Represents the connectivity of atoms of a molecule. More...

#include <Graph.h>

Inheritance diagram for Scine::Molassembler::Graph:

Data Structures
class	InnerBasedIterator
	Templated iterator facade based on PrivateGraph to provide iterative access to atom indices and edge indices. More...

Public Types
Member types
using	AtomIterator = InnerBasedIterator< AtomIndex, false >
	Iterator type yielding all valid atom indices.

using	BondIterator = InnerBasedIterator< BondIndex, false >
	Iterator type yielding all valid bond indices.

using	AdjacencyIterator = InnerBasedIterator< AtomIndex, true >
	Iterator type yielding adjacent atoms to an atom.

using	IncidentEdgesIterator = InnerBasedIterator< BondIndex, true >
	Iterator type yielding incident bonds to an atom.

Public Member Functions
PrivateGraph &	inner ()
	Access to library-internal graph representation class. More...

const PrivateGraph &	inner () const
	Const-access to library-internal graph representation class. More...

Special member functions
	Graph (Graph &&other) noexcept

Graph &	operator= (Graph &&other) noexcept

	Graph (const Graph &other)

Graph &	operator= (const Graph &other)

	~Graph () final

Constructors
	Graph ()
	Wrapping constructor.

	Graph (PrivateGraph &&inner)
	Wrapping constructor.

Modification
AtomIndex	addAtom (Utils::ElementType e, AtomIndex i, BondType type) final

BondIndex	addBond (AtomIndex i, AtomIndex j, BondType type) final

void	setElementType (AtomIndex i, Utils::ElementType type) final

bool	setBondType (AtomIndex i, AtomIndex j, BondType type) final

void	removeAtom (AtomIndex i) final

void	removeBond (const BondIndex &bond) final

Information
bool	adjacent (AtomIndex a, AtomIndex b) const final
	Returns whether two atoms are bonded. More...

std::vector< AtomIndex >	atomsOfElement (Utils::ElementType e) const
	Returns atoms matching an element type. More...

boost::optional< BondIndex >	bond (AtomIndex a, AtomIndex b) const final
	Optionally fetch the bond index of a possibly non-existent bond. More...

Utils::BondOrderCollection	bondOrders () const
	Generate a BondOrderCollection from the graph. More...

BondType	bondType (const BondIndex &edge) const final
	Fetch the bond type at a particular bond. More...

bool	canRemove (AtomIndex a) const final
	Returns whether an atom can be removed without disconnecting the graph. More...

bool	canRemove (const BondIndex &edge) const final
	Returns whether a bond can be removed without disconnecting the graph. More...

const Cycles &	cycles () const final
	Fetch a reference to Cycles. More...

unsigned	degree (AtomIndex a) const final
	Returns the number of bonds incident upon an atom. More...

std::string	dumpGraphviz () const
	Dumps a graphviz representation of the graph.

Utils::ElementTypeCollection	elementCollection () const
	Fetch an element collection of all atoms. More...

Utils::ElementType	elementType (AtomIndex a) const final
	Fetch the element type of an atom. More...

AtomIndex	N () const
	Number of atoms in the graph. More...

AtomIndex	V () const final
	Number of atoms in the graph. More...

unsigned	B () const
	Number of bonds in the graph. More...

unsigned	E () const final
	Number of bonds in the graph. More...

boost::optional< std::vector < AtomIndex > >	modularIsomorphism (const Graph &other, AtomEnvironmentComponents components=AtomEnvironmentComponents::All) const
	Modular isomorphism comparison. More...

std::pair< std::vector < AtomIndex >, std::vector < AtomIndex > >	splitAlongBridge (BondIndex bridge) const
	Determine which vertices belong to which side of a bridge edge. More...

Operators
bool	operator== (const Graph &other) const
	Full isomorphism comparison including element types and bond orders.

bool	operator!= (const Graph &other) const
	Full isomorphism comparison including element types and bond orders.

Ranges
IteratorRange< AtomIterator >	atoms () const
	A begin-end pair of iterators that yield the range of valid atom indices. More...

IteratorRange< BondIterator >	bonds () const
	A begin-end pair of iterators that yield the range of valid bond indices. More...

IteratorRange< AdjacencyIterator >	adjacents (AtomIndex a) const
	Fetch iterator pair yielding adjacents of an atom. More...

IteratorRange < IncidentEdgesIterator >	bonds (AtomIndex a) const
	Fetch iterator pair yielding bonds indices indicent to an atom. More...

Modification
Information

Private Attributes
std::unique_ptr< PrivateGraph >	innerPtr_

Detailed Description

Represents the connectivity of atoms of a molecule.

An undirected graph consisting of atom vertices and bond edges. Vertices store the atomic element type while vertices store a bond type that distinguishes the bond orders one through six as well as a so-called eta bond, which models connections between a central atom and a haptically-bonded subset of atoms (i.e. a contiguous group of atoms all bonded to a transition metal).

The Graph class leaves a consumer a lot of freedom in the specification of the molecule's graph, but does enforce some model limitations.

A molecule's graph must consist of a single connected component, meaning that there must be a path from any atom of the molecule to any other.
Single atoms are not considered molecules, so a molecule must consist of at least two mutually bonded atoms.
Removing atoms or bonds from diatomic molecules are disallowed operations.
Disconnecting a molecule into two logical molecules by removing a particular bond or atom is also disallowed.

Note: This class wraps PrivateGraph so that no Boost Graph types are exposed to library consumers.

