QueryAtom (cdk 2.5 API)

java.lang.Object
- org.openscience.cdk.isomorphism.matchers.QueryChemObject
- - org.openscience.cdk.isomorphism.matchers.QueryAtom

All Implemented Interfaces:

Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope, IQueryAtom

Direct Known Subclasses:

InverseSymbolSetQueryAtom, SMARTSAtom, SymbolAndChargeQueryAtom, SymbolChargeIDQueryAtom, SymbolQueryAtom, SymbolSetQueryAtom
```
public class QueryAtom
extends QueryChemObject
implements IQueryAtom
```
Source code:
master

Belongs to CDK module:
isomorphism

Nested Class Summary
- Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
  IAtomType.Hybridization

Field Summary

Fields
Modifier and Type	Field and Description
`protected Integer`	`atomicNumber` The atomic number for this element giving their position in the periodic table.
`protected Double`	`charge` The partial charge of the atom.
`protected Integer`	`electronValency` The electron Valency of this atom with CDKConstants.UNSET as default.
`Double`	`exactMass` Exact mass of this isotope.
`protected Integer`	`formalCharge` The formal charge of the atom with CDKConstants.UNSET as default.
`protected Integer`	`formalNeighbourCount` The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
`protected javax.vecmath.Point3d`	`fractionalPoint3d` A 3 point specifying the location of this atom in a crystal unit cell.
`protected IAtomType.Hybridization`	`hybridization` The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
`protected Integer`	`hydrogenCount` The number of implicitly bound hydrogen atoms for this atom.
`Double`	`naturalAbundance` Natural abundance of this isotope.
`protected javax.vecmath.Point2d`	`point2d` A 2D point specifying the location of this atom in a 2D coordinate space.
`protected javax.vecmath.Point3d`	`point3d` A 3 point specifying the location of this atom in a 3D coordinate space.
`protected Integer`	`stereoParity` A stereo parity descriptor for the stereochemistry of this atom.
`protected String`	`symbol` The element symbol for this element as listed in the periodic table.

Fields inherited from interface org.openscience.cdk.interfaces.IElement
Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fl, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Lv, Mc, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Nh, Ni, No, Np, O, Og, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, Ts, U, V, W, Wildcard, Xe, Y, Yb, Zn, Zr

Constructor Summary

Constructors
Constructor and Description
`QueryAtom(Expr.Type type)` Create a new query atom with the given an predicate expression type.
`QueryAtom(Expr.Type type, int val)` Create a new query atom with the given an value expression type.
`QueryAtom(Expr expr)` Create a new query atom with the given an expression.
`QueryAtom(IChemObjectBuilder builder)`
`QueryAtom(String symbol, IChemObjectBuilder builder)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Iterable<IBond>`	`bonds()` Returns the bonds connected to this atom.
`IAtom`	`clone()` Returns a deep clone of this IChemObject.
`boolean`	`equals(Object obj)`
`Integer`	`getAtomicNumber()` Returns the atomic number of this element.
`String`	`getAtomTypeName()` Gets the id attribute of the AtomType object.
`IBond`	`getBond(IAtom atom)` Returns the bond connecting 'this' atom to the provided atom.
`int`	`getBondCount()` Get the number of explicit bonds connected to this atom.
`Double`	`getBondOrderSum()` Gets the bondOrderSum attribute of the AtomType object.
`Double`	`getCharge()` Returns the partial charge of this atom.
`IAtomContainer`	`getContainer()` Access the `IAtomContainer` of which this atom is a member of.
`Double`	`getCovalentRadius()` Returns the covalent radius for this AtomType.
`Double`	`getExactMass()` Gets the ExactMass attribute of the Isotope object.
`Expr`	`getExpression()` Get the atom-expression predicate for this query atom.
`Integer`	`getFormalCharge()` Returns the formal charge of this atom.
`Integer`	`getFormalNeighbourCount()` Returns the formal neighbour count of this atom.
`javax.vecmath.Point3d`	`getFractionalPoint3d()` Returns a point specifying the location of this atom in a Crystal unit cell.
`IAtomType.Hybridization`	`getHybridization()` Returns the hybridization of this atom.
`Integer`	`getImplicitHydrogenCount()` Returns the hydrogen count of this atom.
`int`	`getIndex()` Acces the index of an atom in the context of an `IAtomContainer`.
`int`	`getMapIdx()` Access the map index for this atom.
`Integer`	`getMassNumber()` Returns the atomic mass of this element.
`IBond.Order`	`getMaxBondOrder()` Gets the MaxBondOrder attribute of the AtomType object.
`Double`	`getNaturalAbundance()` Gets the NaturalAbundance attribute of the Isotope object.
`javax.vecmath.Point2d`	`getPoint2d()` Returns a point specifying the location of this atom in a 2D space.
`javax.vecmath.Point3d`	`getPoint3d()` Returns a point specifying the location of this atom in a 3D space.
`Integer`	`getStereoParity()` Returns the stereo parity of this atom.
`String`	`getSymbol()` Returns the element symbol of this element.
`Integer`	`getValency()` Gets the the exact electron valency of the AtomType object.
`int`	`hashCode()`
`boolean`	`isAromatic()` Access whether this atom has been marked as aromatic.
`boolean`	`isInRing()` Access whether this atom has been flagged as in a ring.
`boolean`	`matches(IAtom atom)` Returns true of the given `atom` matches this IQueryAtom.
`void`	`setAtomicNumber(Integer atomicNumber)` Sets the atomic number of this element.
`void`	`setAtomTypeName(String identifier)` Sets the if attribute of the AtomType object.
`void`	`setBondOrderSum(Double bondOrderSum)` Sets the the exact bond order sum attribute of the AtomType object.
`void`	`setCharge(Double charge)` Sets the partial charge of this atom.
`void`	`setCovalentRadius(Double radius)` Sets the covalent radius for this AtomType.
`void`	`setExactMass(Double exactMass)` Sets the ExactMass attribute of the Isotope object.
`void`	`setExpression(Expr expr)` Set the atom-expression predicate for this query atom.
`void`	`setFormalCharge(Integer charge)` Sets the formal charge of this atom.
`void`	`setFormalNeighbourCount(Integer count)` Sets the formal neighbour count of this atom.
`void`	`setFractionalPoint3d(javax.vecmath.Point3d point3d)` Sets a point specifying the location of this atom in a Crystal unit cell.
`void`	`setHybridization(IAtomType.Hybridization hybridization)` Sets the hybridization of this atom.
`void`	`setImplicitHydrogenCount(Integer hydrogenCount)` Sets the number of implicit hydrogen count of this atom.
`void`	`setIsAromatic(boolean arom)` Mark this atom as being aromatic.
`void`	`setIsInRing(boolean ring)` Mark this atom as being in a ring.
`void`	`setMapIdx(int mapidx)` Set the map index for this atom.
`void`	`setMassNumber(Integer massNumber)` Sets the atomic mass of this element.
`void`	`setMaxBondOrder(IBond.Order maxBondOrder)` Sets the MaxBondOrder attribute of the AtomType object.
`void`	`setNaturalAbundance(Double naturalAbundance)` Sets the NaturalAbundance attribute of the Isotope object.
`void`	`setPoint2d(javax.vecmath.Point2d point2d)` Sets a point specifying the location of this atom in a 2D space.
`void`	`setPoint3d(javax.vecmath.Point3d point3d)` Sets a point specifying the location of this atom in 3D space.
`void`	`setStereoParity(Integer stereoParity)` Sets the stereo parity for this atom.
`void`	`setSymbol(String symbol)` Sets the element symbol of this element.
`void`	`setValency(Integer valency)` Sets the the exact electron valency of the AtomType object.

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
finalize, getClass, notify, notifyAll, toString, wait, wait, wait

