Class containing a graph representation of a molecule. More...

#include <indigox/graph/molecular.hpp>

Inheritance diagram for MolecularGraph:

Collaboration diagram for MolecularGraph:

Public Types
using	AtomMap = eastl::vector_map< Atom, MGVertex >
	Container for mapping atoms to vertices. More...

using	BondMap = eastl::vector_map< Bond, MGEdge >
	Container for mapping bonds to edges. More...

using	ComponentContain = std::vector< VertContain >
	Type for storing components. More...

using	CycleEdgeContain = std::vector< EdgeContain >
	Type for storing edge cycles. More...

using	CycleVertContain = std::vector< VertContain >
	Type for storing vertex cycles. More...

using	EdgeContain = std::vector< MGEdge >
	Container for edges. More...

using	EdgeIter = EdgeContain::const_iterator
	Type of the iterator returned by GetEdges() method. More...

using	EdgeMap = indigox::utils::SimpleBiMap< MGEdge, EdgeType >
	Type for bidirectional mapping of E to edge descriptor type. More...

using	EdgeType = MGEdge
	Type used for edges. More...

using	graph_type = BaseGraph< MGVertex, MGEdge, MolecularGraph >
	Type of the underlying IXGraphBase. More...

using	NbrsContain = std::map< MGVertex, VertContain >
	Container for neighbours of vertices. More...

using	NbrsIter = NbrsContain::mapped_type::const_iterator
	Type of the iterator returned by GetNeighbours() method. More...

using	PredIter = typename graph_type::inv_adjacency_iterator
	Type for iterator over predecessors of a vertex descriptor. More...

using	SubgraphType = MolecularGraph

using	VertContain = std::vector< MGVertex >
	Container for vertices. More...

using	VertexType = MGVertex
	Type used for vertices. More...

using	VertIter = VertContain::const_iterator
	Type of the iterator returned by GetVertices() method. More...

using	VertMap = indigox::utils::SimpleBiMap< MGVertex, VertType >
	Type for bidirectional mapping of V to vertex descriptor type. More...

using	VertType = typename graph_type::vertex_descriptor
	Type of the graph vertex descriptor. More...

Public Member Functions
	MolecularGraph ()=default
	Construct with a molecule. More...

	MolecularGraph (const MolecularGraph &)=default

	MolecularGraph (MolecularGraph &&)=default

	MolecularGraph (const Molecule &mol)

	~ MolecularGraph ()=default

int64_t	Degree (const MGVertex &v) const
	Degree of a vertex. More...

const CondensedMolecularGraph &	GetCondensedGraph ()

const ComponentContain &	GetConnectedComponents ()
	Get the connected components of the graph. More...

const CycleEdgeContain &	GetCycles ()
	Get the cycles of the graph. More...

const MGEdge &	GetEdge (const Bond &bnd) const
	Get the edge associated with a bond. More...

MGEdge	GetEdge (const MGVertex &u, const MGVertex &v) const
	Get the edge between two vertices. More...

const EdgeContain &	GetEdges () const
	Get the edges of the graph. More...

const Molecule &	GetMolecule () const

const VertContain &	GetNeighbours (const MGVertex &v)
	Get the neighbouring vertices of a vertex. More...

const VertContain &	GetPredecessors (const MGVertex &v)
	Get the predecessor vertices of a vertex. More...

MGVertex	GetSourceVertex (const MGEdge &e) const
	Get the source vertex of an edge. More...

const VertContain &	GetSuccessors (const MGVertex &v)

const MolecularGraph &	GetSuperGraph () const

MGVertex	GetTargetVertex (const MGEdge &e) const
	Get the target vertex of an edge. More...

const MGVertex &	GetVertex (const Atom &atm) const
	Get the vertex associated with an atom. More...

std::pair< MGVertex, MGVertex >	GetVertices (const MGEdge &e) const
	Get the two vertices that make up an edge. More...

const VertContain &	GetVertices () const
	Get the vertices of the graph. More...

bool	HasEdge (const MGEdge &e) const
	Is the edge in the graph. More...

bool	HasEdge (const MGVertex &u, const MGVertex &v) const
	Does an edge exist between two vertices. More...

bool	HasEdge (const Bond &e) const
	Check if the graph has an edge associated with a bond. More...

bool	HasVertex (const MGVertex &v) const
	Is the vertex in the graph. More...

bool	HasVertex (const Atom &v) const
	Check if the graph has a vertex associated with an atom. More...

int64_t	InDegree (const MGVertex &v) const
	Indegree of a vertex. More...

