refine

Bindings for protocols::loops::loop_mover::refine namespace

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub

Bases: LoopMover

add_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, fragset: pyrosetta.rosetta.core.fragment.FragSet) → None

add a fragment set

C++: protocols::loops::loop_mover::LoopMover::add_fragments(class std::shared_ptr<class core::fragment::FragSet>) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::operator=(const class protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub &) –> class protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub &

clear_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → None

clear the list of fragment sets

C++: protocols::loops::loop_mover::LoopMover::clear_fragments() –> void

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.loops.loop_mover.refine.LoopMover_Refine_Backrub) → pyrosetta.rosetta.protocols.moves.Mover

Clone this object

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::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>

false_movemap(*args, **kwargs)

Overloaded function.

1. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap() const –> const class std::shared_ptr<class core::kinematics::MoveMap> &

2. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap(const class std::shared_ptr<class core::kinematics::MoveMap> &) –> void

frag_libs(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t

C++: protocols::loops::loop_mover::LoopMover::frag_libs() const –> const class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > > &

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_checkpoints(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::loops::loop_mover::LoopMover::get_checkpoints() –> class std::shared_ptr<class protocols::checkpoint::CheckPointer> &

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.loops.loop_mover.refine.LoopMover_Refine_Backrub) → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::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_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) → bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::get_redesign_loop() –> bool

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

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

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

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

get_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) → bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::get_task_factory() –> bool

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

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

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

non-const accessor

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

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

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

loops(*args, **kwargs)

Overloaded function.

1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, lptr: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets

the GuardedLoopsFromFile object into a “not in charge” state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data.

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

2. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data: protocols::loops::LoopsFileData) -> None

Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).

C++: protocols::loops::loop_mover::LoopMover::loops(const class protocols::loops::LoopsFileData &) –> void

3. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, setting: protocols::loops::loops_definers::LoopsDefiner) -> None

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>) –> void

4. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops: protocols::loops::GuardedLoopsFromFile) -> None

Set the guarded_loops pointer

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::GuardedLoopsFromFile>) –> void

5. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.protocols.loops.Loops

non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this

before apply() has been called.

C++: protocols::loops::loop_mover::LoopMover::loops() –> class std::shared_ptr<class protocols::loops::Loops>

static mover_name() → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::mover_name() –> std::string

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

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::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

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::LoopMover::scorefxn() const –> 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_default_settings(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::set_default_settings() –> void

set_extended_torsions(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

Extend a loop

C++: protocols::loops::loop_mover::LoopMover::set_extended_torsions(class core::pose::Pose &, const class protocols::loops::Loop &) –> void

set_guarded_loops_not_in_charge(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → None

Inform the GuardedLoopsFromFile object that it is not in charge of

updating its Loops object at the beginning of apply()

C++: protocols::loops::loop_mover::LoopMover::set_guarded_loops_not_in_charge() –> 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_redesign_loop(*args, **kwargs)

Overloaded function.

1. set_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> None

2. set_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub, value: bool) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::set_redesign_loop(bool) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, score_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::LoopMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub, value: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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

torsion_features_string(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin

create a string representing the torsion bins (ABEGX) for the loops defined in the

guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there’s only one Loop object in the guarded_loops_ object).

C++: protocols::loops::loop_mover::LoopMover::torsion_features_string(const class core::pose::Pose &) const –> class utility::vector0<enum core::conformation::ppo_torsion_bin, class std::allocator<enum core::conformation::ppo_torsion_bin> >

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.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator

Bases: MoverCreator

creator for the LoopMover_Refine_BackrubCreator class

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator::operator=(const class protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator &) –> class protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator) → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD

Bases: LoopMover

add_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, fragset: pyrosetta.rosetta.core.fragment.FragSet) → None

add a fragment set

C++: protocols::loops::loop_mover::LoopMover::add_fragments(class std::shared_ptr<class core::fragment::FragSet>) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::operator=(const class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD &) –> class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD &

clear_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → None

clear the list of fragment sets

C++: protocols::loops::loop_mover::LoopMover::clear_fragments() –> void

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.loops.loop_mover.refine.LoopMover_Refine_CCD) → pyrosetta.rosetta.protocols.moves.Mover

Clone this object

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::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>

current_cycle_number(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → int

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::current_cycle_number() const –> unsigned long

false_movemap(*args, **kwargs)

Overloaded function.

1. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap() const –> const class std::shared_ptr<class core::kinematics::MoveMap> &

2. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap(const class std::shared_ptr<class core::kinematics::MoveMap> &) –> void

flank_residue_min(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::flank_residue_min() const –> bool

frag_libs(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t

C++: protocols::loops::loop_mover::LoopMover::frag_libs() const –> const class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > > &

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_checkpoints(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::loops::loop_mover::LoopMover::get_checkpoints() –> class std::shared_ptr<class protocols::checkpoint::CheckPointer> &

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_loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_loops() const –> class std::shared_ptr<const class protocols::loops::Loops>

get_name(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::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_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_redesign_loop() –> bool

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

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

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

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

get_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

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 > > &

inner_cycles(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → int

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::inner_cycles() const –> unsigned long

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

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

loops(*args, **kwargs)

Overloaded function.

1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, lptr: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets

the GuardedLoopsFromFile object into a “not in charge” state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data.

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

2. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data: protocols::loops::LoopsFileData) -> None

Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).

C++: protocols::loops::loop_mover::LoopMover::loops(const class protocols::loops::LoopsFileData &) –> void

3. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, setting: protocols::loops::loops_definers::LoopsDefiner) -> None

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>) –> void

4. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops: protocols::loops::GuardedLoopsFromFile) -> None

Set the guarded_loops pointer

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::GuardedLoopsFromFile>) –> void

5. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.protocols.loops.Loops

non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this

before apply() has been called.

C++: protocols::loops::loop_mover::LoopMover::loops() –> class std::shared_ptr<class protocols::loops::Loops>

max_inner_cycles(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value: int) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::max_inner_cycles(unsigned long) –> void

move_map(*args, **kwargs)

Overloaded function.

1. move_map(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map() const –> class std::shared_ptr<class core::kinematics::MoveMap>

2. move_map(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

static mover_name() → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::mover_name() –> std::string

static name() → str

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

outer_cycles(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value: int) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::outer_cycles(unsigned long) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::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::loops::loop_mover::refine::LoopMover_Refine_CCD::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

repack_neighbors(*args, **kwargs)

Overloaded function.

1. repack_neighbors(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, s: bool) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_neighbors(bool) –> void

2. repack_neighbors(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_neighbors() const –> bool

repack_period(*args, **kwargs)

Overloaded function.

1. repack_period(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value: int) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period(unsigned long) –> void

2. repack_period(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> int

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period() const –> unsigned long

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.loops.loop_mover.LoopMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::LoopMover::scorefxn() const –> 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_default_settings(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_default_settings() –> void

set_extended_torsions(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

Extend a loop

C++: protocols::loops::loop_mover::LoopMover::set_extended_torsions(class core::pose::Pose &, const class protocols::loops::Loop &) –> void

set_flank_residue_min(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value: bool) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_flank_residue_min(bool) –> void

set_fold_tree_from_loops(*args, **kwargs)

Overloaded function.

1. set_fold_tree_from_loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, s: bool) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops(const bool) –> void

2. set_fold_tree_from_loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops() const –> bool

set_guarded_loops_not_in_charge(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → None

Inform the GuardedLoopsFromFile object that it is not in charge of

updating its Loops object at the beginning of apply()

C++: protocols::loops::loop_mover::LoopMover::set_guarded_loops_not_in_charge() –> 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_redesign_loop(*args, **kwargs)

Overloaded function.

1. set_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> None

2. set_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value: bool) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop(bool) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, score_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::LoopMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, task_factory_in: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops, allow_repack: pyrosetta.rosetta.utility.vector1_bool, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

setup an appropriate movemap for the given loops

The loops to model.

Indicates whether or not to allow a position to

repack.

Output movemap, all settings added here.

will enforce the false movemap

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(const class core::pose::Pose &, const class protocols::loops::Loops &, const class utility::vector1<bool, class std::allocator<bool> > &, class std::shared_ptr<class core::kinematics::MoveMap> &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> None

2. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::show(std::ostream &) const –> void

temp_final(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value: float) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final(double) –> void

temp_initial(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value: float) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial(double) –> 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

torsion_features_string(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin

create a string representing the torsion bins (ABEGX) for the loops defined in the

guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there’s only one Loop object in the guarded_loops_ object).

