Classes
struct	access

class	CherryPicker
	CherryPicker parameterisation algorithm class. More...

struct	CMGCallback

struct	CMGPrintCallback

class	ConnectedSubgraphs
	Generate connected subgraphs in G. More...

class	IXAStarOptimisation

class	IXElectronAssigner

class	IXLocalOptimisation
	Local optimisation electron assignment algorithm. More...

struct	MappingCallback

struct	MGCallback

struct	MGPrintCallback

class	PriorityQueue

struct	QueueItem

struct	TraversalResults

Typedefs
using	_ElectronAssigner = std::weak_ptr< IXElectronAssigner >

using	AssignerAlgorithm = IXElectronAssigner::AssignerAlgorithm
	Type for the enum of available assignment algorithms. More...

using	AssignMask = boost::dynamic_bitset<>
	Type of the mask used for assignments. More...

using	ElectronAssigner = std::shared_ptr< IXElectronAssigner >

using	key_t = uint32_t
	Type of the key for a score table. More...

using	LocMask = boost::dynamic_bitset<>

using	queue_t = std::priority_queue< QueueItem, std::vector< QueueItem >, std::greater< QueueItem > >

using	score_t = uint64_t
	Type of the score of an electron assignment. More...

using	ScoreTable = std::map< key_t, score_t >
	Type of a score table. More...

Functions
template<class V , class E , class S , class D , class VP , class EP , class Container >
int64_t	AllCycles (graph::BaseGraph< V, E, S, D, VP, EP > &G, Container &ecycles)

template<class V , class E , class S , class D , class VP , class EP >
void	AllSimplePaths (graph::BaseGraph< V, E, S, D, VP, EP > &G, V source, V target, std::vector< std::vector< E >> &paths, int64_t limit=-1)
	Find all the simple paths between two vertices. More...

template<class V , class E , class S , class D , class VP , class EP >
TraversalResults< V >	BreadthFirstSearch (graph::BaseGraph< V, E, S, D, VP, EP > &G, V source=V(), int64_t limit=-1)

template<class V , class E , class S , class D , class VP , class EP , class Container >
int64_t	ConnectedComponents (graph::BaseGraph< V, E, S, D, VP, EP > &G, Container &bits)

ElectronAssigner	CreateElectronAssigner (const Molecule &m)
	Create an ElectronAssigner. More...

template<class V , class E , class S , class D , class VP , class EP , class Container >
int64_t	CycleBasis (graph::BaseGraph< V, E, S, D, VP, EP > &G, Container &basis)

template<class V , class E , class S , class D , class VP , class EP >
TraversalResults< V >	DepthFirstSearch (graph::BaseGraph< V, E, S, D, VP, EP > &G, V source=V(), int64_t limit=-1)
	Perform a breadth first search of G. More...

std::vector< std::vector< Atom > >	OptimalChargeGroups (const Molecule &mol, int32_t limit=5)

template<class V , class E , class S , class D , class VP , class EP >
std::vector< E >	ShortestPath (graph::BaseGraph< V, E, S, D, VP, EP > &G, V source, V target)
	Find the shortest path between two vertices. More...

void	SubgraphIsomorphisms (graph::CondensedMolecularGraph &G1, graph::CondensedMolecularGraph &G2, CMGCallback &callback)

void	SubgraphIsomorphisms (graph::MolecularGraph &G1, graph::MolecularGraph &G2, MGCallback &callback)

Typedef Documentation

◆ _ElectronAssigner

using _ElectronAssigner = std::weak_ptr<IXElectronAssigner>

◆ AssignerAlgorithm

using AssignerAlgorithm = IXElectronAssigner::AssignerAlgorithm

Type for the enum of available assignment algorithms.

◆ AssignMask

using AssignMask = boost::dynamic_bitset<>

Type of the mask used for assignments.

◆ ElectronAssigner

using ElectronAssigner = std::shared_ptr<IXElectronAssigner>

◆ key_t

using key_t = uint32_t

Type of the key for a score table.

◆ LocMask

using LocMask = boost::dynamic_bitset<>

◆ queue_t

using queue_t = std::priority_queue<QueueItem, std::vector<QueueItem>, std::greater<QueueItem> >

◆ score_t

using score_t = uint64_t

Type of the score of an electron assignment.

◆ ScoreTable

using ScoreTable = std::map<key_t, score_t>

Type of a score table.

Function Documentation

◆ AllCycles()

int64_t indigox::algorithm::AllCycles	(	graph::BaseGraph< V, E, S, D, VP, EP > &	G,
		Container &	ecycles
	)

Referenced by BaseGraph< CMGVertex, CMGEdge, CondensedMolecularGraph >::GetCycles().

