Scine::Molassembler::PrivateGraph Class Reference

Library internal graph class wrapping BGL types. More...

#include <PrivateGraph.h>

Data Structures
struct	EdgeData
	Information stored at each graph edge. More...
struct	Properties
struct	RemovalSafetyData
	Data class to return removal safety information on the graph. More...
struct	VertexData
	Information stored at each graph vertex. More...

Public Types
Member types
using	BglType = boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, VertexData, EdgeData >
using	Vertex = BglType::vertex_descriptor
using	Edge = BglType::edge_descriptor
using	VertexRange = IteratorRange< BglType::vertex_iterator >
using	EdgeRange = IteratorRange< BglType::edge_iterator >
using	AdjacentVertexRange = IteratorRange< BglType::adjacency_iterator >
using	IncidentEdgeRange = IteratorRange< BglType::out_edge_iterator >

Public Member Functions
Constructors
	PrivateGraph ()
	Empty constructor.
	PrivateGraph (Vertex N)
	Preallocating constructor.
Rule of five members
	PrivateGraph (const PrivateGraph &other)
	PrivateGraph (PrivateGraph &&other)
PrivateGraph &	operator= (const PrivateGraph &other)
PrivateGraph &	operator= (PrivateGraph &&other)
	~PrivateGraph ()
Modification
Edge	addEdge (Vertex a, Vertex b, BondType bondType)
	Add an edge to the graph. More...
Vertex	addVertex (Utils::ElementType elementType)
	Add a (disconnected) vertex to the graph. More...
void	applyPermutation (const std::vector< Vertex > &permutation)
	Apply a permutation to the graph. More...
BondType &	bondType (const Edge &edge)
	Fetch the bond type of an edge. More...
BglType &	bgl ()
	Referential access to the underlying BGL graph.
void	clearVertex (Vertex a)
	Removes all bonds involving a vertex. More...
Utils::ElementType &	elementType (Vertex a)
	Fetches the element type of a vertex. More...
void	removeEdge (const Edge &e)
	Removes an edge from the graph. More...
void	removeVertex (Vertex a)
	Removes a vertex from the graph. More...
Information
Utils::ElementType	elementType (Vertex a) const
	Fetches the element type of a vertex. More...
BondType	bondType (const Edge &edge) const
	Fetch the bond type of an edge. More...
const BglType &	bgl () const
	Nonmodifiable access to the underlying BGL graph.
bool	canRemove (Vertex a) const
	Determine whether a vertex can be safely removed. More...
bool	canRemove (const Edge &edge) const
	Determine whether an edge can be safely removed An edge can be safely removed if it is not a bridge edge. More...
unsigned	connectedComponents () const
	Number of connected components. More...
unsigned	connectedComponents (std::vector< unsigned > &componentMap) const
	Connected components, yielding a map from vertices to component index. More...
Edge	edge (Vertex a, Vertex b) const
	Make an edge descriptor from two vertex descriptors. More...
boost::optional< Edge >	edgeOption (Vertex a, Vertex b) const
	Get an edge descriptor from two vertex descriptors, get None if the edge doesn't exist. More...
Vertex	source (const Edge &edge) const
	Source of an edge.
Vertex	target (const Edge &edge) const
	Target of an edge.
Vertex	degree (Vertex a) const
	Number of substituents of a vertex. More...
Vertex	N () const
	Number of vertices in the graph.
Vertex	B () const
	Number of edges in the graph.
boost::optional< std::vector < AtomIndex > >	modularIsomorphism (const PrivateGraph &other, AtomEnvironmentComponents components=AtomEnvironmentComponents::All) const
	Modular isomorphism comparison. More...
bool	identicalGraph (const PrivateGraph &other) const
	Checks whether all edges present in *this are present in other. More...
std::pair< std::vector < AtomIndex >, std::vector < AtomIndex > >	splitAlongBridge (Edge bridge) const
	Determine which vertices belong to which side of a bridge edge. More...
Cached properties access
Call complexity depends on whether the properties have been calculated before. After generation, properties are valid as long as no non-const method is called on this class that modifies state. None of these methods are thread-safe.
void	populateProperties () const
	Access cycle information of the graph.
const Cycles &	cycles () const
	Access cycle information of the graph.
const RemovalSafetyData &	removalSafetyData () const
	Access removal safety information of the graph.
const Cycles &	etaPreservedCycles () const
	Access cycle information of the graph with eta bonds preserved.
Ranges
VertexRange	vertices () const
EdgeRange	edges () const
AdjacentVertexRange	adjacents (Vertex a) const
IncidentEdgeRange	edges (Vertex a) const
Operators
bool	operator== (const PrivateGraph &other) const
	Full isomorphism comparison including element types and bond orders.
bool	operator!= (const PrivateGraph &other) const
	Full isomorphism comparison including element types and bond orders.

Static Public Attributes
Static members
static constexpr Vertex	removalPlaceholder = std::numeric_limits<Vertex>::max()
	Placeholder vertex index used to indicate that a vertex has been removed.

Private Member Functions
Private types
RemovalSafetyData	generateRemovalSafetyData_ () const
Cycles	generateCycles_ () const
Cycles	generateEtaPreservedCycles_ () const

Private Attributes
Private state
BglType	graph_
	A directly owned Boost Library Graph.
Properties	properties_
	Property caching.

Detailed Description

Library internal graph class wrapping BGL types.

Member Typedef Documentation

using Scine::Molassembler::PrivateGraph::AdjacentVertexRange = IteratorRange<BglType::adjacency_iterator>

The type of the BGL graph.

An adjacency list is used due to sparsity of the molecular graph.

using Scine::Molassembler::PrivateGraph::BglType = boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, VertexData, EdgeData >

The type of the BGL graph.