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, toString

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

- Field Detail
  - charge
```
protected Double charge
```
    The partial charge of the atom.
    The default value is CDKConstants.UNSET and serves to provide a check whether the charge has been set or not
  - point2d
```
protected javax.vecmath.Point2d point2d
```
    A 2D point specifying the location of this atom in a 2D coordinate space.
  - point3d
```
protected javax.vecmath.Point3d point3d
```
    A 3 point specifying the location of this atom in a 3D coordinate space.
  - fractionalPoint3d
```
protected javax.vecmath.Point3d fractionalPoint3d
```
    A 3 point specifying the location of this atom in a crystal unit cell.
  - hydrogenCount
```
protected Integer hydrogenCount
```
    The number of implicitly bound hydrogen atoms for this atom.
  - stereoParity
```
protected Integer stereoParity
```
    A stereo parity descriptor for the stereochemistry of this atom.
  - formalCharge
```
protected Integer formalCharge
```
    The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6.
    Note that some constructors e.g. (AtomType(String) and AtomType(String, String) ) will explicitly set this field to 0
  - hybridization
```
protected IAtomType.Hybridization hybridization
```
    The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
  - electronValency
```
protected Integer electronValency
```
    The electron Valency of this atom with CDKConstants.UNSET as default.
  - formalNeighbourCount
```
protected Integer formalNeighbourCount
```
    The formal number of neighbours this atom type can have with CDKConstants_UNSET as default. This includes explicitely and implicitely connected atoms, including implicit hydrogens.
  - exactMass
```
public Double exactMass
```
    Exact mass of this isotope.
  - naturalAbundance
```
public Double naturalAbundance
```
    Natural abundance of this isotope.
  - symbol
```
protected String symbol
```
    The element symbol for this element as listed in the periodic table.
  - atomicNumber
```
protected Integer atomicNumber
```
    The atomic number for this element giving their position in the periodic table.
- Constructor Detail
  - QueryAtom
```
public QueryAtom(String symbol,
                 IChemObjectBuilder builder)
```
  - QueryAtom
```
public QueryAtom(IChemObjectBuilder builder)
```
  - QueryAtom
```
public QueryAtom(Expr expr)
```
    Create a new query atom with the given an expression.
```
 // oxygen in a ring
 Expr expr = new Expr(IS_IN_RING);
 expr.and(new Expr(ELEMENT, 8));
 new QueryAtom(expr);
 
```
    Parameters:
    
    expr - the expr
  - QueryAtom
```
public QueryAtom(Expr.Type type)
```
    Create a new query atom with the given an predicate expression type.
```
 new QueryAtom(IS_IN_RING);
 
```
    Parameters:
    
    type - the expr type
  - QueryAtom
```
public QueryAtom(Expr.Type type,
                 int val)
```
    Create a new query atom with the given an value expression type.
```
 // oxygen
 new QueryAtom(ELEMENT, 8);
 
```
    Parameters:
    
    type - the expr type
    
    val - the expr value
- Method Detail
  - getIndex
```
public int getIndex()
```
    Acces the index of an atom in the context of an IAtomContainer. If the index is not known, < 0 is returned.
    
    Specified by:
    
    getIndex in interface IAtom
    
    Returns:
    
    atom index or < 0 if the index is not known
  - getContainer
```
public IAtomContainer getContainer()
```
    Access the IAtomContainer of which this atom is a member of. Because atoms can be in multiple molecules this method will only work if the atom has been accessed in the context of an IAtomContainer, for example:
```
 IAtomContainer mol  = new AtomContainer();
 IAtom          atom = new Atom(6);

 atom.getContainer(); // null
 mol.add(atom);
 atom.getContainer(); // still null
 mol.getAtom(0).getContainer(); // not-null, returns 'mol'
 
```
    Specified by:
    
    getContainer in interface IAtom
    
    Returns:
    
    the atom container or null if not accessed in the context of a container
  - bonds
```
public Iterable<IBond> bonds()
```
    Returns the bonds connected to this atom. If the bonds are not known an exception is thrown. This method will only throw an exception if IAtom.getIndex() returns < 0 or IAtom.getContainer() returns null.
```
 IAtom atom = ...;

 if (atom.getIndex() >= 0) {
   for (IBond bond : atom.bonds()) {

   }
 }

 if (atom.getContainer() != null) {
   for (IBond bond : atom.bonds()) {

   }
 }

 IAtomContainer mol = ...;
 // guaranteed not throw an exception
 for (IBond bond : mol.getAtom(i).bonds()) {

 }
 
```
    Specified by:
    
    bonds in interface IAtom
    
    Returns:
    
    iterable of bonds
  - getBondCount
```
public int getBondCount()
```
    Get the number of explicit bonds connected to this atom.
    
    Specified by:
    
    getBondCount in interface IAtom
    
    Returns:
    
    the total bond count
  - getBond
```
public IBond getBond(IAtom atom)
```
    Returns the bond connecting 'this' atom to the provided atom. If the atoms are not bonded, null is returned.
    