◆ AllSimplePaths()

void indigox::algorithm::AllSimplePaths	(	graph::BaseGraph< V, E, S, D, VP, EP > &	G,
		V	source,
		V	target,
		std::vector< std::vector< E >> &	paths,
		int64_t	limit = `-1`
	)

Find all the simple paths between two vertices.

Determines all the paths between two vertices, using a modified depth-first search method. The order of the found paths is arbitary, though each path is ordered from source to target.

Parameters

	G	the graph to find paths in.
	source	the source vertex.
	target	the target vertex.
[out]	paths	vector to store all the found paths in.
	limit	the maximum length path to return.

Exceptions

std::runtime_error if you try something stupid.

◆ BreadthFirstSearch()

TraversalResults<V> indigox::algorithm::BreadthFirstSearch	(	graph::BaseGraph< V, E, S, D, VP, EP > &	G,
		V	source = `V()`,
		int64_t	limit = `-1`
	)

◆ ConnectedComponents()

int64_t indigox::algorithm::ConnectedComponents	(	graph::BaseGraph< V, E, S, D, VP, EP > &	G,
		Container &	bits
	)

Referenced by BaseGraph< CMGVertex, CMGEdge, CondensedMolecularGraph >::GetConnectedComponents().

◆ CreateElectronAssigner()

ElectronAssigner indigox::algorithm::CreateElectronAssigner ( const Molecule & m )

inline

Create an ElectronAssigner.

Friendship allows creation of electron assigner instances.

Parameters

m	the molecule this electron assigner is for.

Returns: a new ElectronAssigner.

◆ CycleBasis()

int64_t indigox::algorithm::CycleBasis	(	graph::BaseGraph< V, E, S, D, VP, EP > &	G,
		Container &	basis
	)

◆ DepthFirstSearch()

TraversalResults<V> indigox::algorithm::DepthFirstSearch	(	graph::BaseGraph< V, E, S, D, VP, EP > &	G,
		V	source = `V()`,
		int64_t	limit = `-1`
	)

Perform a breadth first search of G.

Returns ordered vector of vertex pairs. Order is the order in which the vertices were discovered. First member of pair is the discovered vertex, second member is the predecessor of the discovered vertex. If no source is provided, the source is chosen arbitarily until all vertices have been discovered. If source is provided, only vertices within the component containing source will be searched. Limit is the limit of search depth.

◆ OptimalChargeGroups()

std::vector<std::vector<Atom> > indigox::algorithm::OptimalChargeGroups	(	const Molecule &	mol,
		int32_t	limit = `5`
	)

◆ ShortestPath()

std::vector<E> indigox::algorithm::ShortestPath	(	graph::BaseGraph< V, E, S, D, VP, EP > &	G,
		V	source,
		V	target
	)

Find the shortest path between two vertices.

Determines the shortest path between two vertices, using a bi-directional breadth-first search method. If there is no path between the vertices, the returned path is empty. The path is returned has the vertices to traverse in order from the source to the target. Multiple short paths may exist. This function returns only one of them.

Template Parameters

GraphType the type of the graph.

Parameters

G	the graph to find the path in.
source	the source vertex.
target	the target vertex.

Returns: the shortest path from source to target.

Exceptions

std::runtime_error if source and target are the same vertex or either of them is not part of the graph.

◆ SubgraphIsomorphisms() [1/2]

void indigox::algorithm::SubgraphIsomorphisms	(	graph::CondensedMolecularGraph &	G1,
		graph::CondensedMolecularGraph &	G2,
		CMGCallback &	callback
	)

◆ SubgraphIsomorphisms() [2/2]

void indigox::algorithm::SubgraphIsomorphisms	(	graph::MolecularGraph &	G1,
		graph::MolecularGraph &	G2,
		MGCallback &	callback
	)

Classes

Typedefs

Functions

Typedef Documentation

◆ _ElectronAssigner

◆ AssignerAlgorithm

◆ AssignMask

◆ ElectronAssigner

◆ key_t

◆ LocMask

◆ queue_t

◆ score_t

◆ ScoreTable

Function Documentation

◆ AllCycles()

◆ AllSimplePaths()

◆ BreadthFirstSearch()

◆ ConnectedComponents()

◆ CreateElectronAssigner()

◆ CycleBasis()

◆ DepthFirstSearch()

◆ OptimalChargeGroups()

◆ ShortestPath()

◆ SubgraphIsomorphisms() [1/2]

◆ SubgraphIsomorphisms() [2/2]