pose_length_moves

Bindings for protocols::pose_length_moves namespace

class pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::AnalyzeLoopModeling::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling, : pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling) → pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling

C++: protocols::pose_length_moves::AnalyzeLoopModeling::operator=(const class protocols::pose_length_moves::AnalyzeLoopModeling &) –> class protocols::pose_length_moves::AnalyzeLoopModeling &

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.pose_length_moves.AnalyzeLoopModeling) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_length_moves::AnalyzeLoopModeling::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>

generate_lookback_rmsd(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling, pose: pyrosetta.rosetta.core.pose.Pose, position: int) → float

C++: protocols::pose_length_moves::AnalyzeLoopModeling::generate_lookback_rmsd(class core::pose::Pose, unsigned long) –> double

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_loop_rmsd(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling, native_pose: pyrosetta.rosetta.core.pose.Pose, designed_pose: pyrosetta.rosetta.core.pose.Pose, loopStart: int, loopEnd: int) → float

C++: protocols::pose_length_moves::AnalyzeLoopModeling::get_loop_rmsd(class core::pose::Pose, class core::pose::Pose, unsigned long, unsigned long) –> double

get_name(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling) → str

C++: protocols::pose_length_moves::AnalyzeLoopModeling::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

get_valid_resid(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling, resid: int, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::pose_length_moves::AnalyzeLoopModeling::get_valid_resid(int, const class core::pose::Pose) –> 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 > > &

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

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

static mover_name() → str

C++: protocols::pose_length_moves::AnalyzeLoopModeling::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::AnalyzeLoopModeling::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

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

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

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

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

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

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

rmsd_between_coordinates(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling, fragCoordinates: pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t, coordinates: pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t) → float

C++: protocols::pose_length_moves::AnalyzeLoopModeling::rmsd_between_coordinates(class std::vector<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::vector<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> double

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator, : pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator) → pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator

C++: protocols::pose_length_moves::AnalyzeLoopModelingCreator::operator=(const class protocols::pose_length_moves::AnalyzeLoopModelingCreator &) –> class protocols::pose_length_moves::AnalyzeLoopModelingCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_length_moves::AnalyzeLoopModelingCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator) → str

C++: protocols::pose_length_moves::AnalyzeLoopModelingCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::AnalyzeLoopModelingCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_length_moves.BackboneStubRMSDComparator

Bases: pybind11_object

class pyrosetta.rosetta.protocols.pose_length_moves.Chain

Bases: pybind11_object

property poseOP

property rmsd

class pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::ConnectChainsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover, : pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover) → pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover

C++: protocols::pose_length_moves::ConnectChainsMover::operator=(const class protocols::pose_length_moves::ConnectChainsMover &) –> class protocols::pose_length_moves::ConnectChainsMover &

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.pose_length_moves.ConnectChainsMover) → pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

A tag is a unique identifier used to identify structures produced

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover) → str

C++: protocols::pose_length_moves::ConnectChainsMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_length_moves::ConnectChainsMover::mover_name() –> std::string

static name() → str

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

parse_input(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover, individual_chains: pyrosetta.rosetta.utility.vector1_std_string, chains_in_poses: pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t) → None

C++: protocols::pose_length_moves::ConnectChainsMover::parse_input(class utility::vector1<std::string, class std::allocator<std::string > > &, class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > > &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::ConnectChainsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

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

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

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

reletter_chains(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::ConnectChainsMover::reletter_chains(class core::pose::Pose &) –> 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_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator, : pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator) → pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator

C++: protocols::pose_length_moves::ConnectChainsMoverCreator::operator=(const class protocols::pose_length_moves::ConnectChainsMoverCreator &) –> class protocols::pose_length_moves::ConnectChainsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_length_moves::ConnectChainsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator) → str

C++: protocols::pose_length_moves::ConnectChainsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::ConnectChainsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_length_moves.FinalRMSDComparator

Bases: pybind11_object

class pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::FixAllLoopsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover, : pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover) → pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover

C++: protocols::pose_length_moves::FixAllLoopsMover::operator=(const class protocols::pose_length_moves::FixAllLoopsMover &) –> class protocols::pose_length_moves::FixAllLoopsMover &

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.pose_length_moves.FixAllLoopsMover) → pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

A tag is a unique identifier used to identify structures produced

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover) → str

C++: protocols::pose_length_moves::FixAllLoopsMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_length_moves::FixAllLoopsMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::FixAllLoopsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator, : pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator) → pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator

C++: protocols::pose_length_moves::FixAllLoopsMoverCreator::operator=(const class protocols::pose_length_moves::FixAllLoopsMoverCreator &) –> class protocols::pose_length_moves::FixAllLoopsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_length_moves::FixAllLoopsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator) → str

C++: protocols::pose_length_moves::FixAllLoopsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::FixAllLoopsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::InsertResMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover, : pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover) → pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover

C++: protocols::pose_length_moves::InsertResMover::operator=(const class protocols::pose_length_moves::InsertResMover &) –> class protocols::pose_length_moves::InsertResMover &

center_of_mass(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pose_length_moves::InsertResMover::center_of_mass(const class core::pose::Pose &) –> class numeric::xyzVector<double>

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.pose_length_moves.InsertResMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_length_moves::InsertResMover::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>

extendRegion(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover, poseOP: pyrosetta.rosetta.core.pose.Pose, chain_id: int, length: int) → None

