ambit2.sln

Class SLNAtom

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryChemObject

org.openscience.cdk.isomorphism.matchers.QueryAtom

org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

ambit2.sln.SLNAtom

All Implemented Interfaces:

Cloneable, org.openscience.cdk.interfaces.IAtom, org.openscience.cdk.interfaces.IAtomType, org.openscience.cdk.interfaces.ICDKObject, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IElement, org.openscience.cdk.interfaces.IIsotope, org.openscience.cdk.isomorphism.matchers.IQueryAtom

public class SLNAtom
extends org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

Abstract sln atom.

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType

org.openscience.cdk.interfaces.IAtomType.Hybridization

Field Summary

Fields

Modifier and Type	Field and Description
SLNAtomExpression	atomExpression
int	atomID
String	atomName
int	atomType
ISLNDictionaryObject	dictObj
int	numHAtom

Fields inherited from class org.openscience.cdk.isomorphism.matchers.QueryAtom

atomicNumber, charge, electronValency, exactMass, formalCharge, formalNeighbourCount, fractionalPoint3d, hybridization, hydrogenCount, naturalAbundance, point2d, point3d, stereoParity, symbol

Constructor Summary

Constructors

Constructor and Description
SLNAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
SLNAtom	clone()
boolean	matches(org.openscience.cdk.interfaces.IAtom atom)
String	toString()

Methods inherited from class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

chiralityMatches

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryAtom

bonds, getAtomicNumber, getAtomTypeName, getBondCount, getBondOrderSum, getCharge, getContainer, getCovalentRadius, getExactMass, getFormalCharge, getFormalNeighbourCount, getFractionalPoint3d, getHybridization, getImplicitHydrogenCount, getIndex, getMassNumber, getMaxBondOrder, getNaturalAbundance, getPoint2d, getPoint3d, getStereoParity, getSymbol, getValency, isAromatic, isInRing, setAtomicNumber, setAtomTypeName, setBondOrderSum, setCharge, setCovalentRadius, setExactMass, setFormalCharge, setFormalNeighbourCount, setFractionalPoint3d, setHybridization, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMassNumber, setMaxBondOrder, setNaturalAbundance, setPoint2d, setPoint3d, setStereoParity, setSymbol, setValency

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject

addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.IAtom

bonds, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setPoint2d, setPoint3d, setStereoParity

Methods inherited from interface org.openscience.cdk.interfaces.IAtomType

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency

Methods inherited from interface org.openscience.cdk.interfaces.IIsotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Methods inherited from interface org.openscience.cdk.interfaces.IElement

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Field Detail

atomType

public int atomType

atomName

public String atomName

atomID

public int atomID

numHAtom

public int numHAtom

dictObj

public ISLNDictionaryObject dictObj

atomExpression

public SLNAtomExpression atomExpression

Constructor Detail

SLNAtom

public SLNAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Detail

matches

public boolean matches(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

matches in interface org.openscience.cdk.isomorphism.matchers.IQueryAtom

Overrides:

matches in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

toString

public String toString()

Specified by:

toString in interface org.openscience.cdk.interfaces.IChemObject

Overrides:

toString in class Object

clone

public SLNAtom clone()

Specified by:

clone in interface org.openscience.cdk.interfaces.IAtom

Specified by:

clone in interface org.openscience.cdk.interfaces.IChemObject

Overrides:

clone in class org.openscience.cdk.isomorphism.matchers.QueryAtom