movers

Bindings for protocols::rna::movers namespace

class pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover, iterations: int, noise: bool, final_minimize: bool, ang_significance_threshold: float, handle_suites: bool) -> None
3. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover, arg0: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover) -> 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__(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

apply(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNAIdealizeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover, : pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover) → pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover

C++: protocols::rna::movers::RNAIdealizeMover::operator=(const class protocols::rna::movers::RNAIdealizeMover &) –> class protocols::rna::movers::RNAIdealizeMover &

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.rna.movers.RNAIdealizeMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

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

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_iterations(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover) → int

C++: protocols::rna::movers::RNAIdealizeMover::get_iterations() const –> unsigned long

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.rna.movers.RNAIdealizeMover) → str

C++: protocols::rna::movers::RNAIdealizeMover::get_name() const –> std::string

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

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mover_name() → str

C++: protocols::rna::movers::RNAIdealizeMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::rna::movers::RNAIdealizeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

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

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

set_iterations(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover, iterations: int) → None

C++: protocols::rna::movers::RNAIdealizeMover::set_iterations(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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover) -> None
2. show(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::rna::movers::RNAIdealizeMover::show(class std::basic_ostream<char> &) const –> void

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Thread a new sequence over a given RNA scaffold and do a little optimization

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, arg0: str, arg1: str) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, arg0: str, arg1: str, arg2: bool) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, arg0: str, arg1: str, arg2: bool, arg3: str) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, arg0: str, arg1: str, arg2: bool, arg3: str, arg4: str) -> None

doc

5. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, seq: str, template_sequence_from_alignment: str, long_strategy: bool, input_sequence_type: str, mutation_list: str, insertion_list: str) -> None
6. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) -> None
7. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, arg0: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) -> 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__(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) → str

__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).

accomodate_length_change(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose, insertion_begin: int, seqpos: int) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, : pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) → pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::operator=(const class protocols::rna::movers::RNAThreadAndMinimizeMover &) –> class protocols::rna::movers::RNAThreadAndMinimizeMover &

class_name() → str

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::class_name() –> std::string

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.rna.movers.RNAThreadAndMinimizeMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

fresh_instance(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

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

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) → str

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::get_name() const –> std::string

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

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

long_mutate_strategy(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::long_mutate_strategy(class core::pose::Pose &) –> void

mm_from_residues(*args, **kwargs)

Overloaded function.

1. mm_from_residues(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose, changed_pos: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.core.kinematics.MoveMap
2. mm_from_residues(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose, changed_pos: pyrosetta.rosetta.utility.vector1_unsigned_long, add_nearby: bool) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::mm_from_residues(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> class std::shared_ptr<class core::kinematics::MoveMap>

mutate_all_at_once(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::mutate_all_at_once(class core::pose::Pose &) –> void

name() → str

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

obtain_rtypes_for_target_sequence(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::obtain_rtypes_for_target_sequence() –> void

process_deletions(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::process_deletions(class core::pose::Pose &) –> void

process_insertions(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(class core::pose::Pose &) –> void

register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

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

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

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

set_up_target_sequence(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::set_up_target_sequence(class core::pose::Pose &) –> void

setup_alignment_map(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, mapping: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, sequence_from_alignment: str) → None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::setup_alignment_map(class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const class std::basic_string<char> &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) -> None
2. show(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::show(class std::basic_ostream<char> &) const –> void

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler

Bases: pyrosetta.rosetta.protocols.moves.Mover

The RNA de novo structure modeling protocol

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler) -> None
2. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, arg0: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler) -> 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.rna.movers.RNA_HelixAssembler, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::rna::movers::RNA_HelixAssembler::apply(class core::pose::Pose &) –> void

2. apply(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, pose: pyrosetta.rosetta.core.pose.Pose, full_sequence_in: str) -> None

Apply the loop-rebuild protocol to the input pose

C++: protocols::rna::movers::RNA_HelixAssembler::apply(class core::pose::Pose &, const class std::basic_string<char> &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, other: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

build_helix(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::rna::movers::RNA_HelixAssembler::build_helix(class core::pose::Pose &) –> void

build_init_pose(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, seq1: str, seq2: str) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::rna::movers::RNA_HelixAssembler::build_init_pose(const class std::basic_string<char> &, const class std::basic_string<char> &) –> class std::shared_ptr<class core::pose::Pose>

