Class Molecule

java.lang.Object

org.episteme.natural.chemistry.Molecule

All Implemented Interfaces:

Serializable, Commented, ComprehensiveIdentification, Identified<Identification>, Named

Direct Known Subclasses:

AminoAcid, Protein

public class Molecule
extends Object
implements ComprehensiveIdentification

A molecule: collection of atoms connected by bonds.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected final Map<String,Object>	traits

Constructor Summary

Constructors

Constructor	Description
Molecule(String name)

Method Summary

Modifier and Type	Method	Description
void	addAtom(Atom atom)
void	addBond(Bond bond)
int	getAtomCount()
List<Atom>	getAtoms()
int	getBondCount()
List<Bond>	getBonds()
List<Bond>	getBondsFor(Atom atom)	Gets all bonds connected to an atom.
String	getFormula()	Molecular formula (simplified).
Identification	getId()	Returns the unique identifier of this entity.
Quantity<Mass>	getMolecularWeight()	Molecular weight (sum of atomic masses).
String	getName()
List<Atom>	getNeighbors(Atom atom)	Gets all neighbors of an atom.
Map<String,Object>	getTraits()	Returns the traits map for this entity.
void	setName(String name)	Sets the name of this entity.
String	toString()

Methods inherited from class Object

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

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getTrait, setTrait

Field Details

traits

protected final Map<String,Object> traits

Constructor Details

Molecule

public Molecule(String name)

Method Details

getId

public Identification getId()

Description copied from interface: Identified

Returns the unique identifier of this entity.

Specified by:

getId in interface Identified<Identification>

Returns:

the identifier

getTraits

public Map<String,Object> getTraits()

Description copied from interface: ComprehensiveIdentification

Returns the traits map for this entity.

Specified by:

getTraits in interface Commented

Specified by:

getTraits in interface ComprehensiveIdentification

Returns:

the traits map

setName

public void setName(String name)

Description copied from interface: ComprehensiveIdentification

Sets the name of this entity.

Specified by:

setName in interface ComprehensiveIdentification

Parameters:

name - the name to set

addAtom

public void addAtom(Atom atom)

addBond

public void addBond(Bond bond)

getName

public String getName()

Specified by:

getName in interface ComprehensiveIdentification

Specified by:

getName in interface Named

getAtoms

public List<Atom> getAtoms()

getBonds

public List<Bond> getBonds()

getAtomCount

public int getAtomCount()

getBondCount

public int getBondCount()

getBondsFor

public List<Bond> getBondsFor(Atom atom)

Gets all bonds connected to an atom.

getNeighbors

public List<Atom> getNeighbors(Atom atom)

Gets all neighbors of an atom.

getFormula

public String getFormula()

Molecular formula (simplified).

getMolecularWeight

public Quantity<Mass> getMolecularWeight()

Molecular weight (sum of atomic masses). Uses Real for high precision.

toString

public String toString()

Overrides:

toString in class Object