#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).

Definition at line 42 of file RestrictToNeighborhoodOperation.hh.

Member Typedef Documentation

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

Definition at line 45 of file RestrictToNeighborhoodOperation.hh.

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

Definition at line 46 of file RestrictToNeighborhoodOperation.hh.

Constructor & Destructor Documentation

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

Definition at line 45 of file RestrictToNeighborhoodOperation.cc.

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

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

Definition at line 78 of file RestrictToNeighborhoodOperation.cc.

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

Definition at line 64 of file RestrictToNeighborhoodOperation.cc.

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)

Definition at line 58 of file RestrictToNeighborhoodOperation.cc.

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.

Definition at line 48 of file RestrictToNeighborhoodOperation.cc.

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

virtual

Definition at line 70 of file RestrictToNeighborhoodOperation.cc.

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.

Definition at line 138 of file RestrictToNeighborhoodOperation.cc.

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.

Definition at line 73 of file RestrictToNeighborhoodOperation.cc.

References RestrictToNeighborhoodOperation().

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

look up actual calculator object

Definition at line 154 of file RestrictToNeighborhoodOperation.cc.

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

Definition at line 76 of file RestrictToNeighborhoodOperation.hh.

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

Definition at line 172 of file RestrictToNeighborhoodOperation.cc.

References get_calculator().

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

this nontrivially checks the underlying calculator

Definition at line 176 of file RestrictToNeighborhoodOperation.cc.

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

Definition at line 97 of file RestrictToNeighborhoodOperation.cc.

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

Definition at line 114 of file RestrictToNeighborhoodOperation.cc.

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

Definition at line 128 of file RestrictToNeighborhoodOperation.cc.

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

Referenced by make_calculator().

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

assignment operator

Definition at line 85 of file RestrictToNeighborhoodOperation.cc.

References calculator_name_, and get_calculator_name().

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

inline

Definition at line 87 of file RestrictToNeighborhoodOperation.hh.

References calculator_name_.

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