toxTree.query

Class ReallyAnyAtom

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryChemObject

org.openscience.cdk.isomorphism.matchers.QueryAtom

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

org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom

toxTree.query.ReallyAnyAtom

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 ReallyAnyAtom
extends org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom

To be used instead of org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom until its matcher code is fixed

 public boolean matches(IAtom atom) {
        if (atom.getSymbol().equals("H")) {
                Integer massNumber = atom.getMassNumber();
                return massNumber != null;
        }
        return true;
 }
 

Author:

nina

Nested Class Summary

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

org.openscience.cdk.interfaces.IAtomType.Hybridization

Field Summary

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
ReallyAnyAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
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

clone, getAtomicNumber, getAtomTypeName, getBondOrderSum, getCharge, getCovalentRadius, getExactMass, getFormalCharge, getFormalNeighbourCount, getFractionalPoint3d, getHybridization, getImplicitHydrogenCount, 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

clone, getCharge, getFractionalPoint3d, getImplicitHydrogenCount, 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

Constructor Detail

ReallyAnyAtom

public ReallyAnyAtom(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.AnyAtom

toString

public String toString()

Specified by:

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

Overrides:

toString in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom