java.lang.Object
- org.openscience.cdk.ChemObject
- - org.openscience.cdk.Element
  - - org.openscience.cdk.Isotope
    - - org.openscience.cdk.AtomType
      - org.openscience.cdk.Atom
        
        org.openscience.cdk.PseudoAtom
        
        org.openscience.cdk.FragmentAtom
        
        org.openscience.cdk.debug.DebugFragmentAtom

All Implemented Interfaces:

Serializable, Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IFragmentAtom, IIsotope, IPseudoAtom
```
public class DebugFragmentAtom
extends FragmentAtom
```
Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much like the MDL molfile Group concept.

Author:

egonw

See Also:

Serialized Form

Source code:
main

Belongs to CDK module:
datadebug

Nested Class Summary
- Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
  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
- Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
  ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
- 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 Description

DebugFragmentAtom()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addListener(IChemObjectListener col)`	Use this to add yourself to this IChemObject as a listener.
`void`	`addProperties(Map<Object,Object> properties)`	Sets the properties of this object.
`IFragmentAtom`	`clone()`	Clones this atom object and its content.
`Integer`	`getAtomicNumber()`	Returns the atomic number of this element.
`String`	`getAtomTypeName()`	Gets the id attribute of the AtomType object.
`Double`	`getBondOrderSum()`	Gets the bondOrderSum attribute of the AtomType object.
`IChemObjectBuilder`	`getBuilder()`	Returns a `IChemObjectBuilder` for the data classes that extend this class.
`Double`	`getCharge()`	Returns the partial charge of this atom.
`Double`	`getCovalentRadius()`	Returns the covalent radius for this AtomType.
`Double`	`getExactMass()`	The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
`boolean`	`getFlag(int flagType)`	Returns the value of a given flag.
`boolean[]`	`getFlags()`	Returns the whole set of flags.
`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.
`IAtomContainer`	`getFragment()`	Returns the fully expended form of the IFragmentAtom.
`IAtomType.Hybridization`	`getHybridization()`	Returns the hybridization of this atom.
`String`	`getID()`	Returns the identifier (ID) of this object.
`Integer`	`getImplicitHydrogenCount()`	Returns the hydrogen count of this atom.
`String`	`getLabel()`	Returns the label of this PseudoAtom.
`int`	`getListenerCount()`	Returns the number of ChemObjectListeners registered with this object.
`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.
`Map<Object,Object>`	`getProperties()`	Returns a Map with the IChemObject's properties.
`<T> T`	`getProperty(Object description)`	Returns a property for the IChemObject.
`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.
`boolean`	`isExpanded()`	Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.
`void`	`notifyChanged()`	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
`void`	`notifyChanged(IChemObjectChangeEvent evt)`	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
`void`	`removeListener(IChemObjectListener col)`	Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
`void`	`removeProperty(Object description)`	Removes a property for a IChemObject.
`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`	`setExpanded(boolean bool)`	Sets whether this atom is to be fully drawn and not just in the abbreviated form.
`void`	`setFlag(int flagType, boolean flagValue)`	Sets the value of some flag.
`void`	`setFlags(boolean[] flagsNew)`	Sets the whole set of flags.
`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`	`setFragment(IAtomContainer fragment)`	Sets the fully expended form of the IFragmentAtom.
`void`	`setHybridization(IAtomType.Hybridization hybridization)`	Sets the hybridization of this atom.
`void`	`setID(String identifier)`	Sets the identifier (ID) of this object.
`void`	`setImplicitHydrogenCount(Integer hydrogenCount)`	Sets the number of implicit hydrogen count of this atom.
`void`	`setLabel(String label)`	Sets the label of this PseudoAtom.
`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`	`setProperty(Object description, Object property)`	Sets a property for a IChemObject.
`void`	`setStereoParity(Integer stereoParity)`	Dummy method: the stereo parity is undefined, final.
`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.FragmentAtom
toString

Methods inherited from class org.openscience.cdk.PseudoAtom
getAttachPointNum, setAttachPointNum

Methods inherited from class org.openscience.cdk.Atom
bonds, compare, equals, getBond, getBondCount, getContainer, getIndex, getMapIdx, hashCode, setMapIdx

