org.jscience.chemistry
Class Molecule

java.lang.Object
  extended by 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