loop_modeler

• perturbers

Bindings for protocols::loop_modeler namespace

class pyrosetta.rosetta.protocols.loop_modeler.LoopModeler

Bases: pyrosetta.rosetta.protocols.loop_modeling.LoopMover

Attempt to find the native structure for one or more loops.

The typical loop modeling simulation in rosetta has three steps: loop building, centroid refinement, and fullatom refinement. LoopModeler carries out all three of these steps and allows each to to be enabled, disabled, and otherwise configured. By default, nothing needs to be specified and a standard loop modeling simulation will be performed.

Note that this class is a fairly thin wrapper around other LoopMovers. LoopBuilder and LoopProtocol in particular do all the heavy lifting. The main role of this class is actually to provide a reasonable set of default values, some nice tracer output, and a sophisticated parse_my_tag() method for use with rosetta scripts.

Note that LoopModeler doesn’t implement a proper copy constructor. (In fact, no LoopMover does.) This means that if a simulation breaks and nstruct > 1, the remaining simulations will probably break for weird reasons.

__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.

1. __init__(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) -> None
2. __init__(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, arg0: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) -> 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).

apply(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sample the pose in the regions specified by get_loops().

The parent class apply() method automatically sets up a fold tree (if necessary) and keeps track of whether or not the move succeeded. Child classes should reimplement do_apply() instead of this method.

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

assign(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, : pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → pyrosetta.rosetta.protocols.loop_modeler.LoopModeler

C++: protocols::loop_modeler::LoopModeler::operator=(const class protocols::loop_modeler::LoopModeler &) –> class protocols::loop_modeler::LoopModeler &

build_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → protocols::loop_modeling::LoopBuilder

Return a pointer to the build stage mover.

C++: protocols::loop_modeler::LoopModeler::build_stage() –> class std::shared_ptr<class protocols::loop_modeling::LoopBuilder>

centroid_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → protocols::loop_modeling::LoopProtocol

Return a pointer to the centroid stage mover.

C++: protocols::loop_modeler::LoopModeler::centroid_stage() –> class std::shared_ptr<class protocols::loop_modeling::LoopProtocol>

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.loop_modeler.LoopModeler) → pyrosetta.rosetta.protocols.moves.Mover

Return a shallow copy of this object.

C++: protocols::loop_modeler::LoopModeler::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>

define_composition_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition, ct_gen: pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator, subelements: pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList) → None

C++: protocols::loop_modeling::LoopMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &, class utility::tag::XMLSchemaComplexTypeGenerator &, class utility::tag::XMLSchemaSimpleSubelementList &) –> void

disable_build_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Disable the build stage.

C++: protocols::loop_modeler::LoopModeler::disable_build_stage() –> void

disable_centroid_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Disable the centroid stage.

C++: protocols::loop_modeler::LoopModeler::disable_centroid_stage() –> void

disable_fullatom_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Disable the fullatom stage.

C++: protocols::loop_modeler::LoopModeler::disable_fullatom_stage() –> void

enable_build_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Enable the build stage.

C++: protocols::loop_modeler::LoopModeler::enable_build_stage() –> void

enable_centroid_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Enable the centroid stage.

C++: protocols::loop_modeler::LoopModeler::enable_centroid_stage() –> void

enable_fullatom_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Enable the fullatom stage.

C++: protocols::loop_modeler::LoopModeler::enable_fullatom_stage() –> void

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

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

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

fullatom_stage(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → protocols::loop_modeling::LoopProtocol

Return a pointer to the fullatom stage mover.

C++: protocols::loop_modeler::LoopModeler::fullatom_stage() –> class std::shared_ptr<class protocols::loop_modeling::LoopProtocol>

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_children_names(*args, **kwargs)

Overloaded function.

1. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string) -> None
2. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string, indent: str) -> None

Add the names of all the algorithms invoked by this loop mover to

the given list. Indentation is used to represent hierarchy.

C++: protocols::loop_modeling::LoopMover::get_children_names(class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, class std::basic_string<char>) const –> void

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_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, index: int) → pyrosetta.rosetta.protocols.loops.Loop

Return the specified loop.