    Specified by:
    
    getBond in interface IAtom
    
    Parameters:
    
    atom - the other atom
    
    Returns:
    
    the bond connecting the atoms
  - setCharge
```
public void setCharge(Double charge)
```
    Sets the partial charge of this atom.
    
    Specified by:
    
    setCharge in interface IAtom
    
    Parameters:
    
    charge - The partial charge
    
    See Also:
    
    getCharge()
  - getCharge
```
public Double getCharge()
```
    Returns the partial charge of this atom.
    If the charge has not been set the return value is Double.NaN
    
    Specified by:
    
    getCharge in interface IAtom
    
    Returns:
    
    the charge of this atom
    
    See Also:
    
    setCharge(java.lang.Double)
  - setImplicitHydrogenCount
```
public void setImplicitHydrogenCount(Integer hydrogenCount)
```
    Sets the number of implicit hydrogen count of this atom.
    
    Specified by:
    
    setImplicitHydrogenCount in interface IAtom
    
    Parameters:
    
    hydrogenCount - The number of hydrogen atoms bonded to this atom.
    
    See Also:
    
    getImplicitHydrogenCount()
  - getImplicitHydrogenCount
```
public Integer getImplicitHydrogenCount()
```
    Returns the hydrogen count of this atom.
    
    Specified by:
    
    getImplicitHydrogenCount in interface IAtom
    
    Returns:
    
    The hydrogen count of this atom.
    
    See Also:
    
    setImplicitHydrogenCount(java.lang.Integer)
  - setPoint2d
```
public void setPoint2d(javax.vecmath.Point2d point2d)
```
    Sets a point specifying the location of this atom in a 2D space.
    
    Specified by:
    
    setPoint2d in interface IAtom
    
    Parameters:
    
    point2d - A point in a 2D plane
    
    See Also:
    
    getPoint2d()
  - setPoint3d
```
public void setPoint3d(javax.vecmath.Point3d point3d)
```
    Sets a point specifying the location of this atom in 3D space.
    
    Specified by:
    
    setPoint3d in interface IAtom
    
    Parameters:
    
    point3d - A point in a 3-dimensional space
    
    See Also:
    
    getPoint3d()
  - setFractionalPoint3d
```
public void setFractionalPoint3d(javax.vecmath.Point3d point3d)
```
    Sets a point specifying the location of this atom in a Crystal unit cell.
    
    Specified by:
    
    setFractionalPoint3d in interface IAtom
    
    Parameters:
    
    point3d - A point in a 3d fractional unit cell space
    
    See Also:
    
    getFractionalPoint3d(), Crystal
  - setStereoParity
```
public void setStereoParity(Integer stereoParity)
```
    Sets the stereo parity for this atom.
    
    Specified by:
    
    setStereoParity in interface IAtom
    
    Parameters:
    
    stereoParity - The stereo parity for this atom
    
    See Also:
    
    for predefined values., getStereoParity()
  - getPoint2d
```
public javax.vecmath.Point2d getPoint2d()
```
    Returns a point specifying the location of this atom in a 2D space.
    
    Specified by:
    
    getPoint2d in interface IAtom
    
    Returns:
    
    A point in a 2D plane. Null if unset.
    
    See Also:
    
    setPoint2d(javax.vecmath.Point2d)
  - getPoint3d
```
public javax.vecmath.Point3d getPoint3d()
```
    Returns a point specifying the location of this atom in a 3D space.
    
    Specified by:
    
    getPoint3d in interface IAtom
    
    Returns:
    
    A point in 3-dimensional space. Null if unset.
    
    See Also:
    
    setPoint3d(javax.vecmath.Point3d)
  - getFractionalPoint3d
```
public javax.vecmath.Point3d getFractionalPoint3d()
```
    Returns a point specifying the location of this atom in a Crystal unit cell.
    
    Specified by:
    
    getFractionalPoint3d in interface IAtom
    
    Returns:
    
    A point in 3d fractional unit cell space. Null if unset.
    
    See Also:
    
    setFractionalPoint3d(javax.vecmath.Point3d), for predefined values.
  - getStereoParity
```
public Integer getStereoParity()
```
    Returns the stereo parity of this atom. It uses the predefined values found in CDKConstants.
    