bool	IsConnected ()
	Determine if the graph is connected. More...

bool	IsCyclic (const MGVertex &v)
	Determine if a vertex of this graph is cyclic. More...

bool	IsCyclic (const MGVertex &v, uint32_t sz)

bool	IsCyclic (const MGEdge &e)
	Determine if an edge of this graph is cycle. More...

bool	IsCyclic (const MGEdge &e, uint32_t sz)

bool	IsSubgraph () const

int64_t	NumConnectedComponents ()
	Get the number of connected components of the graph. More...

int64_t	NumCycles ()

int64_t	NumEdges () const
	Number of edges in the graph. More...

int64_t	NumVertices () const
	Number of vertices in the graph. More...

	operator bool () const

bool	operator!= (const MolecularGraph &g) const

bool	operator< (const MolecularGraph &g) const

bool	operator<= (const MolecularGraph &g) const

MolecularGraph &	operator= (MolecularGraph &&)=default

MolecularGraph &	operator= (const MolecularGraph &)=default

bool	operator== (const MolecularGraph &g) const

bool	operator> (const MolecularGraph &g) const

bool	operator>= (const MolecularGraph &g) const

MolecularGraph	Subgraph (std::vector< MGVertex > &vertices)
	Induce a subgraph from the range of vertices. More...

MolecularGraph	Subgraph (std::vector< MGVertex > &vertices, std::vector< MGEdge > &edges)

Protected Member Functions
void	AddEdge (const MGVertex &u, const MGVertex &v, const MGEdge &e)
	Add a new edge to the graph. More...

void	AddVertex (const MGVertex &v)
	Add a new vertex to the graph. More...

Protected Attributes
std::shared_ptr< BaseImpl >	m_basedata

Friends
class	cereal::access
	Friendship allows serialisation. More...

class	indigox::Molecule
	Friendship allows an Molecule to own a graph. More...

std::ostream &	operator<< (std::ostream &os, const MolecularGraph &g)

Detailed Description

Class containing a graph representation of a molecule.

The IXMolecularGraph is designed to be maintained by the IXMolecule instance owning it. To that end, all the modifying methods assume that the parameters feed to them are valid. However, all the accessing methods do not make this assumption and so perform sanity checks.

Member Typedef Documentation

◆ AtomMap

using AtomMap = eastl::vector_map<Atom, MGVertex>

Container for mapping atoms to vertices.

◆ BondMap

using BondMap = eastl::vector_map<Bond, MGEdge>

Container for mapping bonds to edges.

◆ ComponentContain

using ComponentContain = std::vector<VertContain>

inherited

Type for storing components.

◆ CycleEdgeContain

using CycleEdgeContain = std::vector<EdgeContain>

inherited

Type for storing edge cycles.

◆ CycleVertContain

using CycleVertContain = std::vector<VertContain>

inherited

Type for storing vertex cycles.

◆ EdgeContain

using EdgeContain = std::vector<MGEdge>

Container for edges.

◆ EdgeIter

using EdgeIter = EdgeContain::const_iterator

Type of the iterator returned by GetEdges() method.

◆ EdgeMap

using EdgeMap = indigox::utils::SimpleBiMap<MGEdge , EdgeType>

inherited

Type for bidirectional mapping of E to edge descriptor type.

◆ EdgeType

using EdgeType = MGEdge

Type used for edges.

◆ graph_type

using graph_type = BaseGraph<MGVertex, MGEdge, MolecularGraph>

Type of the underlying IXGraphBase.

◆ NbrsContain

using NbrsContain = std::map<MGVertex, VertContain>

Container for neighbours of vertices.

◆ NbrsIter

using NbrsIter = NbrsContain::mapped_type::const_iterator

Type of the iterator returned by GetNeighbours() method.

◆ PredIter

using PredIter = typename graph_type::inv_adjacency_iterator

inherited

Type for iterator over predecessors of a vertex descriptor.

◆ SubgraphType

using SubgraphType = MolecularGraph

inherited

◆ VertContain

using VertContain = std::vector<MGVertex>

Container for vertices.

◆ VertexType

using VertexType = MGVertex

Type used for vertices.

◆ VertIter

using VertIter = VertContain::const_iterator

Type of the iterator returned by GetVertices() method.

◆ VertMap

using VertMap = indigox::utils::SimpleBiMap<MGVertex , VertType>

inherited

Type for bidirectional mapping of V to vertex descriptor type.

◆ VertType

using VertType = typename graph_type::vertex_descriptor

inherited

Type of the graph vertex descriptor.

