protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator Class Reference

#include <NeighborhoodByDistanceCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator:

Collaboration diagram for protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator:

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

Public Member Functions
	NeighborhoodByDistanceCalculator (std::set< core::Size > central_residues)
	ctor for positions, dist_cutoff will be initialized using default value from option system More...
	NeighborhoodByDistanceCalculator (std::set< core::Size > central_residues, core::Real dist_cutoff)
	ctor for positions, with custom dist_cutoff supplied by user More...
	NeighborhoodByDistanceCalculator (NeighborhoodByDistanceCalculator const &calculator)
	copy ctor More...
virtual core::pose::metrics::PoseMetricCalculatorOP	clone () const
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 ()
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
std::set< core::Size >	central_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::Size >	num_neighbors_map_
	the number of neighbors for each of the central residues More...
std::set< core::Size >	neighbors_
	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.

Definition at line 42 of file NeighborhoodByDistanceCalculator.hh.

Member Typedef Documentation

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

Definition at line 45 of file NeighborhoodByDistanceCalculator.hh.

Constructor & Destructor Documentation

protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::NeighborhoodByDistanceCalculator

(

std::set< core::Size >

central_residues)

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

Definition at line 49 of file NeighborhoodByDistanceCalculator.cc.

Referenced by clone().

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

ctor for positions, with custom dist_cutoff supplied by user

Definition at line 56 of file NeighborhoodByDistanceCalculator.cc.

protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::NeighborhoodByDistanceCalculator

(

NeighborhoodByDistanceCalculator const &

calculator)

copy ctor

Definition at line 61 of file NeighborhoodByDistanceCalculator.cc.

Member Function Documentation

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

inline

return central residues set

Definition at line 60 of file NeighborhoodByDistanceCalculator.hh.

References central_residues_.

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

virtual

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

Definition at line 64 of file NeighborhoodByDistanceCalculator.cc.

References NeighborhoodByDistanceCalculator().

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

inline

return distance cutoff

Definition at line 63 of file NeighborhoodByDistanceCalculator.hh.

References dist_cutoff_.

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

protectedvirtual

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

Definition at line 68 of file NeighborhoodByDistanceCalculator.cc.

References central_residues_, dist_cutoff_, neighbors_, num_neighbors_, and num_neighbors_map_.

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

protectedvirtual

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

Definition at line 101 of file NeighborhoodByDistanceCalculator.cc.

References central_residues_, dist_cutoff_, core::sequence::end, neighbors_, num_neighbors_, and num_neighbors_map_.

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

protectedvirtual

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

Definition at line 138 of file NeighborhoodByDistanceCalculator.cc.

References central_residues_, core::pose::Pose::conformation(), core::graph::Node::const_edge_list_end(), dist_cutoff_, core::sequence::end, core::graph::Edge::get_node(), neighbors_, num_neighbors_, num_neighbors_map_, core::conformation::residue_point_graph_from_conformation(), and core::pose::Pose::total_residue().

Member Data Documentation

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

private

whose neighbors are we finding?

Definition at line 73 of file NeighborhoodByDistanceCalculator.hh.

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

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

private

stores the input - how far away is a neighbor?

Definition at line 75 of file NeighborhoodByDistanceCalculator.hh.

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

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

private

the set of neighbors, INCLUSIVE of central_residues

Definition at line 81 of file NeighborhoodByDistanceCalculator.hh.

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

core::Size protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::num_neighbors_

private

the number of neighbors, INCLUSIVE of central residues

Definition at line 77 of file NeighborhoodByDistanceCalculator.hh.

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

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

private

the number of neighbors for each of the central residues

Definition at line 79 of file NeighborhoodByDistanceCalculator.hh.

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