rna

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

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

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

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Apply the current rotamer to pose

C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> None

Apply the i-th rotamer to pose

C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::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 &

base_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler) pyrosetta.rosetta.core.chemical.rna.ChiState

Get the base state (WHATEVER / ANTI / SYN)

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::base_state() –> enum core::chemical::rna::ChiState

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.

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.sampler.rna.RNA_ChiStepWiseSampler) str

Name of the class

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::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_t

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler) None

Initialization

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

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

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

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

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

Move to next rotamer

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

pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler) pyrosetta.rosetta.core.chemical.rna.PuckerState

Get the pucker state (NORTH / SOUTH)

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::pucker_state() –> enum core::chemical::rna::PuckerState

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

Check if is random modeler

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

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(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_base_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: pyrosetta.rosetta.core.chemical.rna.ChiState) None

Set the base state (WHATEVER / ANTI / SYN)

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_base_state(const enum core::chemical::rna::ChiState) –> void

set_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: float) None

Set the bin_size (default: 20)

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_bin_size(const double) –> 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_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: bool) None

Set use extra chi (+-60)

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_extra_chi(const bool) –> 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_max_range(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: float) None

Set the max_range of modeler (default: +-20)

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_max_range(const double) –> 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_pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: pyrosetta.rosetta.core.chemical.rna.PuckerState) None

Set the pucker state (NORTH / SOUTH)

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_pucker_state(const enum core::chemical::rna::PuckerState) –> 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_rsd_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: int) None

Set the residue id

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_rsd_id(const unsigned long) –> void

set_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::set_sample_all_chi(const bool &) –> void

set_torsion_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, setting: pyrosetta.rosetta.core.id.TorsionID) None

Set the TorsionID of the sampler

C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::set_torsion_id(const class core::id::TorsionID &) –> void

set_torsions(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion, setting: pyrosetta.rosetta.utility.vector1_double) None

Set the allowed torsions in sampler

C++: protocols::stepwise::sampler::StepWiseSamplerOneTorsion::set_torsions(const class utility::vector1<double, class std::allocator<double> > &) –> 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_values(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue, setting: pyrosetta.rosetta.utility.vector1_double) None

Set the allowed values in sampler

C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::set_values(const class utility::vector1<double, class std::allocator<double> > &) –> 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(std::ostream &, const unsigned long) const –> void

size(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue) int

Get the total number of rotamers in sampler

C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::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_ChiStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType

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

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

value(*args, **kwargs)

Overloaded function.

  1. value(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue) -> float

Get the value of current value

C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::value() const –> double

  1. value(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue, i: int) -> float

Get the value of i-th value

C++: protocols::stepwise::sampler::StepWiseSamplerOneValue::value(const unsigned long) const –> double

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

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

apply(*args, **kwargs)

Overloaded function.

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

Apply the current rotamer to pose

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) -> None

Apply the current rotamer to ref_pose_

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply() –> void

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

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

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>

closable(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) bool

If the chain is closable (random modeler only)

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::closable() const –> bool

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.sampler.rna.RNA_KIC_Sampler) str

Name of the class

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::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 > > &

init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) None

Initialization

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

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

not_end(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) bool

Check if reach the end of rotamer list

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

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

plus_plus(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) None

Move to next rotamer

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator++() –> 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

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

Check if is random modeler

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

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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) None

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

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::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_base_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: pyrosetta.rosetta.core.chemical.rna.ChiState) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_base_state(const enum core::chemical::rna::ChiState) –> void

set_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: float) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_bin_size(const double) –> 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_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_chi(const bool) –> void

set_extra_epsilon(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_extra_epsilon(const bool) –> void

set_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: float) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_fast(const double) –> void

set_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_idealize_coord(const bool) –> 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_max_tries(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: int) None

Max # of step for trying in random sampling

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_max_tries(const unsigned long) –> 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_pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: pyrosetta.rosetta.core.chemical.rna.PuckerState) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_pucker_state(const enum core::chemical::rna::PuckerState) –> void

set_random(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

Set the random modeler state

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_random(const bool) –> void

set_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_all_chi(const bool) –> void

set_sample_nucleoside(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: int) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_sample_nucleoside(const unsigned long) –> void

set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_skip_same_pucker(const bool) –> void

set_torsion_screen(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_torsion_screen(const bool) –> 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_verbose(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler, setting: bool) None

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) -> None

  2. show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, output: pyrosetta.rosetta.std.ostream) -> None

  3. show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, out: pyrosetta.rosetta.std.ostream, indent: int) -> None

output summary of class

C++: protocols::toolbox::SamplerPlusPlus::show(std::ostream &, const unsigned long) 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(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType

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

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

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

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

The RNA de novo structure modeling protocol

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.

