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

#include <LoopModeler.hh>

Inheritance diagram for protocols::loop_modeler::LoopModeler:

Public Member Functions
	LoopModeler ()
	Default constructor. More...

	~LoopModeler () override
	Default destructor. More...

moves::MoverOP	clone () const override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override

void	setup_empty_config ()
	Setup the LoopModeler using a minimal configuration. More...

void	setup_kic_config ()
	Setup the LoopModeler using the "next-gen KIC" configuration. More...

void	setup_kic_with_fragments_config ()
	Setup the LoopModeler using the "KIC with fragments" configuration. More...

void	setup_loophash_kic_config (bool perturb_sequence, std::string seqposes_no_mutate_str)
	Setup the LoopModeler using the LoopHashKIC configuration. More...

loop_modeling::LoopBuilderOP	build_stage ()
	Return a pointer to the build stage mover. More...

loop_modeling::LoopProtocolOP	centroid_stage ()
	Return a pointer to the centroid stage mover. More...

loop_modeling::LoopProtocolOP	fullatom_stage ()
	Return a pointer to the fullatom stage mover. More...

void	enable_build_stage ()
	Enable the build stage. More...

void	disable_build_stage ()
	Disable the build stage. More...

void	enable_centroid_stage ()
	Enable the centroid stage. More...

void	disable_centroid_stage ()
	Disable the centroid stage. More...

void	enable_fullatom_stage ()
	Enable the fullatom stage. More...

void	disable_fullatom_stage ()
	Disable the fullatom stage. More...

core::pack::task::TaskFactoryOP	get_task_factory ()
	Get the task factory to be used on the next call to apply(). More...

core::pack::task::TaskFactoryOP	get_task_factory (core::pack::task::TaskFactoryOP fallback)
	Get the task factory to be used on the next call to apply(). More...

void	set_task_factory (core::pack::task::TaskFactoryOP task_factory)
	Set the task factory to be used on the next call to apply(). More...

core::pack::task::TaskFactoryOP	get_default_task_factory (core::pose::Pose &pose)
	Return a default task factory. More...

void	set_fa_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
	Set the score function to be used for the fullatom stage. More...

void	set_cen_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
	Set the score function to be used for the centroid stage. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::loop_modeling::LoopMover
	LoopMover ()
	Default constructor. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Configure from a RosettaScripts tag. More...

void	apply (Pose &pose) override
	Sample the pose in the regions specified by get_loops(). More...

string	get_name () const override
	Return the name of this mover. More...

virtual void	get_children_names (utility::vector1< std::string > &names, std::string indent="") const
	Add the names of all the algorithms invoked by this loop mover to the given list. Indentation is used to represent hierarchy. More...

bool	was_successful () const
	Return true if the previous move was successful. More...

void	was_successful (bool value)
	Set the success status of a loop mover. More...

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

LoopsCOP	get_loops () const
	Return the loops to be sampled on the next call to apply(). More...

Loop const &	get_loop (core::Size index) const
	Return the specified loop. More...

void	set_loops (LoopsOP loops)
	Set the loops to be sampled on the next call to apply(). More...

void	set_loops (Loops const &loops)
	Set the loops to be sampled on the next call to apply(). More...

void	set_loop (Loop const &loop)
	Set the loop to be sampled on the next call to apply(). More...

template<typename ToolTypeOP >
ToolTypeOP	get_tool (std::string key) const
	Request a tool from this mover or any of its parents. More...

template<typename ToolTypeOP >
ToolTypeOP	get_tool (std::string key, ToolTypeOP fallback) const
	Request a tool from this mover or any of its parents. More...

template<typename ToolTypeOP >
ToolTypeOP	set_tool (std::string key, ToolTypeOP value)
	Provide a tool for this mover or any of its children to use. More...

virtual FoldTreeRequest	request_fold_tree () const
	Return an enum representing the kind of fold tree that is compatible with this mover. More...

void	trust_fold_tree ()
	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. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	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). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	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. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	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. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	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. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::loop_modeling::LoopMover
static void	setup_fold_tree (Pose &pose, LoopsCOP loops, FoldTreeRequest request)
	Setup the given pose with a fold tree that is compatible with the given loops and requests. More...

static void	define_composition_schema (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen, utility::tag::XMLSchemaSimpleSubelementList &subelements)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions
bool	do_apply (Pose &pose) override
	Search for the optimal conformation of the given loops. More...

Protected Member Functions inherited from protocols::loop_modeling::LoopMover
virtual bool	do_apply (Pose &pose, Loop const &loop)
	Perform the loop sampling move. This method can be overwritten in child classes. More...

template<typename ChildSubclassOP >
ChildSubclassOP	add_child (ChildSubclassOP child)
	Add a child to this mover. More...

void	remove_child (LoopMoverOP child)
	Remove a child from this mover. More...

void	clear_children ()
	Remove all children from this mover. More...

LoopMoverOPs	get_children () const
	Return all of this mover's children. More...

core::Size	count_children () const
	Return the number of children this mover has. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Private Attributes
loop_modeling::LoopBuilderOP	build_stage_

loop_modeling::LoopProtocolOP	centroid_stage_

loop_modeling::LoopProtocolOP	fullatom_stage_

loop_modeling::utilities::PrepareForCentroidOP	prepare_for_centroid_

loop_modeling::utilities::PrepareForFullatomOP	prepare_for_fullatom_

bool	use_default_task_factory_

bool	is_build_stage_enabled_

bool	is_centroid_stage_enabled_

bool	is_fullatom_stage_enabled_

Friends
class	::LoopModelerTests

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Detailed Description

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.

