Base class for loop-sampling algorithms. More...

#include <LoopMover.hh>

Inheritance diagram for protocols::loop_modeling::LoopMover:

Public Member Functions
	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 MoverOP	clone () const
	Return a clone of the Mover object. 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 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
virtual bool	do_apply (Pose &pose)
	Perform the loop sampling move. This method can be overwritten in child classes. More...

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
LoopMoverOPs	children_

basic::datacache::HierarchicalDataMapOP	toolbox_

string	parent_name_

bool	trust_fold_tree_

bool	was_successful_

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

Base class for loop-sampling algorithms.

Classes that inherit from LoopMover can plug into the LoopProtocol framework. The only method that subclasses need to provide is do_apply(). Note that the apply() method itself cannot be overwritten, because LoopMover uses it to do some useful setup and teardown work. Instead, there are two versions of do_apply() that subclasses may implement. Both return a boolean to indicate whether or not the move succeeded. The first version of do_apply() accepts only a Pose and is expected to operate on all of the loops returned by get_loops(). The second version accepts a Pose and a Loop, and is only expected to operate on the given loop. By default, the first version simply iterates through the loops provided by get_loops() and calls the second version on each one. This means that if the first version is overwritten, the second version will no longer be called. If neither method is reimplemented, a runtime error will be thrown.

LoopMover provides a handful of features that could be useful to a loop sampling algorithm. As mentioned above, the get_loops() method returns the loops that should be sampled. There are also a number of methods provided for controlling how the fold tree is setup up. The request_fold_tree() method can be reimplemented to return an enum telling what kind of fold tree this mover requires. When apply() is called for the first time, a compatible fold tree will be configured. This behavior is disabled if trust_fold_tree() is called beforehand, in which case responsibility for constructing a compatible fold tree is passed to the calling code.

Constructor & Destructor Documentation

protocols::loop_modeling::LoopMover::LoopMover ( )

Default constructor.

Member Function Documentation

template<typename ChildSubclassOP >

ChildSubclassOP protocols::loop_modeling::LoopMover::add_child ( ChildSubclassOP child )

inlineprotected

Add a child to this mover.

The purpose of calling add_child() is to make it easy to use the child from within the do_apply() method of the parent. Child movers are always configured with the same loops and the same fold tree as their parents. Their toolboxes are linked to their parent's as well, so that the children's tools will default to the parent's tools. Fold tree requests made by child movers will be taken into account by the parent.

References children_, get_name(), and toolbox_.

Referenced by protocols::loop_modeling::utilities::LoopMoverGroup::add_mover().

void protocols::loop_modeling::LoopMover::apply ( Pose & pose )

overridevirtual

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.

Implements protocols::moves::Mover.

References protocols::loops::add_cutpoint_variants(), do_apply(), core::pose::Pose::fold_tree(), get_loops(), core::util::remove_cutpoint_variants(), request_fold_tree(), setup_fold_tree(), trust_fold_tree_, and was_successful_.

void protocols::loop_modeling::LoopMover::clear_children ( )

protected

Remove all children from this mover.

See also: LoopMover::add_child(); LoopMover::remove_child()

References children_.

Referenced by protocols::loop_modeling::utilities::LoopMoverGroup::clear().

Size protocols::loop_modeling::LoopMover::count_children ( ) const

protected

Return the number of children this mover has.

See also: LoopMover::add_child(); LoopMover::get_children()

References children_.

Referenced by protocols::loop_modeling::utilities::LoopMoverGroup::empty().

void protocols::loop_modeling::LoopMover::define_composition_schema	(	utility::tag::XMLSchemaDefinition &	xsd,
		utility::tag::XMLSchemaComplexTypeGenerator &	ct_gen,
		utility::tag::XMLSchemaSimpleSubelementList &	subelements
	)

static

References protocols::loop_modeling::utilities::append_subelement_and_attributes_for_parse_loops_from_tag(), protocols::moves::complex_type_name_for_mover(), and protocols::loop_modeling::LoopMover_subelement_ct_name().

Referenced by protocols::loop_modeling::refiners::RotamerTrialsRefiner::provide_xml_schema(), protocols::loop_modeling::utilities::PrepareForFullatom::provide_xml_schema(), protocols::loop_modeling::refiners::MinimizationRefiner::provide_xml_schema(), and protocols::loop_modeling::refiners::RepackingRefiner::provide_xml_schema().

bool protocols::loop_modeling::LoopMover::do_apply ( Pose & pose )

protectedvirtual

Perform the loop sampling move. This method can be overwritten in child classes.

References core::sequence::end, get_loops(), and was_successful().

Referenced by apply().

bool protocols::loop_modeling::LoopMover::do_apply	(	Pose &	pose,
		Loop const &	loop
	)

protectedvirtual

Perform the loop sampling move. This method can be overwritten in child classes.

Reimplemented in protocols::kinematic_closure::KicMover, protocols::loop_modeling::LoopBuilder, and protocols::loop_modeling::samplers::LegacyKicSampler.

LoopMoverOPs protocols::loop_modeling::LoopMover::get_children ( ) const

protected

Return all of this mover's children.

See also: LoopMover::add_child(); LoopMover::count_children()

References children_.

