toxTree.query
Class ReallyAnyAtom

java.lang.Object
  extended by org.openscience.cdk.ChemObject
      extended by org.openscience.cdk.Element
          extended by org.openscience.cdk.Isotope
              extended by org.openscience.cdk.AtomType
                  extended by org.openscience.cdk.Atom
                      extended by org.openscience.cdk.PseudoAtom
                          extended by org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
                              extended by org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
                                  extended by toxTree.query.ReallyAnyAtom
All Implemented Interfaces:
java.io.Serializable, java.lang.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.interfaces.IPseudoAtom, 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
See Also:
Serialized Form

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.Atom
charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity
 
Fields inherited from class org.openscience.cdk.AtomType
electronValency, formalCharge, formalNeighbourCount, hybridization
 
Fields inherited from class org.openscience.cdk.Isotope
exactMass, naturalAbundance
 
Fields inherited from class org.openscience.cdk.Element
atomicNumber, symbol
 
Constructor Summary
ReallyAnyAtom()
           
 
Method Summary
 boolean matches(org.openscience.cdk.interfaces.IAtom atom)
           
 java.lang.String toString()
           
 
Methods inherited from class org.openscience.cdk.PseudoAtom
clone, getLabel, setLabel, setStereoParity
 
Methods inherited from class org.openscience.cdk.Atom
compare, getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setPoint2d, setPoint3d
 
Methods inherited from class org.openscience.cdk.AtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
 
Methods inherited from class org.openscience.cdk.Isotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
 
Methods inherited from class org.openscience.cdk.Element
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
 
Methods inherited from class org.openscience.cdk.ChemObject
addListener, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
 
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
getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, 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, clone, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, 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()
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 java.lang.String toString()
Specified by:
toString in interface org.openscience.cdk.interfaces.IChemObject
Overrides:
toString in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom


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