org.jscience.chemistry
Class Molecule

java.lang.Object
  org.jscience.chemistry.Molecule

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

ADP, AminoAcid, AMP, ATP, Base, Cholesterol, Citronellol, CO2, Deoxyribose, Fructose, Galactose, Glucose, H2O, Lactose, NAD, O2, PhosphatidylCholine, Ribose, Sucrose, Triacylglycerol

public class Molecule
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable

A class representing molecules.

See Also:

Serialized Form

Constructor Summary

protected

Molecule(Atom a)

Method Summary

java.lang.Object	clone()
double	computeBondingEnergy()
double	computeMolecularWeight()
boolean	containsAtom(Atom a)
boolean	containsBond(Bond b)
java.util.Set	getAtoms()
double	getBoilingPoint()
java.util.Set	getBonds()
java.lang.String	getCASRegistryNumber() Returns the CAS registry number.
double	getCharge()
double	getCombustionEnthaply()
double	getDensity()
double	getEnthropy()
double	getFormationEnthalpy()
java.lang.String	getFormula() Returns the formula in this molecule.
double	getFusionEnthalpy()
double	getFusionEnthropy()
double	getMeltingEnthalpy()
double	getMeltingEnthropy()
double	getMeltingPoint()
double	getMolecularWeight()
double	getSpecificHeat()
double	getVanDerWaalsA()
double	getVanDerWaalsB()
boolean	isBondingIsomer(Molecule m)
boolean	isChemicalIsomer(Molecule m)
boolean	isIon()
boolean	isValidCASNumber()
static boolean	isValidCASNumber(java.lang.String casNumber) Checks wether the registry number is valid.
void	setBoilingPoint(double boilingPoint)
void	setCASRegistryNumber(java.lang.String casRegistryNumber) Sets the CAS registry number.
void	setCombustionEnthaply(double combustionEnthaply)
void	setDensity(double density)
void	setEnthropy(double enthropy)
void	setFormationEnthalpy(double formationEnthalpy)
void	setFusionEnthalpy(double fusionEnthalpy)
void	setFusionEnthropy(double fusionEnthropy)
void	setMeltingEnthalpy(double meltingEnthalpy)
void	setMeltingEnthropy(double meltingEnthropy)
void	setMeltingPoint(double meltingPoint)
void	setMolecularWeight(double molecularWeight)
void	setSpecificHeat(double specificHeat)
void	setVanDerWaalsA(double vanDerWaalsA)
void	setVanDerWaalsB(double vanDerWaalsB)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Molecule

protected Molecule(Atom a)

Method Detail

getFormula

public java.lang.String getFormula()

Returns the formula in this molecule.

computeMolecularWeight

public double computeMolecularWeight()

Returns:

getMolecularWeight

public double getMolecularWeight()

setMolecularWeight

public void setMolecularWeight(double molecularWeight)

getMeltingPoint

public double getMeltingPoint()

setMeltingPoint

public void setMeltingPoint(double meltingPoint)

getBoilingPoint

public double getBoilingPoint()

setBoilingPoint

public void setBoilingPoint(double boilingPoint)

getDensity

public double getDensity()

setDensity

public void setDensity(double density)

getVanDerWaalsA

public double getVanDerWaalsA()

setVanDerWaalsA

public void setVanDerWaalsA(double vanDerWaalsA)

getVanDerWaalsB

public double getVanDerWaalsB()

setVanDerWaalsB

public void setVanDerWaalsB(double vanDerWaalsB)

getFormationEnthalpy

public double getFormationEnthalpy()

setFormationEnthalpy

public void setFormationEnthalpy(double formationEnthalpy)

getMeltingEnthalpy

public double getMeltingEnthalpy()

setMeltingEnthalpy

public void setMeltingEnthalpy(double meltingEnthalpy)

getFusionEnthalpy

public double getFusionEnthalpy()

setFusionEnthalpy

public void setFusionEnthalpy(double fusionEnthalpy)

getCombustionEnthaply

public double getCombustionEnthaply()

setCombustionEnthaply

public void setCombustionEnthaply(double combustionEnthaply)

getEnthropy

public double getEnthropy()

setEnthropy

public void setEnthropy(double enthropy)

getMeltingEnthropy

public double getMeltingEnthropy()

setMeltingEnthropy

public void setMeltingEnthropy(double meltingEnthropy)

getFusionEnthropy

public double getFusionEnthropy()

setFusionEnthropy

public void setFusionEnthropy(double fusionEnthropy)

getSpecificHeat

public double getSpecificHeat()

setSpecificHeat

public void setSpecificHeat(double specificHeat)

getCASRegistryNumber

public java.lang.String getCASRegistryNumber()

Returns the CAS registry number.

setCASRegistryNumber

public void setCASRegistryNumber(java.lang.String casRegistryNumber)

Sets the CAS registry number. Empty means unknown but null is not allowed.

isValidCASNumber

public boolean isValidCASNumber()

isValidCASNumber

public static boolean isValidCASNumber(java.lang.String casNumber)

Checks wether the registry number is valid. See CAS website.

isIon

public boolean isIon()

getCharge

public double getCharge()

getAtoms

public java.util.Set getAtoms()

containsAtom

public boolean containsAtom(Atom a)

getBonds

public java.util.Set getBonds()

containsBond

public boolean containsBond(Bond b)

computeBondingEnergy

public double computeBondingEnergy()

isChemicalIsomer

public boolean isChemicalIsomer(Molecule m)

isBondingIsomer

public boolean isBondingIsomer(Molecule m)

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object