Constructor & Destructor Documentation

◆ MolecularGraph() [1/4]

MolecularGraph ( )

default

Construct with a molecule.

Parameters

mol	the molecule to reference to.

◆ MolecularGraph() [2/4]

MolecularGraph ( const MolecularGraph & )

default

◆ MolecularGraph() [3/4]

MolecularGraph ( MolecularGraph && )

default

◆ ~ MolecularGraph()

~ MolecularGraph ( )

default

◆ MolecularGraph() [4/4]

MolecularGraph ( const Molecule & mol )

Member Function Documentation

◆ AddEdge()

void AddEdge	(	const MGVertex &	u,
		const MGVertex &	v,
		const MGEdge &	e
	)

protectedinherited

Add a new edge to the graph.

Vertex u is used as the source and vertex v as the target. If u and/or v are not already part of the graph, they are added. It is the callers responsibility to ensure that the edge is not part of the graph.

Parameters

u,v	vertices the edge is between.
e	the edge.

◆ AddVertex()

void AddVertex ( const MGVertex & v )

protectedinherited

Add a new vertex to the graph.

It is the callers responsability to ensure that the vertex added is not already part of the graph. If it is, a mismatch between the vertices in the graph and the what the _verts member thinks are in the graph may arise.

Parameters

v	the vertex to add.

◆ Degree()

int64_t Degree ( const MGVertex & v ) const

inherited

Degree of a vertex.

In the case of a directed graph, the degree of a vertex is the number of edges leaving the vertex.

Parameters

v	the vertex to get the degree of.

Returns: pair of the degree of the vertex and if it is valid.

◆ GetCondensedGraph()

const CondensedMolecularGraph& GetCondensedGraph ( )

◆ GetConnectedComponents()

const BaseGraph< MGVertex , MGEdge , MolecularGraph , Undirected , GraphLabel , GraphLabel >::ComponentContain & GetConnectedComponents ( )

inherited

Get the connected components of the graph.

Returns: reference to the connected components of the graph.

◆ GetCycles()

const BaseGraph< MGVertex , MGEdge , MolecularGraph , Undirected , GraphLabel , GraphLabel >::CycleEdgeContain & GetCycles ( )

inherited

Get the cycles of the graph.

Returns: the cycles of the graph.

◆ GetEdge() [1/2]

const MGEdge& GetEdge ( const Bond & bnd ) const

Get the edge associated with a bond.

If the bond is not associated with an edge on this graph, the returned edge is null.

Parameters

bnd	the bond to get the associated edge of.

Returns: the associated edge.

◆ GetEdge() [2/2]

MGEdge GetEdge	(	const MGVertex &	u,
		const MGVertex &	v
	)		const

inherited

Get the edge between two vertices.

It is the callers responsibilty to ensure that the vertices are a part of the graph.

Parameters

u,v	vertices to get the edge between.

Returns: a pair of the edge between the two vertces and if it is valid.

◆ GetEdges()

const BaseGraph< MGVertex , MGEdge , MolecularGraph , Undirected , GraphLabel , GraphLabel >::EdgeContain & GetEdges ( ) const

inherited

Get the edges of the graph.

Parameters

[out] edges the vector where the list of edges will be set. The vector is cleared before any edges are added to it.

Returns: the number of edges added to the vector.

◆ GetMolecule()

const Molecule& GetMolecule ( ) const

◆ GetNeighbours()

const BaseGraph< MGVertex , MGEdge , MolecularGraph , Undirected , GraphLabel , GraphLabel >::VertContain & GetNeighbours ( const MGVertex & v )

inherited

Get the neighbouring vertices of a vertex.

The neighbours of a vertex are those for which the edge v -> u exists within the graph. It is the callers responsibilty to ensure that the vertex is a part of the graph.

Parameters

	v	the vertex to get the neighbours of.
[out]	nbrs	the vector where the list of neighbours will be set. The vector is cleared before any neighbouring vertices are added to it.

Returns: if the vector has been populated or not.

◆ GetPredecessors()

const BaseGraph< MGVertex , MGEdge , MolecularGraph , Undirected , GraphLabel , GraphLabel >::VertContain & GetPredecessors ( const MGVertex & v )

inherited

Get the predecessor vertices of a vertex.

The predecessors of a vertex are those for which the edge u -> v exists within the graph. For an undirected graph, this is equivalent to the neighbours. It is the callers responsibilty to ensure that the vertex is a part of the graph.

Parameters

[in]	v	the vertex to get the predecessors of.
[out]	pres	the vector where the list of predecessors will be set. The vector is cleared before any predecessing vertices are added to it.

Returns: if the vector has been populated or not.

◆ GetSourceVertex()

MGVertex GetSourceVertex ( const MGEdge & e ) const

inherited

Get the source vertex of an edge.

It is the callers responsibilty to ensure that the edge is a part of the graph.

Parameters

e	the edge to get the source of.

Returns: a pair of the source vertex of the edge and if it is valid.

◆ GetSuccessors()

const BaseGraph< MGVertex , MGEdge , MolecularGraph , Undirected , GraphLabel , GraphLabel >::VertContain & GetSuccessors ( const MGVertex & v )

inherited

◆ GetSuperGraph()

const MolecularGraph& GetSuperGraph ( ) const

◆ GetTargetVertex()

MGVertex GetTargetVertex ( const MGEdge & e ) const

inherited

Get the target vertex of an edge.

It is the callers responsibilty to ensure that the edge is a part of the graph.

Parameters

e	the edge to get the target of.

Returns: the target vertex of the edge.

◆ GetVertex()

const MGVertex& GetVertex ( const Atom & atm ) const

Get the vertex associated with an atom.

If the atom is not associated with a vertex of this graph, the returned vertex is null.

Parameters

atm	the atom to get the assocaited vertex of.

Returns: the associated vertex.

◆ GetVertices() [1/2]

std::pair< MGVertex , MGVertex > GetVertices ( const MGEdge & e ) const

inherited

Get the two vertices that make up an edge.

It is the callers responsibility to ensure that the edge is a part of the graph.

Parameters

e	the edge to get vertices of.

Returns: a pair of a pair of the two vertices making up the edge and if they are valid.

◆ GetVertices() [2/2]

const BaseGraph< MGVertex , MGEdge , MolecularGraph , Undirected , GraphLabel , GraphLabel >::VertContain & GetVertices ( ) const

inherited

Get the vertices of the graph.

Parameters

[out] verts the vector where the list of vertices will be set. The vector is cleared before any vertices are added to it.

Returns: the number of vertices added to the vector.

◆ HasEdge() [1/3]

bool HasEdge ( const MGEdge & e ) const

inherited

Is the edge in the graph.

Parameters

e	edge to search for.

Returns: if the requested edge is contained in the graph or not.

◆ HasEdge() [2/3]

bool HasEdge	(	const MGVertex &	u,
		const MGVertex &	v
	)		const

inherited

Does an edge exist between two vertices.

Parameters

u,v	vertices to check between.

Returns: if there is an edge between the two vertices.

◆ HasEdge() [3/3]

bool HasEdge ( const Bond & e ) const

Check if the graph has an edge associated with a bond.

Parameters

e	the bond to check for.

Returns: if the bond is associated with the graph or not.

◆ HasVertex() [1/2]

bool HasVertex ( const MGVertex & v ) const

inherited

Is the vertex in the graph.

Parameters

v	vertex to search for.

Returns: if the requested vertex is contained in the graph or not.

◆ HasVertex() [2/2]

bool HasVertex ( const Atom & v ) const

Check if the graph has a vertex associated with an atom.

Parameters

v	that atom to check for.

Returns: if the atom is associated with the graph or not.

◆ InDegree()

int64_t InDegree ( const MGVertex & v ) const

inherited

Indegree of a vertex.

The indegree of a vertex is the number of edges entering the vertex. For an undirected graph, this is equivalent to Degree(V) const. It is the callers responsibilty to ensure that the vertex is a part of the graph.

Parameters

v	the vertex to get indegree of.

Returns: pair of the indegree of the vertex and if it is valid.

◆ IsConnected()

bool IsConnected ( )

inherited

Determine if the graph is connected.

Returns: if the graph is connected or not.

◆ IsCyclic() [1/4]

bool IsCyclic ( const MGVertex & v )

inherited

Determine if a vertex of this graph is cyclic.

Parameters

v	the vertex to check if in a cycle

Returns: if the vertex is in a cycle or not.

◆ IsCyclic() [2/4]

bool IsCyclic	(	const MGVertex &	v,
		uint32_t	sz
	)

inherited

◆ IsCyclic() [3/4]

bool IsCyclic ( const MGEdge & e )

inherited

Determine if an edge of this graph is cycle.

Parameters

e	the edge to check if in a cycle.

Returns: if the edge is in a cycle or not.

◆ IsCyclic() [4/4]

bool IsCyclic	(	const MGEdge &	e,
		uint32_t	sz
	)

inherited

◆ IsSubgraph()

bool IsSubgraph ( ) const

◆ NumConnectedComponents()

int64_t NumConnectedComponents ( )

inherited

Get the number of connected components of the graph.

