::stepwise::sampler::StepWiseSamplerSized::fast_forward() –> 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_jacobians(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_all_jacobians() const –> class utility::vector1<double, class std::allocator<double> >

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_jacobian(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose: pyrosetta.rosetta.core.pose.Pose) → float

Calculate the jacobian

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_jacobian(class core::pose::Pose &) const –> double

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.sampler.rna.RNA_KinematicCloser) → str

Class name

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::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

id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) → int

C++: protocols::stepwise::sampler::StepWiseSamplerSized::id() const –> const unsigned long &

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 > > &

init(*args, **kwargs)

Overloaded function.

1. init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) -> None

Initialization

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::init() –> void

2. init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose_current: pyrosetta.rosetta.core.pose.Pose, pose_closed: pyrosetta.rosetta.core.pose.Pose) -> None
3. init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, pose_current: pyrosetta.rosetta.core.pose.Pose, pose_closed: pyrosetta.rosetta.core.pose.Pose, use_pose_closed: bool) -> None

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::init(const class core::pose::Pose &, const class core::pose::Pose &, bool) –> void

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

not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) → bool

Check if reach the end of rotamer list

C++: protocols::stepwise::sampler::StepWiseSamplerSized::not_end() const –> bool

plus_plus(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) → None

Move to next rotamer

C++: protocols::stepwise::sampler::StepWiseSamplerSized::operator++() –> void

random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler) → bool

Check if is random modeler

C++: protocols::stepwise::sampler::StepWiseSampler::random() const –> bool

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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) → None

Reset to the first (or random if random()) rotamer.

C++: protocols::stepwise::sampler::StepWiseSamplerSized::reset() –> void

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_calculate_jacobians(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, setting: bool) → None

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_calculate_jacobians(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_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, setting: int) → None

C++: protocols::stepwise::sampler::StepWiseSamplerSized::set_id(const unsigned long) –> 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_random(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler, setting: bool) → None

Set the random modeler state

C++: protocols::stepwise::sampler::StepWiseSampler::set_random(const bool) –> 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_verbose(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser, setting: bool) → None

Set verbose

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_verbose(const bool) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream) -> None
2. show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, out: pyrosetta.rosetta.std.ostream, indent: int) -> None

output summary of class

C++: protocols::stepwise::sampler::StepWiseSamplerSized::show(class std::basic_ostream<char> &, const unsigned long) const –> void

size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) → int

Get the total number of rotamers in sampler

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::size() const –> unsigned long

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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

C++: protocols::stepwise::sampler::rna::RNA_KinematicCloser::type() const –> enum protocols::toolbox::SamplerPlusPlusType

pyrosetta.rosetta.protocols.stepwise.sampler.rna.modeler_sugar_at_five_prime(pose: pyrosetta.rosetta.core.pose.Pose, moving_suite: int) → bool

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

pyrosetta.rosetta.protocols.stepwise.sampler.rna.modeler_sugar_at_three_prime(pose: pyrosetta.rosetta.core.pose.Pose, moving_suite: int) → bool

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

pyrosetta.rosetta.protocols.stepwise.sampler.rna.setup_sampler(pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions, working_parameters: pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters, build_pose_from_scratch: bool, kic_modeler: bool, close_chain: bool) → pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler

C++: protocols::stepwise::sampler::rna::setup_sampler(const class core::pose::Pose &, class std::shared_ptr<const class protocols::stepwise::modeler::options::StepWiseModelerOptions>, class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters>, const bool, const bool, const bool) –> class std::shared_ptr<class protocols::stepwise::sampler::StepWiseSampler>