#include <RestrictToNeighborhoodOperation.hh>

Inheritance diagram for protocols::toolbox::task_operations::RestrictToNeighborhoodOperation:

Collaboration diagram for protocols::toolbox::task_operations::RestrictToNeighborhoodOperation:

Public Types
typedef RestrictOperationsBase	parent

typedef std::set< core::Size >	SizeSet

Public Types inherited from protocols::toolbox::task_operations::RestrictOperationsBase
typedef core::pack::task::operation::TaskOperation	TaskOperation

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef TaskOperation	parent

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr	TagPtr

typedef pose::Pose	Pose

Public Member Functions
	RestrictToNeighborhoodOperation ()

	RestrictToNeighborhoodOperation (RestrictToNeighborhoodOperation const &rhs)

	RestrictToNeighborhoodOperation (std::set< core::Size > const &central_residues, core::Real const dist_cutoff)

	RestrictToNeighborhoodOperation (std::set< core::Size > const &central_residues)
	uses option system default for dist_cutoff More...

	RestrictToNeighborhoodOperation (std::string const &calculator)

virtual	~RestrictToNeighborhoodOperation ()

RestrictToNeighborhoodOperation &	operator= (RestrictToNeighborhoodOperation const &rhs)
	assignment operator More...

virtual core::pack::task::operation::TaskOperationOP	clone () const

virtual void	apply (core::pose::Pose const &, core::pack::task::PackerTask &) const
	Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...

SizeSet const &	get_central_residues () const
	this nontrivially checks the underlying calculator More...

core::Real	get_distance_cutoff () const
	this nontrivially checks the underlying calculator More...

std::string const &	get_calculator_name () const
	trivially returns underlying calculator string name More...

protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculatorCOP	get_calculator () const
	look up actual calculator object More...

void	set_neighborhood_parameters (SizeSet const &central_residues, core::Real dist_cutoff)
	reskin of normal make_calculator More...

void	set_neighborhood_parameters (SizeSet const &central_residues)
	reskin of normal make_calculator More...

void	set_calculator_by_name (std::string const &calculator_name)

Public Member Functions inherited from protocols::toolbox::task_operations::RestrictOperationsBase
	RestrictOperationsBase ()

virtual	~RestrictOperationsBase ()

Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

virtual void	parse_tag (TagPtr)
	Used to parse an xml-like tag to load parameters and properties. More...

virtual void	parse_def (utility::lua::LuaObject const &def)

Private Member Functions
void	make_calculator (std::set< core::Size > const &central_residues, core::Real dist_cutoff)
	constructor helper function - makes the PoseMetricCalculator More...

void	make_calculator (std::set< core::Size > const &central_residues)
	constructor helper function - makes the PoseMetricCalculator More...

void	make_name (std::set< core::Size > const &central_residues)
	constructor helper function - names the PoseMetricCalculator More...

Private Attributes
std::string	calculator_name_

Additional Inherited Members
Protected Member Functions inherited from protocols::toolbox::task_operations::RestrictOperationsBase
void	run_calculator (core::pose::Pose const &pose, std::string const &calculator, std::string const &calculation, utility::vector1_bool &residues) const
	this is the only real function - it takes a calculator name and calculation, and a PackerTask-compatible vector, and flips booleans in the vector according to the calculator More...

Detailed Description

this class is a TaskOperation to prevent repacking of residues not near a neighborhood. Internally it just user NeighborhoodByDistanceCalculator to do all the work. You are allowed a "calculator name" interface to tell it which you-constructed calculator to use, or you can give it a set of residues and a desired distance cutoff to have it define the calculator itself. (There is no need to use both interfaces).

Member Typedef Documentation

typedef RestrictOperationsBase protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::parent

typedef std::set< core::Size > protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::SizeSet

Constructor & Destructor Documentation

protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::RestrictToNeighborhoodOperation ( )

Referenced by clone(), and protocols::toolbox::task_operations::RestrictToNeighborhoodOperationCreator::create_task_operation().

protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::RestrictToNeighborhoodOperation ( RestrictToNeighborhoodOperation const & rhs)

protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::RestrictToNeighborhoodOperation	(	std::set< core::Size > const &	central_residues,
		core::Real const	dist_cutoff
	)

References make_calculator().

protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::RestrictToNeighborhoodOperation ( std::set< core::Size > const & central_residues)

uses option system default for dist_cutoff

this ctor generates calculators (easier to use but will rely on defaults, including default distance cutoff)

References make_calculator().

protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::RestrictToNeighborhoodOperation ( std::string const & calculator)

this ctor assumes a pregenerated Neighborhood and Neighbors calculators - if you want a particular non-default cutoff distance, assemble those calculators separately then pass them to this operation.

protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::~RestrictToNeighborhoodOperation ( )

virtual

Member Function Documentation

void protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::apply	(	core::pose::Pose const &	,
		core::pack::task::PackerTask &
	)		const

virtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements protocols::toolbox::task_operations::RestrictOperationsBase.

References calculator_name_, core::pack::task::PackerTask::restrict_to_residues(), protocols::toolbox::task_operations::RestrictOperationsBase::run_calculator(), and core::pose::Pose::total_residue().

core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::clone ( ) const

virtual

be warned if you use clone that you'll not get a new interface calculator

Implements protocols::toolbox::task_operations::RestrictOperationsBase.

References RestrictToNeighborhoodOperation().

protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculatorCOP protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::get_calculator ( ) const

look up actual calculator object

References calculator_name_.

Referenced by get_central_residues(), and get_distance_cutoff().

std::string const& protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::get_calculator_name ( ) const

inline

trivially returns underlying calculator string name

References calculator_name_.

Referenced by operator=().

std::set< core::Size > const & protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::get_central_residues ( ) const

this nontrivially checks the underlying calculator

References get_calculator().

core::Real protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::get_distance_cutoff ( ) const

this nontrivially checks the underlying calculator

References get_calculator().

void protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::make_calculator	(	std::set< core::Size > const &	central_residues,
		core::Real	dist_cutoff
	)

private

constructor helper function - makes the PoseMetricCalculator

private helper function to make calculator - runs in the ctor

References calculator_name_, and make_name().

Referenced by RestrictToNeighborhoodOperation(), and set_neighborhood_parameters().

void protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::make_calculator ( std::set< core::Size > const & central_residues)

private

constructor helper function - makes the PoseMetricCalculator

private helper function to make calculator - runs in the ctor

References calculator_name_, and make_name().

void protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::make_name ( std::set< core::Size > const & central_residues)

private

constructor helper function - names the PoseMetricCalculator

private helper function to name calculator- runs in the ctor

References calculator_name_, and core::sequence::end.

Referenced by make_calculator().

RestrictToNeighborhoodOperation & protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::operator= ( RestrictToNeighborhoodOperation const & rhs)

assignment operator

References calculator_name_, and get_calculator_name().

void protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::set_calculator_by_name ( std::string const & calculator_name)

inline

References calculator_name_.

void protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::set_neighborhood_parameters	(	SizeSet const &	central_residues,
		core::Real	dist_cutoff
	)