Returns: the number of cnnected components of the graph.

◆ NumCycles()

int64_t NumCycles ( )

inherited

◆ NumEdges()

int64_t NumEdges ( ) const

inherited

Number of edges in the graph.

Returns: the number of edges in the graph.

◆ NumVertices()

int64_t NumVertices ( ) const

inherited

Number of vertices in the graph.

Returns: the number of vertices in the graph.

◆ operator bool()

operator bool ( ) const

inline

◆ operator!=()

bool operator!= ( const MolecularGraph & g ) const

inline

◆ operator<()

bool operator< ( const MolecularGraph & g ) const

◆ operator<=()

bool operator<= ( const MolecularGraph & g ) const

inline

◆ operator=() [1/2]

MolecularGraph& operator= ( MolecularGraph && )

default

◆ operator=() [2/2]

MolecularGraph& operator= ( const MolecularGraph & )

default

◆ operator==()

bool operator== ( const MolecularGraph & g ) const

◆ operator>()

bool operator> ( const MolecularGraph & g ) const

◆ operator>=()

bool operator>= ( const MolecularGraph & g ) const

inline

◆ Subgraph() [1/2]

MolecularGraph Subgraph ( std::vector< MGVertex > & vertices )

virtual

Induce a subgraph from the range of vertices.

Induced subgraph has the same vertices and edges as its parent graph. Additionally, its source Molecule is the same. This is a vertex induced subgraph, meaning that all edges where both vertices are in the provided range will be in the induced graph.

Template Parameters

InputIt type of the iterator range provided.

Parameters

begin,end marking the range of vertices to induce subgraph on.

Returns: a new MolecularGraph.

Implements BaseGraph< MGVertex, MGEdge, MolecularGraph >.

◆ Subgraph() [2/2]

MolecularGraph Subgraph	(	std::vector< MGVertex > &	vertices,
		std::vector< MGEdge > &	edges
	)

virtual

Implements BaseGraph< MGVertex, MGEdge, MolecularGraph >.

Friends And Related Function Documentation

◆ cereal::access

friend class cereal::access

friend

Friendship allows serialisation.

◆ indigox::Molecule

friend class indigox::Molecule

friend

Friendship allows an Molecule to own a graph.

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const MolecularGraph &	g
	)

friend

Member Data Documentation

◆ m_basedata

std::shared_ptr<BaseImpl> m_basedata

protectedinherited

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

include/indigox/graph/molecular.hpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ AtomMap

◆ BondMap

◆ ComponentContain

◆ CycleEdgeContain

◆ CycleVertContain

◆ EdgeContain

◆ EdgeIter

◆ EdgeMap

◆ EdgeType

◆ graph_type

◆ NbrsContain

◆ NbrsIter

◆ PredIter

◆ SubgraphType

◆ VertContain

◆ VertexType

◆ VertIter

◆ VertMap

◆ VertType

Constructor & Destructor Documentation

◆ MolecularGraph() [1/4]

◆ MolecularGraph() [2/4]

◆ MolecularGraph() [3/4]

◆ ~ MolecularGraph()

◆ MolecularGraph() [4/4]

Member Function Documentation

◆ AddEdge()

◆ AddVertex()

◆ Degree()

◆ GetCondensedGraph()

◆ GetConnectedComponents()

◆ GetCycles()

◆ GetEdge() [1/2]

◆ GetEdge() [2/2]

◆ GetEdges()

◆ GetMolecule()

◆ GetNeighbours()

◆ GetPredecessors()

◆ GetSourceVertex()

◆ GetSuccessors()

◆ GetSuperGraph()

◆ GetTargetVertex()

◆ GetVertex()

◆ GetVertices() [1/2]

◆ GetVertices() [2/2]

◆ HasEdge() [1/3]

◆ HasEdge() [2/3]

◆ HasEdge() [3/3]

◆ HasVertex() [1/2]

◆ HasVertex() [2/2]

◆ InDegree()

◆ IsConnected()

◆ IsCyclic() [1/4]

◆ IsCyclic() [2/4]

◆ IsCyclic() [3/4]

◆ IsCyclic() [4/4]

◆ IsSubgraph()

◆ NumConnectedComponents()

◆ NumCycles()

◆ NumEdges()

◆ NumVertices()

◆ operator bool()

◆ operator!=()

◆ operator<()

◆ operator<=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ operator>()

◆ operator>=()

◆ Subgraph() [1/2]

◆ Subgraph() [2/2]

Friends And Related Function Documentation