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protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator Class Reference

#include <NeighborhoodByDistanceCalculator.hh>

Inheritance diagram for protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator:
Inheritance graph
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Public Types

typedef
core::pose::metrics::StructureDependentCalculator 
parent
 

Public Member Functions

 NeighborhoodByDistanceCalculator (std::set< core::Size > const &central_residues)
 ctor for positions, dist_cutoff will be initialized using default value from option system More...
 
 NeighborhoodByDistanceCalculator (std::set< core::Size > const &central_residues, core::Real dist_cutoff)
 ctor for positions, with custom dist_cutoff supplied by user More...
 
core::pose::metrics::PoseMetricCalculatorOP clone () const override
 
std::set< core::Size > const & central_residues () const
 return central residues set More...
 
core::Real dist_cutoff () const
 return distance cutoff More...
 
- Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
 StructureDependentCalculator ()
 
void notify_structure_change () override
 
void get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override
 
std::string get (std::string const &key, Pose const &this_pose) override
 
- Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
 PoseMetricCalculator ()
 
virtual void notify_energy_change ()
 

Protected Member Functions

void lookup (std::string const &key, basic::MetricValueBase *valptr) const override
 
std::string print (std::string const &key) const override
 
void recompute (core::pose::Pose const &pose) override
 

Private Attributes

std::set< core::Sizecentral_residues_
 whose neighbors are we finding? More...
 
core::Real const dist_cutoff_
 stores the input - how far away is a neighbor? More...
 
core::Size num_neighbors_
 the number of neighbors, INCLUSIVE of central residues More...
 
std::map< core::Size, core::Sizenum_neighbors_map_
 the number of neighbors for each of the central residues More...
 
std::set< core::Sizeneighbors_
 the set of neighbors, INCLUSIVE of central_residues More...
 

Detailed Description

this calculator determines the number and resids of residues within X angstroms of a group of given residues. Its intended purpose is the backend for a TaskOperation that allows one to construct a PackerTask based on neighborhoods around a set of particular residues. It can return its set of central residues, the total count of their neighbors as determined by the sub-calculators (inclusive of the central residues), and the identities of those neighbors.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::NeighborhoodByDistanceCalculator ( std::set< core::Size > const &  central_residues)

ctor for positions, dist_cutoff will be initialized using default value from option system

protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::NeighborhoodByDistanceCalculator ( std::set< core::Size > const &  central_residues,
core::Real  dist_cutoff 
)

ctor for positions, with custom dist_cutoff supplied by user

Member Function Documentation

std::set< core::Size > const& protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::central_residues ( ) const
inline

return central residues set

References central_residues_.

core::pose::metrics::PoseMetricCalculatorOP protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::clone ( ) const
overridevirtual
core::Real protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::dist_cutoff ( ) const
inline

return distance cutoff

References dist_cutoff_.

void protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::lookup ( std::string const &  key,
basic::MetricValueBase *  valptr 
) const
overrideprotectedvirtual
std::string protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::print ( std::string const &  key) const
overrideprotectedvirtual
void protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::recompute ( core::pose::Pose const &  pose)
overrideprotectedvirtual

Member Data Documentation

std::set< core::Size > protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::central_residues_
private

whose neighbors are we finding?

Referenced by central_residues(), lookup(), print(), and recompute().

core::Real const protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::dist_cutoff_
private

stores the input - how far away is a neighbor?

Referenced by dist_cutoff(), lookup(), print(), and recompute().

std::set< core::Size > protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::neighbors_
private

the set of neighbors, INCLUSIVE of central_residues

Referenced by lookup(), print(), and recompute().

core::Size protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::num_neighbors_
private

the number of neighbors, INCLUSIVE of central residues

Referenced by lookup(), print(), and recompute().

std::map<core::Size, core::Size> protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::num_neighbors_map_
private

the number of neighbors for each of the central residues

Referenced by lookup(), print(), and recompute().


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