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.rna.movers.RNA_HelixAssembler) → pyrosetta.rosetta.protocols.moves.Mover

Clone this object

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

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

fpd

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

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

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

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler) → str

C++: protocols::rna::movers::RNA_HelixAssembler::get_name() const –> std::string

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

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

name() → str

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

random_perturbation(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, setting: bool) → None

C++: protocols::rna::movers::RNA_HelixAssembler::random_perturbation(const bool &) –> void

register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

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

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

set_dump(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, setting: bool) → None

C++: protocols::rna::movers::RNA_HelixAssembler::set_dump(const bool &) –> void

set_finish_scorefxn(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::rna::movers::RNA_HelixAssembler::set_finish_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_minimize_all(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, setting: bool) → None

C++: protocols::rna::movers::RNA_HelixAssembler::set_minimize_all(const bool &) –> void

set_model_and_remove_capping_residues(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, setting: bool) → None

C++: protocols::rna::movers::RNA_HelixAssembler::set_model_and_remove_capping_residues(bool) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::rna::movers::RNA_HelixAssembler::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

use_phenix_geo(self: pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler, setting: bool) → None

C++: protocols::rna::movers::RNA_HelixAssembler::use_phenix_geo(const bool) –> void

class pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser

Bases: pyrosetta.rosetta.protocols.moves.Mover

The RNA de novo structure modeling protocol

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser) -> None
2. __init__(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, arg0: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser) -> 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.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::rna::movers::RNA_LoopCloser::apply(class core::pose::Pose &) –> void

2. apply(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, connections: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) -> None

Apply the loop-rebuild protocol to the input pose

C++: protocols::rna::movers::RNA_LoopCloser::apply(class core::pose::Pose &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) –> void

3. apply(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, connections: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, cutpoint: int) -> float

Apply the loop-rebuild protocol to the input pose

C++: protocols::rna::movers::RNA_LoopCloser::apply(class core::pose::Pose &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const unsigned long &) –> double

4. apply(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, cutpoint: int) -> float

Apply the loop-rebuild protocol to the input pose

C++: protocols::rna::movers::RNA_LoopCloser::apply(class core::pose::Pose &, const unsigned long &) –> double

5. apply(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, cutpoints: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Apply the loop-rebuild protocol to the input pose

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

assign(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, : pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser) → pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser

C++: protocols::rna::movers::RNA_LoopCloser::operator=(const class protocols::rna::movers::RNA_LoopCloser &) –> class protocols::rna::movers::RNA_LoopCloser &

check_closure(*args, **kwargs)

Overloaded function.

1. check_closure(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> bool
2. check_closure(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, i: int, ccd_tolerance: float) -> bool

C++: protocols::rna::movers::RNA_LoopCloser::check_closure(const class core::pose::Pose &, const unsigned long, double) –> bool

3. check_closure(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
4. check_closure(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, ccd_tolerance: float) -> bool

C++: protocols::rna::movers::RNA_LoopCloser::check_closure(const class core::pose::Pose &, double) –> 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.rna.movers.RNA_LoopCloser) → pyrosetta.rosetta.protocols.moves.Mover

Clone this object

C++: protocols::rna::movers::RNA_LoopCloser::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_scan(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, setting: bool) → None

C++: protocols::rna::movers::RNA_LoopCloser::fast_scan(const bool &) –> 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_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_cutpoints_closed(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::rna::movers::RNA_LoopCloser::get_cutpoints_closed(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_dist_err(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, cutpoint: int) → float

C++: protocols::rna::movers::RNA_LoopCloser::get_dist_err(const class core::pose::Pose &, const unsigned long) const –> double

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.rna.movers.RNA_LoopCloser) → str

C++: protocols::rna::movers::RNA_LoopCloser::get_name() const –> std::string

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

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

name() → str

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

register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_atom_level_domain_map(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, setting: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) → None

C++: protocols::rna::movers::RNA_LoopCloser::set_atom_level_domain_map(class std::shared_ptr<const class protocols::toolbox::AtomLevelDomainMap>) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

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

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

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

set_verbose(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, setting: bool) → None

C++: protocols::rna::movers::RNA_LoopCloser::set_verbose(const bool) –> void

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

pyrosetta.rosetta.protocols.rna.movers.is_blank_seq(c: str) → bool

C++: protocols::rna::movers::is_blank_seq(const char &) –> bool