movers¶

Bindings for protocols::pose_sewing::movers namespace

class pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover¶

Bases: Mover

adds virtual residues to either side of a given Pose

add_flanking_virtual_residues(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::add_flanking_virtual_residues(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, : pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) → pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::operator=(const class protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover &) –> class protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover &

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_sewing.movers.AddFlankingVirtualResiduesMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::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.pose_sewing.movers.AddFlankingVirtualResiduesMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

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

get_C_term_length(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) → int¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_C_term_length() const –> unsigned long

get_N_term_length(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) → int¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_N_term_length() const –> unsigned long

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_chain_to_modify(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) → int¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_chain_to_modify() const –> unsigned long

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_sewing.movers.AddFlankingVirtualResiduesMover) → str¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::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_remove_pre_pose(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) → bool¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_remove_pre_pose() const –> bool

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_vital_selector(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_vital_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

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_sewing::movers::AddFlankingVirtualResiduesMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::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_sewing::movers::AddFlankingVirtualResiduesMover::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_C_term_length(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, : int) → None¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_C_term_length(unsigned long) –> void

set_N_term_length(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, : int) → None¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_N_term_length(unsigned long) –> void

set_chain_to_modify(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, : int) → None¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_chain_to_modify(unsigned long) –> 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_remove_pre_pose(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, : bool) → None¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_remove_pre_pose(bool) –> void

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

Set the ‘type’ string

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

set_vital_selector(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_vital_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) -> None
show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::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.

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

Set the ‘type’ string

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

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_sewing.movers.AddFlankingVirtualResiduesMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator, : pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator) → pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMoverCreator::operator=(const class protocols::pose_sewing::movers::AddFlankingVirtualResiduesMoverCreator &) –> class protocols::pose_sewing::movers::AddFlankingVirtualResiduesMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator) → str¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pose_sewing::movers::AddFlankingVirtualResiduesMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover¶

Bases: Mover

analyzes pairs of interacting elements

apply(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover, : pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover) → pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMover::operator=(const class protocols::pose_sewing::movers::BlockwiseAnalysisMover &) –> class protocols::pose_sewing::movers::BlockwiseAnalysisMover &

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_sewing.movers.BlockwiseAnalysisMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::BlockwiseAnalysisMover::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.pose_sewing.movers.BlockwiseAnalysisMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::BlockwiseAnalysisMover::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_sewing.movers.BlockwiseAnalysisMover) → str¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMover::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_sewing::movers::BlockwiseAnalysisMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

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

provide_citation_info(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMover::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.

show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover) -> None
show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::pose_sewing::movers::BlockwiseAnalysisMover::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.

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

Set the ‘type’ string

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

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_sewing.movers.BlockwiseAnalysisMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator, : pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator) → pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMoverCreator::operator=(const class protocols::pose_sewing::movers::BlockwiseAnalysisMoverCreator &) –> class protocols::pose_sewing::movers::BlockwiseAnalysisMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator) → str¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pose_sewing::movers::BlockwiseAnalysisMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover¶

Bases: Mover

reports information about disulfides

apply(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover, : pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover) → pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover¶: C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::operator=(const class protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover &) –> class protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover &

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_sewing.movers.OmnibusDisulfideAnalysisLabelerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::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.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::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_sewing.movers.OmnibusDisulfideAnalysisLabelerMover) → str¶: C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::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_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

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

provide_citation_info(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

This mover is unpublished. It returns Frank Teets as its author.

C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::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.

show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover) -> None
show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::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.

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

Set the ‘type’ string

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

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_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator, : pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator) → pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator¶: C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMoverCreator::operator=(const class protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMoverCreator &) –> class protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator) → str¶: C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover¶

Bases: Mover

replaces pose with a random starting segment from a segment file

apply(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover, : pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMover::operator=(const class protocols::pose_sewing::movers::PickRandomSegmentMover &) –> class protocols::pose_sewing::movers::PickRandomSegmentMover &

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_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::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>

create_ss_defaults(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.protocols.pose_sewing.movers.SeedSettings¶

Create and return the SS-tunable settings.

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::create_ss_defaults() const –> struct protocols::pose_sewing::movers::SeedSettings

fresh_instance(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::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_sewing.movers.PickRandomSegmentMover) → str¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMover::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_pose_vector(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMover::get_pose_vector() const –> class std::shared_ptr<class protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector>

get_segment_file_paths(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMover::get_segment_file_paths() const –> class utility::vector1<std::string, class std::allocator<std::string > >

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_ss_defaults(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.protocols.pose_sewing.movers.SeedSettings¶

Get the defaults of seed settings.

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::get_ss_defaults() const –> struct protocols::pose_sewing::movers::SeedSettings

get_ss_settings(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → pyrosetta.rosetta.std.map_char_protocols_pose_sewing_movers_SeedSettings¶

Get all SS-specific settings

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::get_ss_settings() const –> class std::map<char, struct protocols::pose_sewing::movers::SeedSettings, struct std::less<char>, class std::allocator<struct std::pair<const char, struct protocols::pose_sewing::movers::SeedSettings> > >

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_sewing::movers::PickRandomSegmentMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::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_sewing::movers::PickRandomSegmentMover::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_segment_file_paths(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover, paths: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMover::set_segment_file_paths(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

set_ss_defaults(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) → None¶

Set the configurable options as defaults.

