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

#include <NeighborsByDistanceCalculator.hh>

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

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

Public Types
typedef core::pose::metrics::StructureDependentCalculator	parent

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)
virtual core::pose::metrics::PoseMetricCalculatorOP	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::Size >	neighbors_
	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

typedef core::pose::metrics::StructureDependentCalculator protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::parent

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

inline

return central residue

References central_residue_.

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

virtual

Implements core::pose::metrics::PoseMetricCalculator.

References NeighborsByDistanceCalculator().

core::Real protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::dist_cutoff ( ) const

inline

return distance cutoff

References dist_cutoff_.

void protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::lookup ( std::string const &  key, basic::MetricValueBase *  valptr  ) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References central_residue_, dist_cutoff_, neighbors_, and num_neighbors_.

std::string protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::print ( std::string const &  key) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References central_residue_, dist_cutoff_, core::sequence::end, neighbors_, and num_neighbors_.

void protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::recompute ( core::pose::Pose const &  pose)

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References central_residue_, core::pose::Pose::conformation(), dist_cutoff_, neighbors_, num_neighbors_, core::conformation::residue_point_graph_from_conformation(), core::pose::Pose::total_residue(), and protocols::toolbox::pose_metric_calculators::TR().

Member Data Documentation

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

private

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_

private

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_

private

the set of neighbors, INCLUSIVE of this residue

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

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

private

the number of neighbors, INCLUSIVE of this residue

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

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

• src/protocols/toolbox/pose_metric_calculators/NeighborsByDistanceCalculator.hh
• src/protocols/toolbox/pose_metric_calculators/NeighborsByDistanceCalculator.cc