    Specified by:
    
    getStereoParity in interface IAtom
    
    Returns:
    
    The stereo parity for this atom
    
    See Also:
    
    CDKConstants, setStereoParity(java.lang.Integer)
  - setAtomTypeName
```
public void setAtomTypeName(String identifier)
```
    Sets the if attribute of the AtomType object.
    
    Specified by:
    
    setAtomTypeName in interface IAtomType
    
    Parameters:
    
    identifier - The new AtomTypeID value. Null if unset.
    
    See Also:
    
    getAtomTypeName()
  - setMaxBondOrder
```
public void setMaxBondOrder(IBond.Order maxBondOrder)
```
    Sets the MaxBondOrder attribute of the AtomType object.
    
    Specified by:
    
    setMaxBondOrder in interface IAtomType
    
    Parameters:
    
    maxBondOrder - The new MaxBondOrder value
    
    See Also:
    
    getMaxBondOrder()
  - setBondOrderSum
```
public void setBondOrderSum(Double bondOrderSum)
```
    Sets the the exact bond order sum attribute of the AtomType object.
    
    Specified by:
    
    setBondOrderSum in interface IAtomType
    
    Parameters:
    
    bondOrderSum - The new bondOrderSum value
    
    See Also:
    
    getBondOrderSum()
  - getAtomTypeName
```
public String getAtomTypeName()
```
    Gets the id attribute of the AtomType object.
    
    Specified by:
    
    getAtomTypeName in interface IAtomType
    
    Returns:
    
    The id value
    
    See Also:
    
    setAtomTypeName(java.lang.String)
  - getMaxBondOrder
```
public IBond.Order getMaxBondOrder()
```
    Gets the MaxBondOrder attribute of the AtomType object.
    
    Specified by:
    
    getMaxBondOrder in interface IAtomType
    
    Returns:
    
    The MaxBondOrder value
    
    See Also:
    
    setMaxBondOrder(org.openscience.cdk.interfaces.IBond.Order)
  - getBondOrderSum
```
public Double getBondOrderSum()
```
    Gets the bondOrderSum attribute of the AtomType object.
    
    Specified by:
    
    getBondOrderSum in interface IAtomType
    
    Returns:
    
    The bondOrderSum value
    
    See Also:
    
    setBondOrderSum(java.lang.Double)
  - setFormalCharge
```
public void setFormalCharge(Integer charge)
```
    Sets the formal charge of this atom.
    
    Specified by:
    
    setFormalCharge in interface IAtomType
    
    Parameters:
    
    charge - The formal charge
    
    See Also:
    
    getFormalCharge()
  - getFormalCharge
```
public Integer getFormalCharge()
```
    Returns the formal charge of this atom.
    
    Specified by:
    
    getFormalCharge in interface IAtomType
    
    Returns:
    
    the formal charge of this atom
    
    See Also:
    
    setFormalCharge(java.lang.Integer)
  - setFormalNeighbourCount
```
public void setFormalNeighbourCount(Integer count)
```
    Sets the formal neighbour count of this atom.
    
    Specified by:
    
    setFormalNeighbourCount in interface IAtomType
    
    Parameters:
    
    count - The neighbour count
    
    See Also:
    
    getFormalNeighbourCount()
  - getFormalNeighbourCount
```
public Integer getFormalNeighbourCount()
```
    Returns the formal neighbour count of this atom.
    
    Specified by:
    
    getFormalNeighbourCount in interface IAtomType
    
    Returns:
    
    the formal neighbour count of this atom
    
    See Also:
    
    setFormalNeighbourCount(java.lang.Integer)
  - setHybridization
```
public void setHybridization(IAtomType.Hybridization hybridization)
```
    Sets the hybridization of this atom.
    
    Specified by:
    
    setHybridization in interface IAtomType
    
    Parameters:
    
    hybridization - The hybridization
    
    See Also:
    
    getHybridization()
  - getHybridization
```
public IAtomType.Hybridization getHybridization()
```
    Returns the hybridization of this atom.
    
    Specified by:
    
    getHybridization in interface IAtomType
    
    Returns:
    
    the hybridization of this atom
    
    See Also:
    
    setHybridization(org.openscience.cdk.interfaces.IAtomType.Hybridization)
  - setNaturalAbundance
```
public void setNaturalAbundance(Double naturalAbundance)
```
    Sets the NaturalAbundance attribute of the Isotope object.
    