Member Function Documentation

bool Scine::Molassembler::Graph::adjacent	(	AtomIndex	a,
		AtomIndex	b
	)		const

finalvirtual

Returns whether two atoms are bonded.

Complexity \(\Theta(1)\)

Implements Scine::Molassembler::GraphInterface.

IteratorRange<AdjacencyIterator> Scine::Molassembler::Graph::adjacents ( AtomIndex a ) const

Fetch iterator pair yielding adjacents of an atom.

Parameters

a	The atom whose adjacents are desired

Complexity \(\Theta(V)\)

Returns: A begin-end pair of iterators that yield adjacent atoms of an atom

IteratorRange<AtomIterator> Scine::Molassembler::Graph::atoms ( ) const

A begin-end pair of iterators that yield the range of valid atom indices.

Complexity \(\Theta(V)\)

std::vector<AtomIndex> Scine::Molassembler::Graph::atomsOfElement ( Utils::ElementType e ) const

Returns atoms matching an element type.

Complexity \(\Theta(V)\)

unsigned Scine::Molassembler::Graph::B ( ) const

Number of bonds in the graph.

Complexity \(\Theta(1)\)

boost::optional<BondIndex> Scine::Molassembler::Graph::bond	(	AtomIndex	a,
		AtomIndex	b
	)		const

finalvirtual

Optionally fetch the bond index of a possibly non-existent bond.

Complexity \(\Theta(1)\)

Implements Scine::Molassembler::GraphInterface.

Utils::BondOrderCollection Scine::Molassembler::Graph::bondOrders ( ) const

Generate a BondOrderCollection from the graph.

Complexity \(\Theta(E)\)

IteratorRange<BondIterator> Scine::Molassembler::Graph::bonds ( ) const

A begin-end pair of iterators that yield the range of valid bond indices.

Complexity \(\Theta(V)\)

IteratorRange<IncidentEdgesIterator> Scine::Molassembler::Graph::bonds ( AtomIndex a ) const

Fetch iterator pair yielding bonds indices indicent to an atom.

Parameters

a	The atom whose incident atoms are desired

Complexity \(\Theta(V)\)

Returns: A begin-end pair of iterators that yield incident bond indices of an atom

BondType Scine::Molassembler::Graph::bondType ( const BondIndex & edge ) const

finalvirtual

Fetch the bond type at a particular bond.

Complexity \(\Theta(1)\)

Implements Scine::Molassembler::GraphInterface.

bool Scine::Molassembler::Graph::canRemove ( AtomIndex a ) const

finalvirtual

Returns whether an atom can be removed without disconnecting the graph.

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

Note: This function is not thread-safe.

Implements Scine::Molassembler::GraphInterface.

bool Scine::Molassembler::Graph::canRemove ( const BondIndex & edge ) const

finalvirtual

Returns whether a bond can be removed without disconnecting the graph.

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

Note: This function is not thread-safe.

Implements Scine::Molassembler::GraphInterface.

const Cycles& Scine::Molassembler::Graph::cycles ( ) const

finalvirtual

Fetch a reference to Cycles.

Complexity \(O(E)\) worst case where \(B\) is the number of bonds in cycles, if cycles are cached \(\Theta(1)\)

Note: This function is not thread-safe.

Implements Scine::Molassembler::GraphInterface.

unsigned Scine::Molassembler::Graph::degree ( AtomIndex a ) const

finalvirtual

Returns the number of bonds incident upon an atom.

Complexity \(\Theta(1)\)

Implements Scine::Molassembler::GraphInterface.

unsigned Scine::Molassembler::Graph::E ( ) const

finalvirtual

Number of bonds in the graph.

Complexity \(\Theta(1)\)

Implements Scine::Molassembler::GraphInterface.

Utils::ElementTypeCollection Scine::Molassembler::Graph::elementCollection ( ) const

Fetch an element collection of all atoms.

Complexity \(\Theta(V)\)

Utils::ElementType Scine::Molassembler::Graph::elementType ( AtomIndex a ) const

finalvirtual

Fetch the element type of an atom.

Complexity \(\Theta(1)\)

Implements Scine::Molassembler::GraphInterface.

PrivateGraph& Scine::Molassembler::Graph::inner ( )

Access to library-internal graph representation class.

Complexity \(\Theta(1)\)

Warning: This function is not intended for library consumers, merely used for implementation purposes.

const PrivateGraph& Scine::Molassembler::Graph::inner ( ) const

Const-access to library-internal graph representation class.

Complexity \(\Theta(1)\)

Warning: This function is not intended for library consumers, merely used for implementation purposes.

boost::optional<std::vector<AtomIndex> > Scine::Molassembler::Graph::modularIsomorphism	(	const Graph &	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.

AtomIndex Scine::Molassembler::Graph::N ( ) const

Number of atoms in the graph.

Complexity \(\Theta(1)\)

std::pair< std::vector<AtomIndex>, std::vector<AtomIndex> > Scine::Molassembler::Graph::splitAlongBridge ( BondIndex bridge ) const

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

Complexity \(\Theta(V)\)

The atoms making up the bond are in the resulting atom lists, too.

Note: This function is not thread-safe.

AtomIndex Scine::Molassembler::Graph::V ( ) const

finalvirtual

Number of atoms in the graph.

Complexity \(\Theta(1)\)

Implements Scine::Molassembler::GraphInterface.

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

Molassembler/Graph.h

Data Structures

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Function Documentation