C++: protocols::loops::loop_mover::LoopMover::torsion_features_string(const class core::pose::Pose &) const –> class utility::vector0<enum core::conformation::ppo_torsion_bin, class std::allocator<enum core::conformation::ppo_torsion_bin> >

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.loops.loop_mover.refine.LoopMover_Refine_CCDCreator

Bases: MoverCreator

creator for the LoopMover_Refine_CCDCreator class

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator::operator=(const class protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator &) –> class protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator) → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC

Bases: LoopMover

add_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, fragset: pyrosetta.rosetta.core.fragment.FragSet) → None

add a fragment set

C++: protocols::loops::loop_mover::LoopMover::add_fragments(class std::shared_ptr<class core::fragment::FragSet>) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::operator=(const class protocols::loops::loop_mover::refine::LoopMover_Refine_KIC &) –> class protocols::loops::loop_mover::refine::LoopMover_Refine_KIC &

clear_fragments(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → None

clear the list of fragment sets

C++: protocols::loops::loop_mover::LoopMover::clear_fragments() –> void

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.loops.loop_mover.refine.LoopMover_Refine_KIC) → pyrosetta.rosetta.protocols.moves.Mover

Clone this object

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::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>

false_movemap(*args, **kwargs)

Overloaded function.

1. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap() const –> const class std::shared_ptr<class core::kinematics::MoveMap> &

2. false_movemap(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

explicit False settings in this MoveMap will override any

automatically generated MoveMap settings during the loop modeling protocol

C++: protocols::loops::loop_mover::LoopMover::false_movemap(const class std::shared_ptr<class core::kinematics::MoveMap> &) –> void

frag_libs(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t

C++: protocols::loops::loop_mover::LoopMover::frag_libs() const –> const class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > > &

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_checkpoints(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::loops::loop_mover::LoopMover::get_checkpoints() –> class std::shared_ptr<class protocols::checkpoint::CheckPointer> &

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.loops.loop_mover.refine.LoopMover_Refine_KIC) → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::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_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) → bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_redesign_loop() –> bool

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

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

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

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

get_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) → bool

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_task_factory() –> bool

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

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

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

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::init(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

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

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

loops(*args, **kwargs)

Overloaded function.

1. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, lptr: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets

the GuardedLoopsFromFile object into a “not in charge” state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data.

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

2. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data: protocols::loops::LoopsFileData) -> None

Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).

C++: protocols::loops::loop_mover::LoopMover::loops(const class protocols::loops::LoopsFileData &) –> void

3. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, setting: protocols::loops::loops_definers::LoopsDefiner) -> None

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::loops_definers::LoopsDefiner>) –> void

4. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops: protocols::loops::GuardedLoopsFromFile) -> None

Set the guarded_loops pointer

C++: protocols::loops::loop_mover::LoopMover::loops(class std::shared_ptr<class protocols::loops::GuardedLoopsFromFile>) –> void

5. loops(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> pyrosetta.rosetta.protocols.loops.Loops

non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this

before apply() has been called.

C++: protocols::loops::loop_mover::LoopMover::loops() –> class std::shared_ptr<class protocols::loops::Loops>

static mover_name() → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::mover_name() –> std::string

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

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::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

scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::LoopMover::scorefxn() const –> 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_default_settings(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_default_settings() –> void

set_extended_torsions(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

Extend a loop

C++: protocols::loops::loop_mover::LoopMover::set_extended_torsions(class core::pose::Pose &, const class protocols::loops::Loop &) –> void

set_flank_residue_min(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, value: bool) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_flank_residue_min(bool) –> void

set_guarded_loops_not_in_charge(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → None

Inform the GuardedLoopsFromFile object that it is not in charge of

updating its Loops object at the beginning of apply()

C++: protocols::loops::loop_mover::LoopMover::set_guarded_loops_not_in_charge() –> 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_movemap_from_kic_segment(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose: pyrosetta.rosetta.core.pose.Pose, cur_mm: pyrosetta.rosetta.core.kinematics.MoveMap, kic_start: int, kic_end: int) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment(class core::pose::Pose &, class core::kinematics::MoveMap &, unsigned long, 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_redesign_loop(*args, **kwargs)

Overloaded function.

1. set_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> None

2. set_redesign_loop(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, value: bool) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop(bool) –> void

set_rottrials_from_kic_segment(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose: pyrosetta.rosetta.core.pose.Pose, rottrials_packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, kic_start: int, kic_end: int) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_rottrials_from_kic_segment(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask> &, unsigned long, unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, score_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::LoopMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, value: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.loops.loop_mover.refine.LoopMover_Refine_KIC) -> None

2. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::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

torsion_features_string(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin

create a string representing the torsion bins (ABEGX) for the loops defined in the

guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there’s only one Loop object in the guarded_loops_ object).