C++: protocols::pose_length_moves::InsertResMover::extendRegion(class std::shared_ptr<class core::pose::Pose>, unsigned long, unsigned long) –> 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.pose_length_moves.InsertResMover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pose_length_moves::InsertResMover::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.pose_length_moves.InsertResMover) → str

C++: protocols::pose_length_moves::InsertResMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_length_moves::InsertResMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::InsertResMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator, : pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator) → pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator

C++: protocols::pose_length_moves::InsertResMoverCreator::operator=(const class protocols::pose_length_moves::InsertResMoverCreator &) –> class protocols::pose_length_moves::InsertResMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_length_moves::InsertResMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator) → str

C++: protocols::pose_length_moves::InsertResMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::InsertResMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::NearNativeLoopCloser::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, : pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser) → pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser

C++: protocols::pose_length_moves::NearNativeLoopCloser::operator=(const class protocols::pose_length_moves::NearNativeLoopCloser &) –> class protocols::pose_length_moves::NearNativeLoopCloser &

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.pose_length_moves.NearNativeLoopCloser) → pyrosetta.rosetta.protocols.moves.Mover

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

close_loop(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::pose_length_moves::NearNativeLoopCloser::close_loop(class core::pose::Pose &) –> double

combine_chains(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(class core::pose::Pose &) –> void

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>

create_maximum_length_pose(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, resTypeBeforeLoop: str, resTypeAfterLoop: str, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose(char, char, class core::pose::Pose) –> class std::shared_ptr<class core::pose::Pose>

create_potential_loops(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_pose_length_moves_PossibleLoop_t

C++: protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(class core::pose::Pose) –> class utility::vector1<class std::shared_ptr<class protocols::pose_length_moves::PossibleLoop>, class std::allocator<class std::shared_ptr<class protocols::pose_length_moves::PossibleLoop> > >

extendRegion(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, towardCTerm: bool, resStart: int, neighborResType: str, numberAddRes: int, poseOP: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(bool, unsigned long, char, unsigned long, class std::shared_ptr<class core::pose::Pose> &) –> 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.pose_length_moves.NearNativeLoopCloser) → pyrosetta.rosetta.core.pose.Pose

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

get_additional_output_with_rmsd(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, return_rmsd: float) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output_with_rmsd(double &) –> 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.pose_length_moves.NearNativeLoopCloser) → str

C++: protocols::pose_length_moves::NearNativeLoopCloser::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_length_moves::NearNativeLoopCloser::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::NearNativeLoopCloser::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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(std::ostream &) const –> void

switch_chain_order(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser, pose: pyrosetta.rosetta.core.pose.Pose, new_chain_order: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::pose_length_moves::NearNativeLoopCloser::switch_chain_order(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator, : pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator) → pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator

C++: protocols::pose_length_moves::NearNativeLoopCloserCreator::operator=(const class protocols::pose_length_moves::NearNativeLoopCloserCreator &) –> class protocols::pose_length_moves::NearNativeLoopCloserCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_length_moves::NearNativeLoopCloserCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator) → str

C++: protocols::pose_length_moves::NearNativeLoopCloserCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::pose_length_moves::NearNativeLoopCloserCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop, : pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop

C++: protocols::pose_length_moves::PossibleLoop::operator=(const class protocols::pose_length_moves::PossibleLoop &) –> class protocols::pose_length_moves::PossibleLoop &

evaluate_distance_closure(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → None

C++: protocols::pose_length_moves::PossibleLoop::evaluate_distance_closure() –> void

generate_output_pose(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop, output_closed: bool, ideal_loop: bool, rms_threshold: float, allowed_loop_abegos: str, closure_type: str) → None

C++: protocols::pose_length_moves::PossibleLoop::generate_output_pose(bool, bool, double, std::string, std::string) –> void

generate_stub_rmsd(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop, stubRmsdThreshold: float) → None

C++: protocols::pose_length_moves::PossibleLoop::generate_stub_rmsd(double) –> void

get_below_distance_threshold(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → bool

C++: protocols::pose_length_moves::PossibleLoop::get_below_distance_threshold() –> bool

get_description(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → str

C++: protocols::pose_length_moves::PossibleLoop::get_description() –> std::string

get_finalPoseOP(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pose_length_moves::PossibleLoop::get_finalPoseOP() –> class std::shared_ptr<class core::pose::Pose>

get_final_RMSD(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → float

C++: protocols::pose_length_moves::PossibleLoop::get_final_RMSD() –> double

get_stubRMSD(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → float

C++: protocols::pose_length_moves::PossibleLoop::get_stubRMSD() –> double

label_loop(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop, label: str) → None

C++: protocols::pose_length_moves::PossibleLoop::label_loop(std::string) –> void

outputed(*args, **kwargs)

Overloaded function.

1. outputed(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) -> bool

C++: protocols::pose_length_moves::PossibleLoop::outputed() –> bool

2. outputed(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop, outputed: bool) -> None

C++: protocols::pose_length_moves::PossibleLoop::outputed(bool) –> void

setup_finalPose_copy_labels(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → None

C++: protocols::pose_length_moves::PossibleLoop::setup_finalPose_copy_labels() –> void

setup_finalPose_copy_rotamers(self: pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop) → None

C++: protocols::pose_length_moves::PossibleLoop::setup_finalPose_copy_rotamers() –> void

class pyrosetta.rosetta.protocols.pose_length_moves.chain_lt

Bases: pybind11_object