Namespaces
namespace	primitive
	Functions for generating primitive rings.

Classes
struct	primitive::Vertex
	This is a collection of elements, for each point, required for graph traversal. More...
struct	primitive::Graph
	This is a per-frame object, containing all the vertices for the particular frame, along with the vector of rings generated. More...
class	primitive::RingUpdater
	Exact frame-to-frame maintenance of the primitive ring network. More...

Functions
std::vector< std::vector< int > >	primitive::ringNetwork (const std::vector< std::vector< int > > &nList, int maxDepth)
Graph	primitive::populateGraphFromNListID (molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::vector< std::vector< int > > &neighHbondList)
Graph	primitive::populateGraphFromIndices (const std::vector< std::vector< int > > &nList)
void	primitive::restoreEdgesFromIndices (Graph &fullGraph, const std::vector< std::vector< int > > &nList)
Graph	primitive::countAllRingsFromIndex (const std::vector< std::vector< int > > &neighHbondList, int maxDepth)
	Creates a vector of vectors of all possible rings.
void	primitive::removeNonSPrings (Graph &fullGraph)
	Removes the non-SP rings, using the Franzblau shortest path criterion.
int	primitive::findRings (Graph &fullGraph, int v, std::vector< int > &visited, int maxDepth, int depth, int root=-1)
	Main function that searches for all rings.
int	primitive::shortestPath (Graph &fullGraph, int v, int goal, std::vector< int > &path, std::vector< int > &visited, int maxDepth, int depth=1)
	Calculates the shortest path.
Graph	primitive::clearGraph (Graph &currentGraph)
	Function for clearing vectors in Graph after multiple usage.
	primitive::RingUpdater::RingUpdater (int maxDepth)
	primitive::RingUpdater::~RingUpdater ()
	primitive::RingUpdater::RingUpdater (RingUpdater &&) noexcept
RingUpdater &	primitive::RingUpdater::operator= (RingUpdater &&) noexcept
	primitive::RingUpdater::RingUpdater (const RingUpdater &)=delete
RingUpdater &	primitive::RingUpdater::operator= (const RingUpdater &)=delete
const std::vector< std::vector< int > > &	primitive::RingUpdater::update (const std::vector< std::vector< int > > &nList)
int	primitive::RingUpdater::lastRecomputedSources () const
int	primitive::RingUpdater::lastBallsRefreshed () const
	Vertices whose bounded balls were rebuilt on the last update.

Variables
int	primitive::Vertex::atomIndex
std::vector< int >	primitive::Vertex::neighListIndex
	This is the index according to pointCloud.
bool	primitive::Vertex::inGraph
std::vector< Vertex >	primitive::Graph::pts
std::vector< std::vector< int > >	primitive::Graph::rings

Detailed Description

Function Documentation

◆ clearGraph()

Graph primitive::clearGraph ( Graph & currentGraph )

Function for clearing vectors in Graph after multiple usage.

◆ countAllRingsFromIndex()

Graph primitive::countAllRingsFromIndex	(	const std::vector< std::vector< int > > &	neighHbondList,
		int	maxDepth )

Creates a vector of vectors of all possible rings.

◆ findRings()

int primitive::findRings	(	Graph &	fullGraph,
		int	v,
		std::vector< int > &	visited,
		int	maxDepth,
		int	depth,
		int	root = -1 )

nodiscard

Main function that searches for all rings.

◆ lastBallsRefreshed()

int primitive::RingUpdater::lastBallsRefreshed ( ) const

nodiscard

Vertices whose bounded balls were rebuilt on the last update.