C++: protocols::loops::loop_mover::LoopMover::torsion_features_string(const class core::pose::Pose &) const –> class utility::vector0<enum core::conformation::ppo_torsion_bin, class std::allocator<enum core::conformation::ppo_torsion_bin> >

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 &

update_allow_sc_vectors(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose: pyrosetta.rosetta.core.pose.Pose, allow_sc_vectors: pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) → None

update the vector of vectors of moveable side-chain positions, one for each loop in loops_

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_allow_sc_vectors(class core::pose::Pose &, class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > > &) –> void

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator

Bases: MoverCreator

creator for the LoopMover_Perturb_KICCreator class

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator::operator=(const class protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator &) –> class protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator) → str

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, rhs: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::operator=(const class protocols::loops::loop_mover::refine::LoopRefineInnerCycle &) –> class protocols::loops::loop_mover::refine::LoopRefineInnerCycle &

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>

debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → bool

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug() const –> bool

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.loops.loop_mover.refine.LoopRefineInnerCycle) → str

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::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

loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover() const –> class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>

mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc() const –> class std::shared_ptr<class protocols::moves::MonteCarlo>

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

Associates relevant options with the LoopRefineInnerCycle class

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::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.loops.loop_mover.refine.LoopRefineInnerCycle) → bool

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::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.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn() 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_debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug: bool) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_debug(bool) –> 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_loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town: pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_loop_mover(class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>) –> void

set_mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.loops.loop_mover.refine.LoopRefineInnerCycle) -> None

2. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

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.loops.loop_mover.refine.LoopRefineInnerCycleContainer

Bases: LoopRefineInnerCycle

add_inner_cycle_step(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, inner_cycle_step: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::add_inner_cycle_step(class std::shared_ptr<class protocols::loops::loop_mover::refine::LoopRefineInnerCycle>) –> void

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, rhs: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::operator=(const class protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer &) –> class protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer &

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.loops.loop_mover.refine.LoopRefineInnerCycleContainer) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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>

debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → bool

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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.loops.loop_mover.refine.LoopRefineInnerCycleContainer) → str

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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

loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover() const –> class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>

mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc() const –> class std::shared_ptr<class protocols::moves::MonteCarlo>

static mover_name() → str

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::mover_name() –> std::string

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

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Associates relevant options with the LoopRefineInnerCycleContainer class

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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.loops.loop_mover.refine.LoopRefineInnerCycleContainer) → bool

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::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.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn() 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_debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug: bool) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_debug(bool) –> 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_loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, new_owner_in_town: pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_loop_mover(class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>) –> void

set_mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> None

2. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

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.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator

Bases: MoverCreator

creator for the LoopRefineInnerCycleContainer class

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator::operator=(const class protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator &) –> class protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator) → str

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory

Bases: SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t

Create LoopMover Reporters

create_inner_cycle(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory, type_name: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName, loop_mover: pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle

Create a LoopRefineInnerCycle giving it a pointer to the data it needs to function

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory::create_inner_cycle(enum protocols::loops::loop_mover::refine::LoopRefineInnerCycleName, class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>, class std::shared_ptr<class protocols::moves::MonteCarlo>, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::pack::task::TaskFactory>) const –> class std::shared_ptr<class protocols::loops::loop_mover::refine::LoopRefineInnerCycle>

static get_instance() → protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory

C++: utility::SingletonBase<protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory>::get_instance() –> class protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory *

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName

Bases: pybind11_object

Members:

IC_SmallMinCCDTrial

IC_ShearMinCCDTrial

IC_RepackTrial

IC_RefineCCDStandard

number_of_loop_refine_inner_cycle_names

IC_RefineCCDStandard = <LoopRefineInnerCycleName.IC_RefineCCDStandard: 4>

IC_RepackTrial = <LoopRefineInnerCycleName.IC_RepackTrial: 3>

IC_ShearMinCCDTrial = <LoopRefineInnerCycleName.IC_ShearMinCCDTrial: 2>

IC_SmallMinCCDTrial = <LoopRefineInnerCycleName.IC_SmallMinCCDTrial: 1>

property name

number_of_loop_refine_inner_cycle_names = <LoopRefineInnerCycleName.IC_RefineCCDStandard: 4>

property value

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial

Bases: LoopRefineInnerCycle

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::RepackTrial::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial, rhs: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial

C++: protocols::loops::loop_mover::refine::RepackTrial::operator=(const class protocols::loops::loop_mover::refine::RepackTrial &) –> class protocols::loops::loop_mover::refine::RepackTrial &

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.loops.loop_mover.refine.RepackTrial) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::RepackTrial::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>

debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → bool

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::RepackTrial::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.loops.loop_mover.refine.RepackTrial) → str