    Specified by:
    
    setNaturalAbundance in interface IIsotope
    
    Parameters:
    
    naturalAbundance - The new NaturalAbundance value
    
    See Also:
    
    getNaturalAbundance()
  - setExactMass
```
public void setExactMass(Double exactMass)
```
    Sets the ExactMass attribute of the Isotope object.
    
    Specified by:
    
    setExactMass in interface IIsotope
    
    Parameters:
    
    exactMass - The new ExactMass value
    
    See Also:
    
    getExactMass()
  - getNaturalAbundance
```
public Double getNaturalAbundance()
```
    Gets the NaturalAbundance attribute of the Isotope object.
    Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:
```
   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 
```
    Specified by:
    
    getNaturalAbundance in interface IIsotope
    
    Returns:
    
    The NaturalAbundance value
    
    See Also:
    
    setNaturalAbundance(java.lang.Double)
  - getExactMass
```
public Double getExactMass()
```
    Gets the ExactMass attribute of the Isotope object.
    Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:
```
   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 
```
    Specified by:
    
    getExactMass in interface IIsotope
    
    Returns:
    
    The ExactMass value
    
    See Also:
    
    setExactMass(java.lang.Double)
  - getMassNumber
```
public Integer getMassNumber()
```
    Returns the atomic mass of this element.
    Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:
```
   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 
```
    Specified by:
    
    getMassNumber in interface IIsotope
    
    Returns:
    
    The atomic mass of this element
    
    See Also:
    
    setMassNumber(Integer)
  - setMassNumber
```
public void setMassNumber(Integer massNumber)
```
    Sets the atomic mass of this element.
    
    Specified by:
    
    setMassNumber in interface IIsotope
    
    Parameters:
    
    massNumber - The atomic mass to be assigned to this element
    
    See Also:
    
    getMassNumber()
  - getAtomicNumber
```
public Integer getAtomicNumber()
```
    Returns the atomic number of this element.
    Once instantiated all field not filled by passing parameters to the constructor are null. Elements can be configured by using the IsotopeFactory.configure() method:
```
   Element element = new Element("C");
   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
   if.configure(element);
 
```
    Specified by:
    
    getAtomicNumber in interface IElement
    
    Returns:
    
    The atomic number of this element
    
    See Also:
    
    setAtomicNumber(java.lang.Integer)
  - setAtomicNumber
```
public void setAtomicNumber(Integer atomicNumber)
```
    Sets the atomic number of this element.
    
    Specified by:
    
    setAtomicNumber in interface IElement
    
    Parameters:
    
    atomicNumber - The atomic mass to be assigned to this element
    
    See Also:
    
    getAtomicNumber()
  - getSymbol
```
public String getSymbol()
```
    Returns the element symbol of this element.
    
    Specified by:
    
    getSymbol in interface IElement
    
    Returns:
    
    The element symbol of this element. Null if unset.
    
    See Also:
    
    setSymbol(java.lang.String)
  - setSymbol
```
public void setSymbol(String symbol)
```
    Sets the element symbol of this element.
    
    Specified by:
    
    setSymbol in interface IElement
    
    Parameters:
    
    symbol - The element symbol to be assigned to this atom
    
    See Also:
    
    getSymbol()
  - setCovalentRadius
```
public void setCovalentRadius(Double radius)
```
    Sets the covalent radius for this AtomType.
    
    Specified by:
    
    setCovalentRadius in interface IAtomType
    
    Parameters:
    
    radius - The covalent radius for this AtomType
    
    See Also:
    
    getCovalentRadius()
  - getCovalentRadius
```
public Double getCovalentRadius()
```
    Returns the covalent radius for this AtomType.
    
    Specified by:
    
    getCovalentRadius in interface IAtomType
    
    Returns:
    
    The covalent radius for this AtomType
    
    See Also:
    
    setCovalentRadius(java.lang.Double)
  - setValency
```
public void setValency(Integer valency)
```
    Sets the the exact electron valency of the AtomType object.
    
    Specified by:
    
    setValency in interface IAtomType
    
    Parameters:
    
    valency - The new valency value
    
    See Also:
    
    getValency()
  - getValency
```
public Integer getValency()
```
    Gets the the exact electron valency of the AtomType object.
    
