movers

Bindings for protocols::rna::movers namespace

class pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol

Bases: Mover

Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job

apply(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol, pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the mover

C++: protocols::rna::movers::ERRASER2Protocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol, : pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol) → pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol

C++: protocols::rna::movers::ERRASER2Protocol::operator=(const class protocols::rna::movers::ERRASER2Protocol &) –> class protocols::rna::movers::ERRASER2Protocol &

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::rna::movers::ERRASER2Protocol::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

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

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

fresh_instance(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::rna::movers::ERRASER2Protocol::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.rna.movers.ERRASER2Protocol) → str

C++: protocols::rna::movers::ERRASER2Protocol::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::rna::movers::ERRASER2Protocol::mover_name() –> std::string

n_rounds(*args, **kwargs)

Overloaded function.

1. n_rounds(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol, n_rounds: int) -> None

C++: protocols::rna::movers::ERRASER2Protocol::n_rounds(const unsigned long) –> void

2. n_rounds(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol) -> int

C++: protocols::rna::movers::ERRASER2Protocol::n_rounds() const –> unsigned long

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol, 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::rna::movers::ERRASER2Protocol::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::rna::movers::ERRASER2Protocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

rebuild_residue_selector(*args, **kwargs)

Overloaded function.

1. rebuild_residue_selector(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol, residue_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

2. rebuild_residue_selector(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

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

score_function(*args, **kwargs)

Overloaded function.

1. score_function(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::rna::movers::ERRASER2Protocol::score_function(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

2. score_function(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::rna::movers::ERRASER2Protocol::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.rna.movers.ERRASER2Protocol) -> None

2. show(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::rna::movers::ERRASER2Protocol::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator, : pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator) → pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator

C++: protocols::rna::movers::ERRASER2ProtocolCreator::operator=(const class protocols::rna::movers::ERRASER2ProtocolCreator &) –> class protocols::rna::movers::ERRASER2ProtocolCreator &

create_mover(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rna::movers::ERRASER2ProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator) → str

C++: protocols::rna::movers::ERRASER2ProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::rna::movers::ERRASER2ProtocolCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover

Bases: Mover

add_fixed_res_constraints(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, pose: pyrosetta.rosetta.core.pose.Pose, fixed_res_num: int, my_anchor: int) → None

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

add_virtual_res(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(class core::pose::Pose &) –> int

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

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

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

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

constrain_phosphate(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, setting: bool) → None

C++: protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate(const bool) –> void

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

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

edens_scorefxn(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

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

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

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

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

fpd

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

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

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

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

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

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

A tag is a unique identifier used to identify structures produced

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

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

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

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

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

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

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

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

C++: protocols::rna::movers::ErraserMinimizerMover::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

i_want_this_atom_to_move(*args, **kwargs)

Overloaded function.

1. i_want_this_atom_to_move(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, residue_type: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) -> bool

C++: protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(const class core::chemical::ResidueType &, const unsigned long &) –> bool

2. i_want_this_atom_to_move(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, pose: pyrosetta.rosetta.core.pose.Pose, atom_id: pyrosetta.rosetta.core.id.AtomID) -> bool

C++: protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(const class core::pose::Pose &, const class core::id::AtomID &) –> bool

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 > > &

initialize_from_options(*args, **kwargs)

Overloaded function.

1. initialize_from_options(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, options: pyrosetta.rosetta.utility.options.OptionCollection) -> None

2. initialize_from_options(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, options: pyrosetta.rosetta.utility.options.OptionCollection, initialize_scorefxn: bool) -> None

C++: protocols::rna::movers::ErraserMinimizerMover::initialize_from_options(const class utility::options::OptionCollection &, const bool) –> void

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

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

minimize_protein(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, setting: bool) → None

C++: protocols::rna::movers::ErraserMinimizerMover::minimize_protein(const bool) –> void

movemap_setup(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, pose: pyrosetta.rosetta.core.pose.Pose, cut_upper: pyrosetta.rosetta.std.set_unsigned_long_t, cut_lower: pyrosetta.rosetta.std.set_unsigned_long_t, allow_insert: pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::rna::movers::ErraserMinimizerMover::movemap_setup(class core::pose::Pose &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, class ObjexxFCL::FArray1D<bool> &) –> class core::kinematics::MoveMap

static mover_name() → str

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

static name() → str

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

nproc(*args, **kwargs)

Overloaded function.

1. nproc(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, nproc: int) -> None

C++: protocols::rna::movers::ErraserMinimizerMover::nproc(const int) –> void

2. nproc(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover) -> int

C++: protocols::rna::movers::ErraserMinimizerMover::nproc() const –> int

nstruct(*args, **kwargs)

Overloaded function.

1. nstruct(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, nstruct: int) -> None

C++: protocols::rna::movers::ErraserMinimizerMover::nstruct(const unsigned long) –> void

2. nstruct(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover) -> int

C++: protocols::rna::movers::ErraserMinimizerMover::nstruct() –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

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

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

C++: protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(class core::pose::Pose &) –> 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::rna::movers::ErraserMinimizerMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

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

rank(*args, **kwargs)

Overloaded function.