C++: protocols::loops::loop_mover::refine::RepackTrial::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

loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover() const –> class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>

mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc() const –> class std::shared_ptr<class protocols::moves::MonteCarlo>

static mover_name() → str

C++: protocols::loops::loop_mover::refine::RepackTrial::mover_name() –> std::string

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

C++: protocols::loops::loop_mover::refine::RepackTrial::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Associates relevant options with the LoopRefineInnerCycle class

C++: protocols::loops::loop_mover::refine::RepackTrial::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.loops.loop_mover.refine.RepackTrial) → bool

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::loops::loop_mover::refine::RepackTrial::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.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn() 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_debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug: bool) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_debug(bool) –> 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_loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town: pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_loop_mover(class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>) –> void

set_mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.loops.loop_mover.refine.RepackTrial) -> None

2. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_mover::refine::RepackTrial::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

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.loops.loop_mover.refine.RepackTrialCreator

Bases: MoverCreator

creator for the RepackTrial class

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator

C++: protocols::loops::loop_mover::refine::RepackTrialCreator::operator=(const class protocols::loops::loop_mover::refine::RepackTrialCreator &) –> class protocols::loops::loop_mover::refine::RepackTrialCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::RepackTrialCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator) → str

C++: protocols::loops::loop_mover::refine::RepackTrialCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::loops::loop_mover::refine::RepackTrialCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial

Bases: LoopRefineInnerCycle

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial, rhs: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::operator=(const class protocols::loops::loop_mover::refine::ShearMinCCDTrial &) –> class protocols::loops::loop_mover::refine::ShearMinCCDTrial &

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.loops.loop_mover.refine.ShearMinCCDTrial) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::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>

debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → bool

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::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.loops.loop_mover.refine.ShearMinCCDTrial) → str

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::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

loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover() const –> class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>

mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc() const –> class std::shared_ptr<class protocols::moves::MonteCarlo>

static mover_name() → str

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::mover_name() –> std::string

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

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Associates relevant options with the LoopRefineInnerCycle class

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::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.loops.loop_mover.refine.ShearMinCCDTrial) → bool

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::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.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn() 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_debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug: bool) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_debug(bool) –> 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_loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town: pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_loop_mover(class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>) –> void

set_mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.loops.loop_mover.refine.ShearMinCCDTrial) -> None

2. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrial::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

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.loops.loop_mover.refine.ShearMinCCDTrialCreator

Bases: MoverCreator

creator for the ShearMinCCDTrial class

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator::operator=(const class protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator &) –> class protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator) → str

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial

Bases: LoopRefineInnerCycle

apply(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, rhs: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::operator=(const class protocols::loops::loop_mover::refine::SmallMinCCDTrial &) –> class protocols::loops::loop_mover::refine::SmallMinCCDTrial &

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.loops.loop_mover.refine.SmallMinCCDTrial) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::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>

debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → bool

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::debug() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::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.loops.loop_mover.refine.SmallMinCCDTrial) → str

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::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

loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::loop_mover() const –> class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>

mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::mc() const –> class std::shared_ptr<class protocols::moves::MonteCarlo>

minimizer_options(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) → pyrosetta.rosetta.core.optimization.MinimizerOptions

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::minimizer_options() const –> class std::shared_ptr<class core::optimization::MinimizerOptions>

static mover_name() → str

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::mover_name() –> std::string

static name() → str

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

number_of_moves(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) → int

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::number_of_moves() const –> unsigned long

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

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Associates relevant options with the LoopRefineInnerCycle class

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::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.loops.loop_mover.refine.SmallMinCCDTrial) → bool

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::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.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::scorefxn() 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_debug(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug: bool) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_debug(bool) –> 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_loop_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town: pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_loop_mover(class std::weak_ptr<class protocols::loops::loop_mover::refine::LoopMover_Refine_CCD>) –> void

set_mc(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_minimizer_options(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, minimizer_options: pyrosetta.rosetta.core.optimization.MinimizerOptions) → None

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::set_minimizer_options(class std::shared_ptr<class core::optimization::MinimizerOptions>) –> 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_number_of_moves(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, nmoves: int) → None

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::set_number_of_moves(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.loops.loop_mover.refine.SmallMinCCDTrial) -> None

2. show(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrial::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::loops::loop_mover::refine::LoopRefineInnerCycle::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

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.loops.loop_mover.refine.SmallMinCCDTrialCreator

Bases: MoverCreator

creator for the SmallMinCCDTrial class

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator, : pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator) → pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator::operator=(const class protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator &) –> class protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator &

create_mover(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator) → str

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void