ambit2.structure2name

Class IUPACNameGenerator

java.lang.Object

ambit2.structure2name.IUPACNameGenerator

public class IUPACNameGenerator
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected List<org.openscience.cdk.interfaces.IAtom>	acyclicAtoms
protected List<AcyclicComponent>	acyclicComponents
protected Map<org.openscience.cdk.interfaces.IAtom,int[]>	atomRingNumbers
protected List<IIUPACComponent>	components
protected org.openscience.cdk.graph.Cycles	cycles
protected List<org.openscience.cdk.interfaces.IAtom>	cyclicAtoms
protected List<CyclicComponent>	cyclicComponents
protected int	cyclomaticNum
protected List<ComponentConnection>	initialConnections
protected org.openscience.cdk.interfaces.IAtomContainer	molecule
protected org.openscience.cdk.interfaces.IAtomContainer	originalMolecule
protected org.openscience.cdk.interfaces.IRingSet	ringSet
protected IUPACRuleDataBase	ruleDataBase
protected List<org.openscience.cdk.interfaces.IAtom>	spiroAtoms

Constructor Summary

Constructors

Constructor and Description
IUPACNameGenerator()

Method Summary

Modifier and Type	Method and Description
protected void	findCyclicAndAcyclicComponets()
protected void	findSpiroAtoms()
protected AcyclicComponent	generateAcyclicComponent(org.openscience.cdk.interfaces.IAtom startAtom)
protected void	generateComponents()
String	generateIUPACName(org.openscience.cdk.interfaces.IAtomContainer mol)
protected IIUPACComponent	getBestRankComponent()
String	getComponentDataAsString()
protected CyclicComponent	getCyclicComponentForAtom(org.openscience.cdk.interfaces.IAtom at)
protected CyclicComponent	getCyclicComponentFusedToRing(org.openscience.cdk.interfaces.IAtomContainer ring)
protected ComponentConnection	getInitialConnection(IIUPACComponent c0, IIUPACComponent c1)
protected int	getRingNumber(org.openscience.cdk.interfaces.IAtomContainer ring)
IUPACRuleDataBase	getRuleDataBase()
protected void	init()
protected void	makeRindData()
protected void	nullify()
protected void	processAcyclicComponent(AcyclicComponent acomp)

Methods inherited from class java.lang.Object

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

Field Detail

ruleDataBase

protected IUPACRuleDataBase ruleDataBase

originalMolecule

protected org.openscience.cdk.interfaces.IAtomContainer originalMolecule

molecule

protected org.openscience.cdk.interfaces.IAtomContainer molecule

cyclomaticNum

protected int cyclomaticNum

cycles

protected org.openscience.cdk.graph.Cycles cycles

ringSet

protected org.openscience.cdk.interfaces.IRingSet ringSet

atomRingNumbers

protected Map<org.openscience.cdk.interfaces.IAtom,int[]> atomRingNumbers

spiroAtoms

protected List<org.openscience.cdk.interfaces.IAtom> spiroAtoms

acyclicAtoms

protected List<org.openscience.cdk.interfaces.IAtom> acyclicAtoms

cyclicAtoms

protected List<org.openscience.cdk.interfaces.IAtom> cyclicAtoms

cyclicComponents

protected List<CyclicComponent> cyclicComponents

acyclicComponents

protected List<AcyclicComponent> acyclicComponents

components

protected List<IIUPACComponent> components

initialConnections

protected List<ComponentConnection> initialConnections

Constructor Detail

IUPACNameGenerator

public IUPACNameGenerator()
                   throws Exception

Throws:

Exception

Method Detail

getRuleDataBase

public IUPACRuleDataBase getRuleDataBase()

generateIUPACName

public String generateIUPACName(org.openscience.cdk.interfaces.IAtomContainer mol)
                         throws Exception

Throws:

Exception

nullify

protected void nullify()

init

protected void init()

makeRindData

protected void makeRindData()

findSpiroAtoms

protected void findSpiroAtoms()

getRingNumber

protected int getRingNumber(org.openscience.cdk.interfaces.IAtomContainer ring)

generateComponents

protected void generateComponents()

findCyclicAndAcyclicComponets

protected void findCyclicAndAcyclicComponets()

generateAcyclicComponent

protected AcyclicComponent generateAcyclicComponent(org.openscience.cdk.interfaces.IAtom startAtom)

getCyclicComponentFusedToRing

protected CyclicComponent getCyclicComponentFusedToRing(org.openscience.cdk.interfaces.IAtomContainer ring)

getCyclicComponentForAtom

protected CyclicComponent getCyclicComponentForAtom(org.openscience.cdk.interfaces.IAtom at)

getInitialConnection

protected ComponentConnection getInitialConnection(IIUPACComponent c0,
                                                   IIUPACComponent c1)

processAcyclicComponent

protected void processAcyclicComponent(AcyclicComponent acomp)

getBestRankComponent

protected IIUPACComponent getBestRankComponent()

getComponentDataAsString

public String getComponentDataAsString()