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protocols::toolbox::ResidueNetwork Class Referenceabstract

residuenetwork base class More...

#include <NetworkAlgorithms.hh>

Inheritance diagram for protocols::toolbox::ResidueNetwork:
Inheritance graph
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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< NodeOPnodes_
 

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 ( )
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)
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

Member Data Documentation

std::list< NodeOP > protocols::toolbox::ResidueNetwork::nodes_
private

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