loop_modeler¶

perturbers

Bindings for protocols::loop_modeler namespace

class pyrosetta.rosetta.protocols.loop_modeler.LoopModeler¶

Bases: 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.

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>

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition, ct_gen: utility::tag::XMLSchemaComplexTypeGenerator, subelements: 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.

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_children_names(*args, **kwargs)¶

Overloaded function.

get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string) -> None
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<std::string, class std::allocator<std::string > > &, std::string) 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_default_task_factory(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pack.task.TaskFactory¶

Return a default task factory

C++: protocols::loop_modeler::LoopModeler::get_default_task_factory(class core::pose::Pose &) –> class std::shared_ptr<class core::pack::task::TaskFactory>

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.

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>

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_t¶

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::loop_modeler::LoopModeler::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModeler, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

LoopMover::parse_my_tag

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

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¶: 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_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.

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

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¶

Set the ‘type’ string

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

static 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, std::string) –> 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(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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

was_successful(*args, **kwargs)¶

Overloaded function.

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

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

class pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator, : pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator) → pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator¶: C++: protocols::loop_modeler::LoopModelerCreator::operator=(const class protocols::loop_modeler::LoopModelerCreator &) –> class protocols::loop_modeler::LoopModelerCreator &

create_mover(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::loop_modeler::LoopModelerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator) → str¶: C++: protocols::loop_modeler::LoopModelerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::loop_modeler::LoopModelerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void