movers

Bindings for protocols::pose_sewing::movers namespace

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

Bases: pyrosetta.rosetta.protocols.moves.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.

  1. show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover) -> None

  2. 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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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.

  1. show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover) -> None

  2. 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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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.

  1. show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover) -> None

  2. 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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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.

  1. show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover) -> None

  2. 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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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_builtins.pybind11_object

property max_terminal_length_
property min_terminal_length_
class pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

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

align(*args, **kwargs)

Overloaded function.

  1. 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

  2. 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.

  1. show(self: pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover) -> None

  2. 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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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