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_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_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

  1. 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

  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, 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

static 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

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

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

Move to next rotamer

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

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

Check if is random modeler

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

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(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

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_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

Set the ‘type’ string

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

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

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

add_external_loop_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, rotamer: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None

Add one more rotamer sampler to this sampler

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::add_external_loop_rotamer(const class std::shared_ptr<class protocols::stepwise::sampler::StepWiseSamplerSized> &) –> void

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Apply the current rotamer to pose

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> None

Apply the i-th rotamer to pose

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

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

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

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

clear_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None

Clear all rotamer samplers stored in this sampler

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::clear_rotamer() –> 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.

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.sampler.rna.RNA_NucleosideStepWiseSampler) str

Name of the class

C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::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_t

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler) None

Initialization wrapper

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

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

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

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

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

Move to next rotamer

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::operator++() –> 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

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

Check if is random modeler

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

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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None

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

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::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_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: float) None

C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_bin_size(const double) –> 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_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None

Set functions

C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_extra_chi(const bool) –> void

set_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None

Just sample the center chi torsion.

C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_fast(const bool) –> 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_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_idealize_coord(const bool) –> 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_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_sample_all_chi(const bool) –> void

set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::set_skip_same_pucker(const bool) –> 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.

  1. show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, out: pyrosetta.rosetta.std.ostream) -> None

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

output summary of class

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::show(std::ostream &, const unsigned long) const –> void

size(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) int

Get the total number of rotamers in sampler

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::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_NucleosideStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType

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

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

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

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

apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, pose: pyrosetta.rosetta.core.pose.Pose, i: int) None

Apply the i-th rotamer to pose

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

assign(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, : pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler

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

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.

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.sampler.rna.RNA_SugarStepWiseSampler) str

Name of the class

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::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_t

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) None

Initialization

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

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

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

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

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

Move to next rotamer

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

pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) pyrosetta.rosetta.core.chemical.rna.PuckerState

Get the current pucker state.

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::pucker() const –> enum core::chemical::rna::PuckerState

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

Check if is random modeler

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

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(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

rsd_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler) int

Get the residue id being sampled

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::rsd_id() const –> const unsigned long &

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_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized, setting: int) None

C++: protocols::stepwise::sampler::StepWiseSamplerSized::set_id(const unsigned long) –> void

set_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: bool) None

Set if using RNA_IdealCoord to sample puckers

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_idealize_coord(const bool) –> 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_pucker_state(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: pyrosetta.rosetta.core.chemical.rna.PuckerState) None

Set the pucker_state (WHATEVER / NORTH / SOUTH)

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_pucker_state(const enum core::chemical::rna::PuckerState) –> 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_rsd_id(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: int) None

Set the residue id being sampled

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_rsd_id(const unsigned long) –> void

set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler, setting: bool) None

Set if the sampler will skip pucker applying when input pose has

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::set_skip_same_pucker(const bool) –> 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.

  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(std::ostream &, const unsigned long) const –> void

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

Get the total number of rotamers in sampler

C++: protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::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_SugarStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType

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

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

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

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

add_external_loop_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, rotamer: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized) None

Add one more rotamer sampler to this sampler

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::add_external_loop_rotamer(const class std::shared_ptr<class protocols::stepwise::sampler::StepWiseSamplerSized> &) –> void

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Apply the current rotamer to pose

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::apply(class core::pose::Pose &) –> void

  1. apply(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> None

Apply the i-th rotamer to pose

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

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

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

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

clear_rotamer(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None

Clear all rotamer samplers stored in this sampler

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::clear_rotamer() –> 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.

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.sampler.rna.RNA_SuiteStepWiseSampler) str

Name of the class

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::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_t

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) None

Initialization wrapper

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

init_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) None

Initialization for fast mode

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_fast() –> void

init_standard(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler) None

Initialization for standard modeler

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard() –> void

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

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

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

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

Move to next rotamer

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::operator++() –> 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

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

Check if is random modeler

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

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(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) None

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

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::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_bin_size(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: float) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_bin_size(const double) –> 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_extra_beta(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_beta(const bool) –> void

set_extra_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_chi(const bool) –> void

set_extra_epsilon(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_extra_epsilon(const bool) –> void

set_fast(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

Fast mode: just sample popular center torsions

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_fast(const bool) –> 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_idealize_coord(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_idealize_coord(const bool) –> 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_sample_all_chi(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_all_chi(const bool) –> void

set_sample_nucleoside_lower(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

Set functions

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_nucleoside_lower(const bool) –> void

set_sample_nucleoside_upper(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_sample_nucleoside_upper(const bool) –> void

set_skip_same_pucker(self: pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler, setting: bool) None

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::set_skip_same_pucker(const bool) –> 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.

  1. show(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny, out: pyrosetta.rosetta.std.ostream) -> None

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

output summary of class

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::show(std::ostream &, const unsigned long) const –> void

size(self: pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny) int

Get the total number of rotamers in sampler

C++: protocols::stepwise::sampler::StepWiseSamplerSizedAny::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_SuiteStepWiseSampler) pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType

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

C++: protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::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>