Apply the legacy KinematicMover. More...

#include <LegacyKicSampler.hh>

Inheritance diagram for protocols::loop_modeling::samplers::LegacyKicSampler:

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

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

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 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, Loop const &loop) override
	Apply the legacy KinematicMover algorithm. More...

Protected Member Functions inherited from protocols::loop_modeling::LoopMover
virtual bool	do_apply (Pose &pose)
	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
protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP	mover_

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

Apply the legacy KinematicMover.

The old KinematicMover works just as well as the new KicMover, but it is not written as well and is therefore much harder to understand and maintain. Largely for this reason, development will shift towards the new implementation and the old one will grow more and more out of date. This sampler was written to compare the two algorithms and is only meant to be a debugging tool. However, it may be useful in the short term while features like next-gen KIC are still being ported to the new implementation.

Constructor & Destructor Documentation

protocols::loop_modeling::samplers::LegacyKicSampler::LegacyKicSampler ( )

Default constructor.

Member Function Documentation

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

overrideprotectedvirtual

Apply the legacy KinematicMover algorithm.

Reimplemented from protocols::loop_modeling::LoopMover.

References protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

std::string protocols::loop_modeling::samplers::LegacyKicSampler::get_name ( ) const

overridevirtual

Return the name of this mover.

Reimplemented from protocols::loop_modeling::LoopMover.

std::string protocols::loop_modeling::samplers::LegacyKicSampler::mover_name ( )

static

void protocols::loop_modeling::samplers::LegacyKicSampler::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Member Data Documentation

protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP protocols::loop_modeling::samplers::LegacyKicSampler::mover_

private

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

src/protocols/loop_modeling/samplers/LegacyKicSampler.hh
src/protocols/loop_modeling/samplers/LegacyKicSampler.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation