residuenetwork base class More...

#include <NetworkAlgorithms.hh>

Inheritance diagram for protocols::toolbox::ResidueNetwork:

Public Member Functions
	ResidueNetwork ()
	default constructor More...

	~ResidueNetwork () override
	destructor More...

void	create_from_pose (core::pose::Pose const &pose)
	create a network from a pose More...

virtual void	generate_edges (core::pose::Pose const &pose)=0
	generate a list of edges from the pose – MUST be reimplemented for each type of network More...

void	clear_edges ()
	empties edges More...

void	dijkstras (core::Size const resi) const
	run Dijkstra's shortest path algorithm on the given list of nodes after execution, the "distanceFromStart" variable of each node will contain the distance from residue resi More...

core::Real	connectivity_index (core::Size const resi) const
	calculates the connectivity index of residue resi in the context of the network More...

core::Real	average_shortest_path_length () const
	calculates the average shortest path length of the network More...

std::list< NodeOP > const &	nodes () const

Private Attributes
std::list< NodeOP >	nodes_

Detailed Description

residuenetwork base class

Constructor & Destructor Documentation

protocols::toolbox::ResidueNetwork::ResidueNetwork ( )

default

default constructor

protocols::toolbox::ResidueNetwork::~ResidueNetwork ( )

overridedefault

destructor

Member Function Documentation

core::Real protocols::toolbox::ResidueNetwork::average_shortest_path_length ( ) const

calculates the average shortest path length of the network

References dijkstras(), nodes_, core::chemical::shortest_path(), and protocols::TR().

Referenced by protocols::simple_filters::AveragePathLengthFilter::compute().

void protocols::toolbox::ResidueNetwork::clear_edges ( )

empties edges

References nodes().

Referenced by protocols::toolbox::DistanceResidueNetwork::generate_edges(), and protocols::toolbox::CovalentResidueNetwork::generate_edges().

core::Real protocols::toolbox::ResidueNetwork::connectivity_index ( core::Size const resi ) const

calculates the connectivity index of residue resi in the context of the network

References dijkstras(), nodes_, core::chemical::shortest_path(), and protocols::TR().

void protocols::toolbox::ResidueNetwork::create_from_pose ( core::pose::Pose const & pose )

create a network from a pose

create a network from an input pose

References generate_edges(), core::conformation::Residue::name3(), nodes_, core::pose::Pose::residue(), core::pose::Pose::size(), core::id::to_string(), and protocols::TR().

Referenced by protocols::simple_filters::AveragePathLengthFilter::compute().

void protocols::toolbox::ResidueNetwork::dijkstras ( core::Size const resi ) const

run Dijkstra's shortest path algorithm on the given list of nodes after execution, the "distanceFromStart" variable of each node will contain the distance from residue resi

References protocols::toolbox::AdjacentRemainingNodes(), core::kinematics::distance(), protocols::toolbox::ExtractSmallest(), nodes(), nodes_, and protocols::TR().

Referenced by average_shortest_path_length(), and connectivity_index().

virtual void protocols::toolbox::ResidueNetwork::generate_edges ( core::pose::Pose const & pose )

pure virtual

generate a list of edges from the pose – MUST be reimplemented for each type of network

Implemented in protocols::toolbox::CovalentResidueNetwork, and protocols::toolbox::DistanceResidueNetwork.

Referenced by create_from_pose().

std::list< NodeOP > const& protocols::toolbox::ResidueNetwork::nodes ( ) const

inline

References nodes_.

Referenced by clear_edges(), dijkstras(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), and protocols::toolbox::CovalentResidueNetwork::generate_edges().