Referenced by protocols::loop_modeling::utilities::LoopMoverGroup::do_apply(), protocols::loop_modeling::utilities::LoopMoverGroup::get_children_names(), get_children_names(), and request_fold_tree().

void protocols::loop_modeling::LoopMover::get_children_names	(	utility::vector1< std::string > &	names,
		std::string	indent = `""`
	)		const

virtual

Add the names of all the algorithms invoked by this loop mover to the given list. Indentation is used to represent hierarchy.

Reimplemented in protocols::kinematic_closure::KicMover, and protocols::loop_modeling::utilities::LoopMoverGroup.

References get_children(), and get_name().

Loop const & protocols::loop_modeling::LoopMover::get_loop ( core::Size index ) const

Return the specified loop.

References get_loops().

LoopsOP protocols::loop_modeling::LoopMover::get_loops ( void )

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

References protocols::loop_modeling::ToolboxKeys::LOOPS.

Referenced by apply(), do_apply(), and get_loop().

LoopsCOP protocols::loop_modeling::LoopMover::get_loops ( void ) const

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

References protocols::loop_modeling::ToolboxKeys::LOOPS.

string protocols::loop_modeling::LoopMover::get_name ( ) const

inlineoverridevirtual

Return the name of this mover.

Implements protocols::moves::Mover.

Referenced by add_child(), and get_children_names().

template<typename ToolTypeOP >

ToolTypeOP protocols::loop_modeling::LoopMover::get_tool ( std::string key ) const

inline

Request a tool from this mover or any of its parents.

If the tool cannot be found, an exception will be thrown.

References toolbox_.

Referenced by protocols::loop_modeling::utilities::TrajectoryLogger::init().

template<typename ToolTypeOP >

ToolTypeOP protocols::loop_modeling::LoopMover::get_tool	(	std::string	key,
		ToolTypeOP	fallback
	)		const

inline

Request a tool from this mover or any of its parents.

If the tool isn't be found, the given fallback will be returned.

References toolbox_.

void protocols::loop_modeling::LoopMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Configure from a RosettaScripts tag.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::loop_modeling::LoopProtocol, protocols::loop_modeling::utilities::PrepareForFullatom, protocols::loop_modeling::refiners::RepackingRefiner, protocols::loop_modeling::refiners::MinimizationRefiner, and protocols::loop_modeling::refiners::RotamerTrialsRefiner.

References protocols::loop_modeling::utilities::parse_loops_from_tag(), and set_loops().

Referenced by protocols::loop_modeling::refiners::RotamerTrialsRefiner::parse_my_tag(), protocols::loop_modeling::refiners::MinimizationRefiner::parse_my_tag(), protocols::loop_modeling::refiners::RepackingRefiner::parse_my_tag(), and protocols::loop_modeling::utilities::PrepareForFullatom::parse_my_tag().

void protocols::loop_modeling::LoopMover::remove_child ( LoopMoverOP child )

protected

Remove a child from this mover.

See also: LoopMover::add_child(); LoopMover::clear_children()

References children_.

FoldTreeRequest protocols::loop_modeling::LoopMover::request_fold_tree ( ) const

virtual

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.

Reimplemented in protocols::kinematic_closure::KicMover.

References protocols::loop_modeling::FTR_DONT_CARE, and get_children().

Referenced by apply().

void protocols::loop_modeling::LoopMover::set_loop ( Loop const & loop )

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

References set_loops().

void protocols::loop_modeling::LoopMover::set_loops ( LoopsOP loops )

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

References protocols::loop_modeling::ToolboxKeys::LOOPS, and set_tool().

Referenced by parse_my_tag(), set_loop(), and set_loops().

void protocols::loop_modeling::LoopMover::set_loops ( Loops const & loops )

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

References set_loops().

template<typename ToolTypeOP >

ToolTypeOP protocols::loop_modeling::LoopMover::set_tool	(	std::string	key,
		ToolTypeOP	value
	)

inline

Provide a tool for this mover or any of its children to use.

References toolbox_.

Referenced by set_loops(), protocols::loop_modeling::refiners::RepackingRefiner::set_score_function(), protocols::loop_modeling::utilities::PrepareForFullatom::set_score_function(), and protocols::loop_modeling::refiners::RepackingRefiner::set_task_factory().

void protocols::loop_modeling::LoopMover::setup_fold_tree	(	Pose &	pose,
		LoopsCOP	loops,
		FoldTreeRequest	request
	)

static

Setup the given pose with a fold tree that is compatible with the given loops and requests.

References protocols::loops::add_cutpoint_variants(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::loop_modeling::FTR_DONT_CARE, protocols::loop_modeling::FTR_LOOPS_WITH_CUTS, protocols::loop_modeling::FTR_SIMPLE_TREE, and core::pose::Pose::size().

Referenced by apply().

void protocols::loop_modeling::LoopMover::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.

References trust_fold_tree_.

bool protocols::loop_modeling::LoopMover::was_successful ( ) const

Return true if the previous move was successful.

References was_successful_.

Referenced by do_apply().

void protocols::loop_modeling::LoopMover::was_successful ( bool value )

inline

Set the success status of a loop mover.

References was_successful_.