protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator Class Reference

#include <NonlocalContactsCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator:

Collaboration diagram for protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator:

Public Member Functions
	NonlocalContactsCalculator (core::Size min_sequence_separation=basic::options::option[basic::options::OptionKeys::pose_metrics::min_sequence_separation], core::Real contact_cutoffE=basic::options::option[basic::options::OptionKeys::pose_metrics::contact_cutoffE])
	NonlocalContactsCalculator (std::set< core::Size > const &special_region, core::Size min_sequence_separation=basic::options::option[basic::options::OptionKeys::pose_metrics::min_sequence_separation], core::Real contact_cutoffE=basic::options::option[basic::options::OptionKeys::pose_metrics::contact_cutoffE])
	NonlocalContactsCalculator (std::set< core::Size > const &special_region1, std::set< core::Size > const &special_region2, core::Size min_sequence_separation=basic::options::option[basic::options::OptionKeys::pose_metrics::min_sequence_separation], core::Real contact_cutoffE=basic::options::option[basic::options::OptionKeys::pose_metrics::contact_cutoffE])
	~NonlocalContactsCalculator ()
core::pose::metrics::PoseMetricCalculatorOP	clone () const
Public Member Functions inherited from core::pose::metrics::EnergyDependentCalculator
	EnergyDependentCalculator ()
void	notify_energy_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_structure_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 &this_pose)

Private Attributes
core::Size	total_nlcontacts_
core::Size	special_region1_nlcontacts_
core::Size	special_region2_nlcontacts_
core::Size	special_region1_intra_nlcontacts_
core::Size	special_region1_to_other_nlcontacts_
core::Size	region1_region2_nlcontacts_
utility::vector1< core::Size >	residue_nlcontacts_
utility::vector1< core::Real >	residue_nlscore_
core::graph::GraphOP	nlcontacts_graph_
core::Size	min_seq_separation_
core::Real	cutoffE_
std::set< core::Size >	special_region1_
std::set< core::Size >	special_region2_

Constructor & Destructor Documentation

protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::NonlocalContactsCalculator	(	core::Size	min_sequence_separation = basic::options::option[basic::options::OptionKeys::pose_metrics::min_sequence_separation],
		core::Real	contact_cutoffE = basic::options::option[basic::options::OptionKeys::pose_metrics::contact_cutoffE]
	)

References residue_nlcontacts_, residue_nlscore_, special_region1_, and special_region2_.

Referenced by clone().

protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::NonlocalContactsCalculator	(	std::set< core::Size > const &	special_region,
		core::Size	min_sequence_separation = basic::options::option[basic::options::OptionKeys::pose_metrics::min_sequence_separation],
		core::Real	contact_cutoffE = basic::options::option[basic::options::OptionKeys::pose_metrics::contact_cutoffE]
	)

References residue_nlcontacts_, residue_nlscore_, and special_region2_.

protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::NonlocalContactsCalculator	(	std::set< core::Size > const &	special_region1,
		std::set< core::Size > const &	special_region2,
		core::Size	min_sequence_separation = basic::options::option[basic::options::OptionKeys::pose_metrics::min_sequence_separation],
		core::Real	contact_cutoffE = basic::options::option[basic::options::OptionKeys::pose_metrics::contact_cutoffE]
	)

References residue_nlcontacts_, and residue_nlscore_.

protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::~NonlocalContactsCalculator

(

)

Member Function Documentation

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

inlinevirtual

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

References cutoffE_, min_seq_separation_, NonlocalContactsCalculator(), special_region1_, and special_region2_.

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

protectedvirtual

Implements core::pose::metrics::EnergyDependentCalculator.

References nlcontacts_graph_, region1_region2_nlcontacts_, residue_nlcontacts_, residue_nlscore_, special_region1_intra_nlcontacts_, special_region1_nlcontacts_, special_region1_to_other_nlcontacts_, special_region2_nlcontacts_, and total_nlcontacts_.

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

protectedvirtual

Implements core::pose::metrics::EnergyDependentCalculator.

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

protectedvirtual

Implements core::pose::metrics::EnergyDependentCalculator.

References core::graph::Node::const_upper_edge_list_begin(), core::graph::Node::const_upper_edge_list_end(), cutoffE_, core::scoring::EnergyEdge::dot(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Graph::get_node(), core::chemical::ResidueType::is_protein(), min_seq_separation_, nlcontacts_graph_, region1_region2_nlcontacts_, residue_nlcontacts_, residue_nlscore_, core::pose::Pose::residue_type(), special_region1_, special_region1_intra_nlcontacts_, special_region1_nlcontacts_, special_region1_to_other_nlcontacts_, special_region2_, special_region2_nlcontacts_, total_nlcontacts_, core::pose::Pose::total_residue(), protocols::toolbox::pose_metric_calculators::TR(), and core::scoring::Energies::weights().

Member Data Documentation

core::Real protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::cutoffE_

private

Referenced by clone(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::min_seq_separation_

private

Referenced by clone(), and recompute().

core::graph::GraphOP protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::nlcontacts_graph_

private

Referenced by lookup(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::region1_region2_nlcontacts_

private

Referenced by lookup(), and recompute().

utility::vector1< core::Size > protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::residue_nlcontacts_

private

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

utility::vector1< core::Real > protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::residue_nlscore_

private

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

std::set< core::Size > protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::special_region1_

private

Referenced by clone(), NonlocalContactsCalculator(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::special_region1_intra_nlcontacts_

private

Referenced by lookup(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::special_region1_nlcontacts_

private

Referenced by lookup(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::special_region1_to_other_nlcontacts_

private

Referenced by lookup(), and recompute().

std::set< core::Size > protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::special_region2_

private

Referenced by clone(), NonlocalContactsCalculator(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::special_region2_nlcontacts_

private

Referenced by lookup(), and recompute().

core::Size protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::total_nlcontacts_

private

Referenced by lookup(), and recompute().

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

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