C++: protocols::loop_modeling::LoopMover::get_loop(unsigned long) const –> const class protocols::loops::Loop &

get_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loops.Loops

Return the loops to be sampled on the next call to apply().

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

get_name(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → str

C++: protocols::loop_modeler::LoopModeler::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_task_factory(*args, **kwargs)

Overloaded function.

1. get_task_factory(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) -> pyrosetta.rosetta.core.pack.task.TaskFactory

Get the task factory to be used on the next call to apply().

If no task factory has been set, this will raise an exception.

C++: protocols::loop_modeler::LoopModeler::get_task_factory() –> class std::shared_ptr<class core::pack::task::TaskFactory>

2. get_task_factory(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, fallback: pyrosetta.rosetta.core.pack.task.TaskFactory) -> pyrosetta.rosetta.core.pack.task.TaskFactory

Get the task factory to be used on the next call to apply().

If no task factory has been set, the fallback will be returned.

C++: protocols::loop_modeler::LoopModeler::get_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> class std::shared_ptr<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_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

mover_name() → str

C++: protocols::loop_modeler::LoopModeler::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::loop_modeler::LoopModeler::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

request_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest

Return an enum representing the kind of fold tree that is

compatible with this mover.

The FoldTreeRequest enum values can be combined using the bitwise logical operators. For example, you can request either the standard fold tree or a simple fold tree with FTR_LOOPS_WITH_CUTS | FTR_SIMPLE_TREE.

C++: protocols::loop_modeling::LoopMover::request_fold_tree() const –> enum protocols::loop_modeling::FoldTreeRequest

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

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

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

set_cen_scorefxn(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set the score function to be used for the centroid stage.

C++: protocols::loop_modeler::LoopModeler::set_cen_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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_fa_scorefxn(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set the score function to be used for the fullatom stage.

C++: protocols::loop_modeler::LoopModeler::set_fa_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

Set the loop to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loop(const class protocols::loops::Loop &) –> void

set_loops(*args, **kwargs)

Overloaded function.

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

Set the loops to be sampled on the next call to apply().

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

2. set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(const class protocols::loops::Loops &) –> 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_task_factory(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

Set the task factory to be used on the next call to apply().

C++: protocols::loop_modeler::LoopModeler::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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

setup_empty_config(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Setup the LoopModeler using a minimal configuration.

C++: protocols::loop_modeler::LoopModeler::setup_empty_config() –> void

setup_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops, request: pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest) → None

Setup the given pose with a fold tree that is compatible with the

given loops and requests.

C++: protocols::loop_modeling::LoopMover::setup_fold_tree(class core::pose::Pose &, class std::shared_ptr<const class protocols::loops::Loops>, enum protocols::loop_modeling::FoldTreeRequest) –> void

setup_kic_config(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Setup the LoopModeler using the “next-gen KIC” configuration.

C++: protocols::loop_modeler::LoopModeler::setup_kic_config() –> void

setup_kic_with_fragments_config(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler) → None

Setup the LoopModeler using the “KIC with fragments”

configuration.

C++: protocols::loop_modeler::LoopModeler::setup_kic_with_fragments_config() –> void

setup_loophash_kic_config(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, perturb_sequence: bool, seqposes_no_mutate_str: str) → None

Setup the LoopModeler using the LoopHashKIC configuration

C++: protocols::loop_modeler::LoopModeler::setup_loophash_kic_config(bool, class std::basic_string<char>) –> 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(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

trust_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → None

Promise that the calling code will setup a fold tree compatible

with request_fold_tree(). If this method is not called, this mover will setup a fold tree on its own every time apply() is called.

C++: protocols::loop_modeling::LoopMover::trust_fold_tree() –> void

type(*args, **kwargs)

Overloaded function.

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

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

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

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

was_successful(*args, **kwargs)

Overloaded function.

1. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) -> bool

Return true if the previous move was successful.

C++: protocols::loop_modeling::LoopMover::was_successful() const –> bool

2. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, value: bool) -> None

Set the success status of a loop mover

C++: protocols::loop_modeling::LoopMover::was_successful(bool) –> void