Constructor & Destructor Documentation

protocols::loop_modeler::LoopModeler::LoopModeler ( )

Default constructor.

References protocols::loops::get_cen_scorefxn(), and protocols::loops::get_fa_scorefxn().

protocols::loop_modeler::LoopModeler::~LoopModeler ( )

overridedefault

Default destructor.

Member Function Documentation

loop_modeling::LoopBuilderOP protocols::loop_modeler::LoopModeler::build_stage ( )

Return a pointer to the build stage mover.

loop_modeling::LoopProtocolOP protocols::loop_modeler::LoopModeler::centroid_stage ( )

Return a pointer to the centroid stage mover.

MoverOP protocols::loop_modeler::LoopModeler::clone ( ) const

overridevirtual

Return a shallow copy of this object.

Reimplemented from protocols::moves::Mover.

void protocols::loop_modeler::LoopModeler::disable_build_stage ( )

Disable the build stage.

void protocols::loop_modeler::LoopModeler::disable_centroid_stage ( )

Disable the centroid stage.

void protocols::loop_modeler::LoopModeler::disable_fullatom_stage ( )

Disable the fullatom stage.

bool protocols::loop_modeler::LoopModeler::do_apply ( Pose & pose )

overrideprotectedvirtual

Search for the optimal conformation of the given loops.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::loop_modeler::LoopModeler::enable_build_stage ( )

Enable the build stage.

void protocols::loop_modeler::LoopModeler::enable_centroid_stage ( )

Enable the centroid stage.

void protocols::loop_modeler::LoopModeler::enable_fullatom_stage ( )

Enable the fullatom stage.

loop_modeling::LoopProtocolOP protocols::loop_modeler::LoopModeler::fullatom_stage ( )

Return a pointer to the fullatom stage mover.

core::pack::task::TaskFactoryOP protocols::loop_modeler::LoopModeler::get_default_task_factory ( core::pose::Pose & pose )

Return a default task factory.

References protocols::loops::select_loop_residues(), core::pose::Pose::size(), and core::pose::Pose::update_residue_neighbors().

std::string protocols::loop_modeler::LoopModeler::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

TaskFactoryOP protocols::loop_modeler::LoopModeler::get_task_factory ( )

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.

core::pack::task::TaskFactoryOP protocols::loop_modeler::LoopModeler::get_task_factory ( core::pack::task::TaskFactoryOP fallback )

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.

std::string protocols::loop_modeler::LoopModeler::mover_name ( )

static

void protocols::loop_modeler::LoopModeler::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Reimplemented from protocols::moves::Mover.

References protocols::loop_modeling::utilities::loop_mover_from_tag(), core::scoring::parse_score_function(), and protocols::loop_modeling::utilities::set_task_factory_from_tag().

void protocols::loop_modeler::LoopModeler::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::loop_modeling::utilities::attributes_for_set_task_factory_from_tag().

void protocols::loop_modeler::LoopModeler::set_cen_scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

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

void protocols::loop_modeler::LoopModeler::set_fa_scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

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

void protocols::loop_modeler::LoopModeler::set_task_factory ( core::pack::task::TaskFactoryOP task_factory )

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

void protocols::loop_modeler::LoopModeler::setup_empty_config ( )

Setup the LoopModeler using a minimal configuration.

void protocols::loop_modeler::LoopModeler::setup_kic_config ( )

Setup the LoopModeler using the "next-gen KIC" configuration.

void protocols::loop_modeler::LoopModeler::setup_kic_with_fragments_config ( )

Setup the LoopModeler using the "KIC with fragments" configuration.

References protocols::loops::read_loop_fragments().

void protocols::loop_modeler::LoopModeler::setup_loophash_kic_config	(	bool	perturb_sequence,
		std::string	seqposes_no_mutate_str
	)

Setup the LoopModeler using the LoopHashKIC configuration.

Friends And Related Function Documentation

friend class ::LoopModelerTests

friend

Member Data Documentation

loop_modeling::LoopBuilderOP protocols::loop_modeler::LoopModeler::build_stage_

private

loop_modeling::LoopProtocolOP protocols::loop_modeler::LoopModeler::centroid_stage_

private

loop_modeling::LoopProtocolOP protocols::loop_modeler::LoopModeler::fullatom_stage_

private

bool protocols::loop_modeler::LoopModeler::is_build_stage_enabled_

private

bool protocols::loop_modeler::LoopModeler::is_centroid_stage_enabled_

private

bool protocols::loop_modeler::LoopModeler::is_fullatom_stage_enabled_

private

loop_modeling::utilities::PrepareForCentroidOP protocols::loop_modeler::LoopModeler::prepare_for_centroid_

private

loop_modeling::utilities::PrepareForFullatomOP protocols::loop_modeler::LoopModeler::prepare_for_fullatom_

private

bool protocols::loop_modeler::LoopModeler::use_default_task_factory_

private

The documentation for this class was generated from the following files:

src/protocols/loop_modeler/LoopModeler.hh
src/protocols/loop_modeler/LoopModeler.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation