#include <KinematicWrapper.hh>

Inheritance diagram for protocols::loops::loop_closure::kinematic_closure::KinematicWrapper:

Public Member Functions
	KinematicWrapper (KinematicMoverOP kinmover_in, protocols::loops::Loop loop, core::Size cycles=0)
	ctor with Loop More...

	KinematicWrapper (KinematicMoverOP kinmover_in, core::Size loop_begin, core::Size loop_end, core::Size cycles=0)
	ctor with explicit loop begin/end More...

	~KinematicWrapper () override

void	apply (core::pose::Pose &pose) override
	re-applies KinematicMover with different pivots until success More...

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

void	respect_this_movemap (core::kinematics::MoveMapCOP mm)
	this function derives the allowed_positions_ vector from mm and the loop begin/end 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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

Private Member Functions
void	ctor ()
	two ctors have same functions, just different initialization lists; de-duplicated here More...

void	init_allowed_pos ()
	initializes allowed positions - for constructors and resetting More...

Private Attributes
KinematicMoverOP	kinmover_
	OP for KinematicMover. More...

core::Size const	loop_begin_
	the loop this object-instance remodels More...

core::Size const	loop_end_
	the loop this object-instance remodels More...

core::Size const	limit_
	a limit on the number of cycles the mover will run More...

utility::vector1< core::Size >	allowed_positions_
	vector of positions allowed as pivots More...

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

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 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...

Detailed Description

This class extends KinematicMover by composition (has-a KinematicMover). The idea is to make KinematicMover useful when ONLY the apply() function is available (as in MoverContainers, etc.). It will reapply KinematicMover until the KinematicMover reports a success. This class uses searches through loop begin/middle/end points while searching for solutions. You can pass a MoveMap; it will refuse to put pivots where the MoveMap is not mobile.

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::KinematicWrapper	(	KinematicMoverOP	kinmover_in,
		protocols::loops::Loop	loop,
		core::Size	cycles = `0`
	)

ctor with Loop

References ctor().

protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::KinematicWrapper	(	KinematicMoverOP	kinmover_in,
		core::Size	loop_begin,
		core::Size	loop_end,
		core::Size	cycles = `0`
	)

ctor with explicit loop begin/end

References ctor().

protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::~KinematicWrapper ( )

overridedefault

Member Function Documentation

void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply ( core::pose::Pose & pose )

overridevirtual

re-applies KinematicMover with different pivots until success

the responsiblity of apply() is to use the underlying KinematicMover to close the loop, taking care of moving the KinematicMover's begin/middle/end and ensuring that closure does occur.

Implements protocols::moves::Mover.

References allowed_positions_, protocols::moves::FAIL_RETRY, kinmover_, limit_, protocols::moves::MS_SUCCESS, core::scoring::rg, protocols::moves::Mover::set_last_move_status(), and protocols::loops::loop_closure::kinematic_closure::TR().

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), and protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub().

void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::ctor ( )

private

two ctors have same functions, just different initialization lists; de-duplicated here

trivial wrapper around stuff needed in two ctors (de-duplicating the code)

References init_allowed_pos(), loop_begin_, and loop_end_.

Referenced by KinematicWrapper().

std::string protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::init_allowed_pos ( )

private

initializes allowed positions - for constructors and resetting

initializes the allowed_positions vector with every position in the loop as an allowed pivot

References allowed_positions_, loop_begin_, and loop_end_.

Referenced by ctor(), and respect_this_movemap().

void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::respect_this_movemap ( core::kinematics::MoveMapCOP mm )

this function derives the allowed_positions_ vector from mm and the loop begin/end

this function compares positions in the allowed_positions vector with the movemap, and removes non-mobile positions

References allowed_positions_, init_allowed_pos(), and protocols::loops::loop_closure::kinematic_closure::TR().

Member Data Documentation

utility::vector1<core::Size> protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::allowed_positions_

private

vector of positions allowed as pivots

Referenced by apply(), init_allowed_pos(), and respect_this_movemap().

KinematicMoverOP protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::kinmover_

private

OP for KinematicMover.

Referenced by apply().

core::Size const protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::limit_

private

a limit on the number of cycles the mover will run

Referenced by apply().

core::Size const protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::loop_begin_

private

the loop this object-instance remodels

Referenced by ctor(), and init_allowed_pos().

core::Size const protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::loop_end_

private

the loop this object-instance remodels

Referenced by ctor(), and init_allowed_pos().

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

src/protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.hh
src/protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation