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protocols::task_operations::RestrictToNeighborhoodOperation Class Reference

#include <RestrictToNeighborhoodOperation.hh>

Inheritance diagram for protocols::task_operations::RestrictToNeighborhoodOperation:
Inheritance graph
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Public Types

typedef RestrictOperationsBase parent
 
typedef std::set< core::SizeSizeSet
 
- Public Types inherited from protocols::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::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
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)
 
 ~RestrictToNeighborhoodOperation () override
 
RestrictToNeighborhoodOperationoperator= (RestrictToNeighborhoodOperation const &rhs)
 assignment operator More...
 
core::pack::task::operation::TaskOperationOP clone () const override
 
void apply (core::pose::Pose const &, core::pack::task::PackerTask &) const override
 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::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::task_operations::RestrictOperationsBase
 RestrictOperationsBase ()
 
 ~RestrictOperationsBase () override
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
 ~TaskOperation () override
 
virtual void parse_tag (TagCOP, DataMap &)
 Used to parse an xml-like tag to load parameters and properties. More...
 
virtual bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static std::string keyname ()
 

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::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

Constructor & Destructor Documentation

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

References make_calculator().

protocols::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::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::task_operations::RestrictToNeighborhoodOperation::~RestrictToNeighborhoodOperation ( )
overridedefault

Member Function Documentation

void protocols::task_operations::RestrictToNeighborhoodOperation::apply ( core::pose::Pose const &  ,
core::pack::task::PackerTask  
) const
overridevirtual
core::pack::task::operation::TaskOperationOP protocols::task_operations::RestrictToNeighborhoodOperation::clone ( ) const
overridevirtual

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

Implements protocols::task_operations::RestrictOperationsBase.

protocols::pose_metric_calculators::NeighborhoodByDistanceCalculatorCOP protocols::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::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::task_operations::RestrictToNeighborhoodOperation::get_central_residues ( ) const

this nontrivially checks the underlying calculator

References get_calculator().

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

this nontrivially checks the underlying calculator

References get_calculator().

static std::string protocols::task_operations::RestrictToNeighborhoodOperation::keyname ( )
inlinestatic
void protocols::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_, make_name(), and protocols::task_operations::TR().

Referenced by RestrictToNeighborhoodOperation(), and set_neighborhood_parameters().

void protocols::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_, make_name(), and protocols::task_operations::TR().

void protocols::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::id::to_string().

Referenced by make_calculator().

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

assignment operator

References calculator_name_, and get_calculator_name().

void protocols::task_operations::RestrictToNeighborhoodOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::task_operations::RestrictToNeighborhoodOperation::set_calculator_by_name ( std::string const &  calculator_name)
inline

References calculator_name_.

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

reskin of normal make_calculator

References make_calculator().

void protocols::task_operations::RestrictToNeighborhoodOperation::set_neighborhood_parameters ( SizeSet const &  central_residues)

reskin of normal make_calculator

References make_calculator().

Member Data Documentation

std::string protocols::task_operations::RestrictToNeighborhoodOperation::calculator_name_
private

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