    Specified by:
    
    getValency in interface IAtomType
    
    Returns:
    
    The valency value
    
    See Also:
    
    setValency(java.lang.Integer)
  - isAromatic
```
public boolean isAromatic()
```
    Access whether this atom has been marked as aromatic. The default value is false and you must explicitly perceive aromaticity with one of the available models.
    
    Specified by:
    
    isAromatic in interface IAtom
    
    Returns:
    
    aromatic status
    
    See Also:
    
    IChemObject.getFlag(int), Aromaticity
  - setIsAromatic
```
public void setIsAromatic(boolean arom)
```
    Mark this atom as being aromatic.
    
    Specified by:
    
    setIsAromatic in interface IAtom
    
    Parameters:
    
    arom - aromatic status
    
    See Also:
    
    IChemObject.setFlag(int, boolean)
  - isInRing
```
public boolean isInRing()
```
    Access whether this atom has been flagged as in a ring. The default value is false and you must explicitly find rings first.
    
    Specified by:
    
    isInRing in interface IAtom
    
    Returns:
    
    ring status
    
    See Also:
    
    IChemObject.getFlag(int), RingSearch
  - setIsInRing
```
public void setIsInRing(boolean ring)
```
    Mark this atom as being in a ring.
    
    Specified by:
    
    setIsInRing in interface IAtom
    
    Parameters:
    
    ring - ring status
    
    See Also:
    
    IChemObject.setFlag(int, boolean)
  - getMapIdx
```
public int getMapIdx()
```
    Access the map index for this atom.
    
    Specified by:
    
    getMapIdx in interface IAtom
    
    Returns:
    
    the map index (0 if not set)
  - setMapIdx
```
public void setMapIdx(int mapidx)
```
    Set the map index for this atom.
    
    Specified by:
    
    setMapIdx in interface IAtom
    
    Parameters:
    
    mapidx - the new map index
  - setExpression
```
public void setExpression(Expr expr)
```
    Set the atom-expression predicate for this query atom.
    
    Parameters:
    
    expr - the expression
  - getExpression
```
public Expr getExpression()
```
    Get the atom-expression predicate for this query atom.
    
    Returns:
    
    the expression
  - matches
```
public boolean matches(IAtom atom)
```
    Returns true of the given atom matches this IQueryAtom.
    
    Specified by:
    
    matches in interface IQueryAtom
    
    Overrides:
    
    matches in class QueryChemObject
    
    Parameters:
    
    atom - IAtom to match against
    
    Returns:
    
    true, if this IQueryAtom matches the given IAtom
  - clone
```
public IAtom clone()
            throws CloneNotSupportedException
```
    Description copied from interface: IChemObject
    
    Returns a deep clone of this IChemObject.
    
    Specified by:
    
    clone in interface IAtom
    
    Specified by:
    
    clone in interface IChemObject
    
    Overrides:
    
    clone in class QueryChemObject
    
    Returns:
    
    Object the clone of this IChemObject.
    
    Throws:
    
    CloneNotSupportedException - if the IChemObject cannot be cloned
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object

Class QueryAtom

Nested Class Summary

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

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

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

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

Field Detail

charge

point2d

point3d

fractionalPoint3d

hydrogenCount

stereoParity

formalCharge

hybridization

electronValency

formalNeighbourCount

exactMass

naturalAbundance

symbol

atomicNumber

Constructor Detail

QueryAtom

QueryAtom

QueryAtom

QueryAtom

QueryAtom

Method Detail

getIndex

getContainer

bonds

getBondCount

getBond

setCharge

getCharge

setImplicitHydrogenCount

getImplicitHydrogenCount

setPoint2d

setPoint3d

setFractionalPoint3d

setStereoParity

getPoint2d

getPoint3d

getFractionalPoint3d

getStereoParity

setAtomTypeName

setMaxBondOrder

setBondOrderSum

getAtomTypeName

getMaxBondOrder

getBondOrderSum

setFormalCharge

getFormalCharge

setFormalNeighbourCount

getFormalNeighbourCount

setHybridization

getHybridization

setNaturalAbundance

setExactMass

getNaturalAbundance

getExactMass

getMassNumber

setMassNumber

getAtomicNumber

setAtomicNumber

getSymbol

setSymbol

setCovalentRadius

getCovalentRadius

setValency

getValency

isAromatic

setIsAromatic

isInRing

setIsInRing