1. rank(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, rank: int) -> None

C++: protocols::rna::movers::ErraserMinimizerMover::rank(const int) –> void

2. rank(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover) -> int

C++: protocols::rna::movers::ErraserMinimizerMover::rank() const –> int

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

scorefxn(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::rna::movers::ErraserMinimizerMover::scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> 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

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

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

turn_off_for_chunks(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, chunk: pyrosetta.rosetta.std.set_unsigned_long_t) → None

C++: protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks(class core::kinematics::MoveMap &, const class core::pose::Pose &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

vary_bond_geometry(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, allow_insert: pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t, chunk: pyrosetta.rosetta.std.set_unsigned_long_t) → None

C++: protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(class core::kinematics::MoveMap &, class core::pose::Pose &, class ObjexxFCL::FArray1D<bool> &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

work_partition(*args, **kwargs)

Overloaded function.

1. work_partition(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover, work_partition: bool) -> None

C++: protocols::rna::movers::ErraserMinimizerMover::work_partition(const bool) –> void

2. work_partition(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover) -> int

C++: protocols::rna::movers::ErraserMinimizerMover::work_partition() const –> int

class pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator

Bases: MoverCreator

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

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

create_mover(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator) → str

C++: protocols::rna::movers::ErraserMinimizerMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

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

Bases: Mover

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

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

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

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

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

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

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

clear_info is called by jd2 before calling apply

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

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

required in the context of the parser/scripting scheme

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

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

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

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

required in the context of the parser/scripting scheme

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_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::rna::movers::RNAIdealizeMover::mover_name() –> std::string

static name() → str

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

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

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

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

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

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

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

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.rna.movers.RNAIdealizeMover) -> None

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

C++: protocols::rna::movers::RNAIdealizeMover::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator

Bases: MoverCreator

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

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

create_mover(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator) → str

C++: protocols::rna::movers::RNAIdealizeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

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

Bases: Mover

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

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

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

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

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

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

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

static class_name() → str

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

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

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

clear_info is called by jd2 before calling apply

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

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

required in the context of the parser/scripting scheme

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

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

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

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

required in the context of the parser/scripting scheme

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

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

fpd

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

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.rna.movers.RNAThreadAndMinimizeMover) → str

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

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

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

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

mm_from_residues(*args, **kwargs)

Overloaded function.

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

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

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

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

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

static name() → str

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

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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover, 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::rna::movers::RNAThreadAndMinimizeMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

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

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

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

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 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

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

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

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

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover) -> None

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

C++: protocols::rna::movers::RNAThreadAndMinimizeMover::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator

Bases: MoverCreator

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

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

create_mover(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator) → str

C++: protocols::rna::movers::RNAThreadAndMinimizeMoverCreator::keyname() const –> std::string

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

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify

Bases: Mover

Make a fullatom RNA pose into a coarse representation.

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

Apply the mover

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

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

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

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

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

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

required in the context of the parser/scripting scheme

C++: protocols::rna::movers::RNA_Coarsify::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.rna.movers.RNA_Coarsify) → str

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify, 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::rna::movers::RNA_Coarsify::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::rna::movers::RNA_Coarsify::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.rna.movers.RNA_Coarsify) -> None

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

C++: protocols::rna::movers::RNA_Coarsify::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator

Bases: MoverCreator

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

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

create_mover(self: pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator) → str

C++: protocols::rna::movers::RNA_CoarsifyCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer

Bases: Mover

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

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

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

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

cycles(self: pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer) → int

C++: protocols::rna::movers::RNA_DeNovoOptimizer::cycles() const –> unsigned long

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

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

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

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

fpd

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

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

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

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

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

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

A tag is a unique identifier used to identify structures produced

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

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

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

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

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

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

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

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

C++: protocols::rna::movers::RNA_DeNovoOptimizer::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 name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

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 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

rna_fragment_monte_carlo(self: pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer) → pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo

C++: protocols::rna::movers::RNA_DeNovoOptimizer::rna_fragment_monte_carlo() const –> class std::shared_ptr<const class protocols::rna::denovo::RNA_FragmentMonteCarlo>

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_cycles(self: pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer, setting: int) → None

C++: protocols::rna::movers::RNA_DeNovoOptimizer::set_cycles(const unsigned long &) –> void

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify

Bases: Mover

Make a coarse RNA pose into a fullatom representation.

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

Apply the mover

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

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

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

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

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

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

required in the context of the parser/scripting scheme

C++: protocols::rna::movers::RNA_Decoarsify::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.rna.movers.RNA_Decoarsify) → str

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify, 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::rna::movers::RNA_Decoarsify::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::rna::movers::RNA_Decoarsify::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.rna.movers.RNA_Decoarsify) -> None

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

C++: protocols::rna::movers::RNA_Decoarsify::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator

Bases: MoverCreator

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

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

create_mover(self: pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator) → str

C++: protocols::rna::movers::RNA_DecoarsifyCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

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

Bases: Mover

The RNA de novo structure modeling protocol

apply(*args, **kwargs)

Overloaded function.

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

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

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

Apply the loop-rebuild protocol to the input pose

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

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

Apply the loop-rebuild protocol to the input pose

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

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

Apply the loop-rebuild protocol to the input pose

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

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

Apply the loop-rebuild protocol to the input pose

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

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

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

check_closure(*args, **kwargs)

Overloaded function.

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

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

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

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

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

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

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser) → pyrosetta.rosetta.protocols.moves.Mover

Clone this object

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

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

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

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

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

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

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

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

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

fpd

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

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_cutpoints_closed(self: pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_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 name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

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 register_options() → None

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

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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