loop_mover¶

Bindings for protocols::loops::loop_mover namespace

class pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

The loop-rebuild protocol

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> None
__init__(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, loops_in: pyrosetta.rosetta.protocols.loops.Loops) -> None
__init__(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, loops_from_file: protocols::loops::LoopsFileData) -> None
__init__(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops: protocols::loops::GuardedLoopsFromFile) -> None
__init__(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, arg0: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.LoopMover, : pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the loop-build protocol to the input pose

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

assign(self: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover, rhs: pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover) → pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover¶

assignment operator

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

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.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>

false_movemap(*args, **kwargs)¶

Overloaded function.

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> &

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.

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.LoopMover) → str¶: C++: protocols::loops::loop_mover::LoopMover::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_std_allocator_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.

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

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

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

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>

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

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¶

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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_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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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(class std::basic_ostream<char> &) 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.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.loops.loop_mover.loops_set_chainbreak_weight(*args, **kwargs)¶

Overloaded function.

loops_set_chainbreak_weight(scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
loops_set_chainbreak_weight(scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, round: int) -> None

C++: protocols::loops::loop_mover::loops_set_chainbreak_weight(class std::shared_ptr<class core::scoring::ScoreFunction>, const unsigned long) –> void