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::set_ss_defaults() –> 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.

show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) -> None
show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::pose_sewing::movers::PickRandomSegmentMover::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.

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

Set the ‘type’ string

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

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_sewing.movers.PickRandomSegmentMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator, : pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator) → pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMoverCreator::operator=(const class protocols::pose_sewing::movers::PickRandomSegmentMoverCreator &) –> class protocols::pose_sewing::movers::PickRandomSegmentMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator) → str¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pose_sewing::movers::PickRandomSegmentMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.pose_sewing.movers.SeedSettings¶

Bases: pybind11_object

property max_terminal_length_¶

property min_terminal_length_¶

class pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover¶

Bases: Mover

perform SEWING-like chimerization-based addition of supersecondary structural segments into previously virtual residues

align(*args, **kwargs)¶

Overloaded function.

align(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, stationary_pose: pyrosetta.rosetta.core.pose.Pose, stationary_residue: int, mobile_pose: pyrosetta.rosetta.core.pose.Pose, mobile_residue: int, window_width: int, tolerance: float) -> bool
align(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, stationary_pose: pyrosetta.rosetta.core.pose.Pose, stationary_residue: int, mobile_pose: pyrosetta.rosetta.core.pose.Pose, mobile_residue: int, window_width: int, tolerance: float, check_alignment: bool) -> bool

C++: protocols::pose_sewing::movers::SewAnythingAddMover::align(const class core::pose::Pose &, unsigned long, class core::pose::Pose &, unsigned long, unsigned long, double, bool) const –> bool

apply(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

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

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, : pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::operator=(const class protocols::pose_sewing::movers::SewAnythingAddMover &) –> class protocols::pose_sewing::movers::SewAnythingAddMover &

clashes(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, nterm_pose: pyrosetta.rosetta.core.pose.Pose, first_nterm_res: int, last_nterm_res: int, cterm_pose: pyrosetta.rosetta.core.pose.Pose, first_cterm_res: int, last_cterm_res: int, clash_radius: float, check_all_backbone: bool) → bool¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::clashes(const class core::pose::Pose &, unsigned long, unsigned long, const class core::pose::Pose &, unsigned long, unsigned long, double, bool) const –> bool

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::SewAnythingAddMover::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>

find_mod_terminus(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, pose: pyrosetta.rosetta.core.pose.Pose, : Tuple[int, int]) → str¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::find_mod_terminus(class core::pose::Pose &, struct std::pair<unsigned long, unsigned long>) –> char

find_sewable_region(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, pose: pyrosetta.rosetta.core.pose.Pose) → Tuple[int, int]¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::find_sewable_region(class core::pose::Pose &) –> struct std::pair<unsigned long, unsigned long>

fresh_instance(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::pose_sewing::movers::SewAnythingAddMover::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_clash_radius(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → float¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::get_clash_radius() const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

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

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_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_max_attempts(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → int¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::get_max_attempts() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → str¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::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_permissible_segment_ends(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → str¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::get_permissible_segment_ends() const –> std::string

get_permissible_termini(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → str¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::get_permissible_termini() const –> std::string

get_pose_vector(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::get_pose_vector() const –> class std::shared_ptr<class protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector>

get_segment_file_paths(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::get_segment_file_paths() const –> class utility::vector1<std::string, class std::allocator<std::string > >

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_trim_terminal_loops(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) → bool¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::get_trim_terminal_loops() const –> bool

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_sewing::movers::SewAnythingAddMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::pose_sewing::movers::SewAnythingAddMover::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_sewing::movers::SewAnythingAddMover::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

segment_vector_dssp(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, mod_terminus: str, mod_terminus_dssp: str, permissible_segment_ends: str) → Tuple[str, str]¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::segment_vector_dssp(char, char, const std::string &) const –> struct std::pair<std::string, std::string >

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_permissible_segment_ends(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, : str) → None¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::set_permissible_segment_ends(std::string) –> void

set_segment_file_paths(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, segment_file_paths: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::pose_sewing::movers::SewAnythingAddMover::set_segment_file_paths(class utility::vector1<std::string, class std::allocator<std::string > >) –> 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.

show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) -> None
show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::pose_sewing::movers::SewAnythingAddMover::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.

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

Set the ‘type’ string

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

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_sewing.movers.SewAnythingAddMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator, : pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator) → pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator¶: C++: protocols::pose_sewing::movers::SewAnythingAddMoverCreator::operator=(const class protocols::pose_sewing::movers::SewAnythingAddMoverCreator &) –> class protocols::pose_sewing::movers::SewAnythingAddMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::pose_sewing::movers::SewAnythingAddMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator) → str¶: C++: protocols::pose_sewing::movers::SewAnythingAddMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::pose_sewing::movers::SewAnythingAddMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void