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protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator Class Reference

#include <NeighborsByDistanceCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator:
Inheritance graph
Collaboration diagram for protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator:
Collaboration graph

Public Types


Public Member Functions

 NeighborsByDistanceCalculator (core::Size central_residue, core::Real dist_cutoff=basic::options::option[basic::options::OptionKeys::pose_metrics::neighbor_by_distance_cutoff])
 central_residue is the residue whose neighbors we find More...
 NeighborsByDistanceCalculator (NeighborsByDistanceCalculator const &calculator)
clone () const
core::Size central_residue () const
 return central residue More...
core::Real dist_cutoff () const
 return distance cutoff More...
- Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
 StructureDependentCalculator ()
void notify_structure_change ()
void get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose)
std::string get (std::string const &key, Pose const &this_pose)
- Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
 PoseMetricCalculator ()
virtual void notify_energy_change ()

Protected Member Functions

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

Private Attributes

core::Size const central_residue_
 stores the input - 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 this residue More...
std::set< core::Sizeneighbors_
 the set of neighbors, INCLUSIVE of this residue More...

Detailed Description

this calculator determines the number and resids of residues within X angstroms of the given residue. 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 combines with a NeighborhoodByDistanceCalculator for that purpose). It can return the identity of its seeded central residue and distance (just get functions) and calculate the neighbors and count of neighbors around that residue within that distance. It uses the PointGraph class to do this; if you have a better/faster implementation please code it up and replace this one. Note that returned data is INCLUSIVE of the central residue - it is part of the count and part of the std::set.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::NeighborsByDistanceCalculator ( core::Size  central_residue,
core::Real  dist_cutoff = basic::options::option[basic::options::OptionKeys::pose_metrics::neighbor_by_distance_cutoff] 

central_residue is the residue whose neighbors we find

Referenced by clone().

protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::NeighborsByDistanceCalculator ( NeighborsByDistanceCalculator const &  calculator)

Member Function Documentation

core::Size protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::central_residue ( ) const

return central residue

References central_residue_.

core::pose::metrics::PoseMetricCalculatorOP protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::clone ( ) const
core::Real protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::dist_cutoff ( ) const

return distance cutoff

References dist_cutoff_.

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

Member Data Documentation

core::Size const protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::central_residue_

stores the input - whose neighbors are we finding?

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

core::Real const protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::dist_cutoff_

stores the input - how far away is a neighbor?

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

std::set< core::Size > protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::neighbors_

the set of neighbors, INCLUSIVE of this residue

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

core::Size protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::num_neighbors_

the number of neighbors, INCLUSIVE of this residue

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

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