An adjacency list is used due to sparsity of the molecular graph.

using Scine::Molassembler::PrivateGraph::Edge = BglType::edge_descriptor

The type of the BGL graph.

An adjacency list is used due to sparsity of the molecular graph.

using Scine::Molassembler::PrivateGraph::EdgeRange = IteratorRange<BglType::edge_iterator>

The type of the BGL graph.

An adjacency list is used due to sparsity of the molecular graph.

using Scine::Molassembler::PrivateGraph::IncidentEdgeRange = IteratorRange<BglType::out_edge_iterator>

The type of the BGL graph.

An adjacency list is used due to sparsity of the molecular graph.

using Scine::Molassembler::PrivateGraph::Vertex = BglType::vertex_descriptor

The type of the BGL graph.

An adjacency list is used due to sparsity of the molecular graph.

using Scine::Molassembler::PrivateGraph::VertexRange = IteratorRange<BglType::vertex_iterator>

The type of the BGL graph.

An adjacency list is used due to sparsity of the molecular graph.

Member Function Documentation

Edge Scine::Molassembler::PrivateGraph::addEdge	(	Vertex	a,
		Vertex	b,
		BondType	bondType
	)

Add an edge to the graph.

Complexity \(\Theta(1)\)

Exceptions

std::logic_error

if the edge already exists

Vertex Scine::Molassembler::PrivateGraph::addVertex

(

Utils::ElementType

elementType

)

Add a (disconnected) vertex to the graph.

Complexity \(\Theta(1)\)

void Scine::Molassembler::PrivateGraph::applyPermutation

(

const std::vector< Vertex > &

permutation

)

Apply a permutation to the graph.

Complexity \(\Theta(V)\)

BondType& Scine::Molassembler::PrivateGraph::bondType

(

const Edge &

edge

)

Fetch the bond type of an edge.

Complexity \(\Theta(1)\)

Precondition

The edge exists

BondType Scine::Molassembler::PrivateGraph::bondType

(

const Edge &

edge

)

const

Fetch the bond type of an edge.

Complexity \(\Theta(1)\)

Precondition

The edge exists

bool Scine::Molassembler::PrivateGraph::canRemove

(

Vertex

a

)

const

Determine whether a vertex can be safely removed.

A Vertex can be safely removed if it is not an articulation vertex or if the number of vertices is more than one.

Complexity \(O(V)\) worst case, if removal data is cached \(\Theta(1)\)

Note

This function is not thread-safe.

bool Scine::Molassembler::PrivateGraph::canRemove

(

const Edge &

edge

)

const

Determine whether an edge can be safely removed An edge can be safely removed if it is not a bridge edge.

Complexity \(O(V)\) worst case, if removal data is cached \(\Theta(1)\)

Note

This function is not thread-safe.

void Scine::Molassembler::PrivateGraph::clearVertex

(

Vertex

a

)

Removes all bonds involving a vertex.

Complexity \(\Theta(1)\)

unsigned Scine::Molassembler::PrivateGraph::connectedComponents

(

)

const

Number of connected components.

Complexity \(\Theta(V)\)

unsigned Scine::Molassembler::PrivateGraph::connectedComponents

(

std::vector< unsigned > &

componentMap

)

const

Connected components, yielding a map from vertices to component index.

Complexity \(\Theta(V)\)

Vertex Scine::Molassembler::PrivateGraph::degree

(

Vertex

a

)

const

Number of substituents of a vertex.

Complexity \(\Theta(1)\)

Edge Scine::Molassembler::PrivateGraph::edge	(	Vertex	a,
		Vertex	b
	)		const

Make an edge descriptor from two vertex descriptors.

Exceptions

std::out_of_range

if the edge doesn't exist in the graph Complexity \(\Theta(1)\)

boost::optional<Edge> Scine::Molassembler::PrivateGraph::edgeOption	(	Vertex	a,
		Vertex	b
	)		const

Get an edge descriptor from two vertex descriptors, get None if the edge doesn't exist.

Complexity \(\Theta(1)\)

Utils::ElementType& Scine::Molassembler::PrivateGraph::elementType

(

Vertex

a

)

Fetches the element type of a vertex.

Complexity \(\Theta(1)\)

Precondition

The vertex exists

Utils::ElementType Scine::Molassembler::PrivateGraph::elementType

(

Vertex

a

)

const

Fetches the element type of a vertex.

Complexity \(\Theta(1)\)

Precondition

The vertex exists

bool Scine::Molassembler::PrivateGraph::identicalGraph

(

const PrivateGraph &

other

)

const

Checks whether all edges present in *this are present in other.

Complexity \(O(B)\)

boost::optional<std::vector<AtomIndex> > Scine::Molassembler::PrivateGraph::modularIsomorphism	(	const PrivateGraph &	other,
		AtomEnvironmentComponents	components = AtomEnvironmentComponents::All
	)		const

Modular isomorphism comparison.

Returns None if the molecules are not isomorphic. Returns an index mapping from this to other otherwise.

void Scine::Molassembler::PrivateGraph::removeEdge

(

const Edge &

e

)

Removes an edge from the graph.

Complexity \(\Theta(1)\)

void Scine::Molassembler::PrivateGraph::removeVertex

(

Vertex

a

)

Removes a vertex from the graph.

Complexity \(\Theta(1)\)

Warning

This invalidates ALL vertex and edge descriptors!

std::pair< std::vector<AtomIndex>, std::vector<AtomIndex> > Scine::Molassembler::PrivateGraph::splitAlongBridge

(

Edge

bridge

)

const

Determine which vertices belong to which side of a bridge edge.

Complexity \(\Theta(N)\)

Note

This function is not thread-safe.

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

• Molassembler/Graph/PrivateGraph.h