Class MolecularGraph

java.lang.Object

org.episteme.natural.chemistry.MolecularGraph

All Implemented Interfaces:

Graph<Atom>

public class MolecularGraph
extends Object
implements Graph<Atom>

Represents a molecule as a graph of atoms and bonds.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MolecularGraph.Bond
static enum	MolecularGraph.BondType

Nested classes/interfaces inherited from interface Graph

Graph.Edge<V>

Constructor Summary

Constructors

Constructor	Description
MolecularGraph()

Method Summary

Modifier and Type	Method	Description
void	addAtom(Atom atom)
void	addBond(Atom a, Atom b, MolecularGraph.BondType type)
boolean	addEdge(Atom source, Atom target)	Adds an edge between two vertices.
boolean	addVertex(Atom vertex)	Adds a vertex to the graph.
int	degree(Atom vertex)	Returns the degree (number of edges) of a vertex.
Set<Graph.Edge<Atom>>	edges()	Returns all edges in this graph.
List<Atom>	getAtoms()
List<MolecularGraph.Bond>	getBonds()
Map<Atom, List<MolecularGraph.Bond>>	getConnections()	connection table: Mapinvalid input: '<'Atom, List>
String	getFormula()	Returns the formula (e.g.
double	getMolecularMass()	Calculates molecular mass.
boolean	isDirected()	Checks if this graph is directed.
Set<Atom>	neighbors(Atom vertex)	Returns neighbors of a vertex.
String	toString()
int	vertexCount()	Returns the number of vertices in the graph.
Set<Atom>	vertices()	Returns all vertices in this graph.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface Graph

bfs, dfs

Constructor Details

MolecularGraph

public MolecularGraph()

Method Details

addAtom

public void addAtom(Atom atom)

addBond

public void addBond(Atom a,
 Atom b,
 MolecularGraph.BondType type)

getAtoms

public List<Atom> getAtoms()

getBonds

public List<MolecularGraph.Bond> getBonds()

getConnections

public Map<Atom, List<MolecularGraph.Bond>> getConnections()

connection table: Mapinvalid input: '<'Atom, List>

getMolecularMass

public double getMolecularMass()

Calculates molecular mass.

getFormula

public String getFormula()

Returns the formula (e.g. C6H6).

toString

public String toString()

Overrides:

toString in class Object

vertices

public Set<Atom> vertices()

Description copied from interface: Graph

Returns all vertices in this graph.

Specified by:

vertices in interface Graph<Atom>

Returns:

unmodifiable set of vertices

edges

public Set<Graph.Edge<Atom>> edges()

Description copied from interface: Graph

Returns all edges in this graph.

Specified by:

edges in interface Graph<Atom>

Returns:

unmodifiable set of edges

addVertex

public boolean addVertex(Atom vertex)

Description copied from interface: Graph

Adds a vertex to the graph.

Specified by:

addVertex in interface Graph<Atom>

Parameters:

vertex - the vertex to add

Returns:

true if vertex was added, false if already present

addEdge

public boolean addEdge(Atom source,
 Atom target)

Description copied from interface: Graph

Adds an edge between two vertices.

Specified by:

addEdge in interface Graph<Atom>

Parameters:

source - the source vertex

target - the target vertex

Returns:

true if edge was added

neighbors

public Set<Atom> neighbors(Atom vertex)

Description copied from interface: Graph

Returns neighbors of a vertex.

Specified by:

neighbors in interface Graph<Atom>

Parameters:

vertex - the vertex

Returns:

set of adjacent vertices

degree

public int degree(Atom vertex)

Description copied from interface: Graph

Returns the degree (number of edges) of a vertex.

Specified by:

degree in interface Graph<Atom>

Parameters:

vertex - the vertex

Returns:

degree of vertex

isDirected

public boolean isDirected()

Description copied from interface: Graph

Checks if this graph is directed.

Specified by:

isDirected in interface Graph<Atom>

Returns:

true if directed, false if undirected

vertexCount

public int vertexCount()

Description copied from interface: Graph

Returns the number of vertices in the graph.

Specified by:

vertexCount in interface Graph<Atom>

Returns:

the number of vertices