◆ lastRecomputedSources()

int primitive::RingUpdater::lastRecomputedSources ( ) const

nodiscard

Sources re-enumerated by the last update; the full vertex count on the first frame, zero when nothing changed

◆ operator=() [1/2]

RingUpdater & primitive::RingUpdater::operator= ( const RingUpdater & )

delete

◆ operator=() [2/2]

RingUpdater & primitive::RingUpdater::operator= ( RingUpdater && )

noexcept

◆ populateGraphFromIndices()

Graph primitive::populateGraphFromIndices ( const std::vector< std::vector< int > > & nList )

Creates a graph object and fills it with the information from a neighbour list of INDICES NOT ATOM IDs created before. NOTE: the neighbourListIndex contains the indices and NOT the atom IDs as in the neighbour list

◆ populateGraphFromNListID()

Graph primitive::populateGraphFromNListID	(	molSys::PointCloud< molSys::Point< double >, double > &	yCloud,
		const std::vector< std::vector< int > > &	neighHbondList )

Creates a graph object and fills it with the information from a neighbour list and pointCloud created before. NOTE: the neighbourListIndex contains the indices and NOT the atom IDs as in the neighbour list

◆ removeNonSPrings()

void primitive::removeNonSPrings ( Graph & fullGraph )

Removes the non-SP rings, using the Franzblau shortest path criterion.

◆ restoreEdgesFromIndices()

void primitive::restoreEdgesFromIndices	(	Graph &	fullGraph,
		const std::vector< std::vector< int > > &	nList )

Re-fills the neighbour lists of a graph object from a neighbour list of INDICES NOT ATOM IDs created before. NOTE: the neighbourListIndex contains the indices and NOT the atom IDs as in the neighbour list

◆ ringNetwork()

std::vector< std::vector< int > > primitive::ringNetwork	(	const std::vector< std::vector< int > > &	nList,
		int	maxDepth )

Returns a vector of vectors containing the rings (of all sizes), by atom index, given the neighbour list also by index (preferably the hydrogen-bonded neighbour list). Internally uses the Graph and Vertex objects.

◆ RingUpdater() [1/3]

primitive::RingUpdater::RingUpdater ( const RingUpdater & )

delete

◆ RingUpdater() [2/3]

primitive::RingUpdater::RingUpdater ( int maxDepth )

explicit

◆ RingUpdater() [3/3]

primitive::RingUpdater::RingUpdater ( RingUpdater && )

noexcept

◆ shortestPath()

int primitive::shortestPath	(	Graph &	fullGraph,
		int	v,
		int	goal,
		std::vector< int > &	path,
		std::vector< int > &	visited,
		int	maxDepth,
		int	depth = 1 )

nodiscard

Calculates the shortest path.

◆ update()

const std::vector< std::vector< int > > & primitive::RingUpdater::update ( const std::vector< std::vector< int > > & nList )

Primitive rings for this frame's neighbour list (row-ordered, by index, first element of each row the vertex itself)

◆ ~RingUpdater()

primitive::RingUpdater::~RingUpdater ( )

Variable Documentation

◆ atomIndex

int primitive::Vertex::atomIndex

Definition at line 90 of file franzblau.hpp.

◆ inGraph

bool primitive::Vertex::inGraph

Initial value:

=

true

Contains the INDICES (not the atomIDs) of the neighbouring vertices

Definition at line 93 of file franzblau.hpp.

◆ neighListIndex

std::vector<int> primitive::Vertex::neighListIndex

This is the index according to pointCloud.

Definition at line 91 of file franzblau.hpp.

◆ pts

std::vector<Vertex> primitive::Graph::pts

Definition at line 108 of file franzblau.hpp.

◆ rings

std::vector<std::vector<int> > primitive::Graph::rings

Collection of vertices. The index of each should be the same as that in pointCloud

Definition at line 111 of file franzblau.hpp.

Namespaces

Classes

Functions

Variables

Detailed Description

Function Documentation

◆ clearGraph()

◆ countAllRingsFromIndex()

◆ findRings()

◆ lastBallsRefreshed()

◆ lastRecomputedSources()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ populateGraphFromIndices()

◆ populateGraphFromNListID()

◆ removeNonSPrings()

◆ restoreEdgesFromIndices()

◆ ringNetwork()

◆ RingUpdater() [1/3]

◆ RingUpdater() [2/3]

◆ RingUpdater() [3/3]

◆ shortestPath()

◆ update()

◆ ~RingUpdater()

Variable Documentation

◆ atomIndex

◆ inGraph

◆ neighListIndex

◆ pts

◆ rings