Methods inherited from class org.openscience.cdk.ChemObject
clear, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties, shallowCopy

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.IAtom
bonds, getBond, getBondCount, getContainer, getIndex, getMapIdx, getTotalHydrogenCount, isAromatic, isInRing, neighbors, setIsAromatic, setIsInRing, setMapIdx

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
clear, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties

Methods inherited from interface org.openscience.cdk.interfaces.IPseudoAtom
getAttachPointNum, setAttachPointNum

- Constructor Detail
  - DebugFragmentAtom
```
public DebugFragmentAtom()
```
- Method Detail
  - isExpanded
```
public boolean isExpanded()
```
    Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.
    
    Specified by:
    
    isExpanded in interface IFragmentAtom
    
    Overrides:
    
    isExpanded in class FragmentAtom
    
    Returns:
    
    true, if it should be considered in expended form
  - setExpanded
```
public void setExpanded(boolean bool)
```
    Sets whether this atom is to be fully drawn and not just in the abbreviated form.
    
    Specified by:
    
    setExpanded in interface IFragmentAtom
    
    Overrides:
    
    setExpanded in class FragmentAtom
    
    Parameters:
    
    bool - true if the full structure should be drawn
  - getFragment
```
public IAtomContainer getFragment()
```
    Returns the fully expended form of the IFragmentAtom.
    
    Specified by:
    
    getFragment in interface IFragmentAtom
    
    Overrides:
    
    getFragment in class FragmentAtom
    
    Returns:
    
    the fully expanded form as an IAtomContainer object
  - setFragment
```
public void setFragment(IAtomContainer fragment)
```
    Sets the fully expended form of the IFragmentAtom.
    
    Specified by:
    
    setFragment in interface IFragmentAtom
    
    Overrides:
    
    setFragment in class FragmentAtom
    
    Parameters:
    
    fragment - The fragment
  - setCharge
```
public void setCharge(Double charge)
```
    Sets the partial charge of this atom.
    
    Specified by:
    
    setCharge in interface IAtom
    
    Overrides:
    
    setCharge in class Atom
    
    Parameters:
    
    charge - The partial charge
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    getCharge in class Atom
    
    Returns:
    
    the charge of this atom
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    setImplicitHydrogenCount in class Atom
    
    Parameters:
    
    hydrogenCount - The number of hydrogen atoms bonded to this atom.
    
    See Also:
    
    Atom.getImplicitHydrogenCount()
  - getImplicitHydrogenCount
```
public Integer getImplicitHydrogenCount()
```
    Returns the hydrogen count of this atom.
    
    Specified by:
    
    getImplicitHydrogenCount in interface IAtom
    
    Overrides:
    
    getImplicitHydrogenCount in class Atom
    
    Returns:
    
    The hydrogen count of this atom.
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    setPoint2d in class Atom
    
    Parameters:
    
    point2d - A point in a 2D plane
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    setPoint3d in class Atom
    
    Parameters:
    
    point3d - A point in a 3-dimensional space
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    setFractionalPoint3d in class Atom
    
    Parameters:
    
    point3d - A point in a 3d fractional unit cell space
    
    See Also:
    
    Atom.getFractionalPoint3d(), Crystal
  - setStereoParity
```
public void setStereoParity(Integer stereoParity)
```
    Dummy method: the stereo parity is undefined, final.
    
    Specified by:
    
    setStereoParity in interface IAtom
    
    Overrides:
    
    setStereoParity in class PseudoAtom
    
    Parameters:
    
    stereoParity - The stereo parity for this atom
    
    See Also:
    
    for predefined values., Atom.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
    
    Overrides:
    
    getPoint2d in class Atom
    
    Returns:
    
    A point in a 2D plane. Null if unset.
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    getPoint3d in class Atom
    
    Returns:
    
    A point in 3-dimensional space. Null if unset.
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    getFractionalPoint3d in class Atom
    
    Returns:
    
    A point in 3d fractional unit cell space. Null if unset.
    
    See Also:
    
    Atom.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
    
    Overrides:
    
    getStereoParity in class Atom
    
    Returns:
    
    The stereo parity for this atom
    
    See Also:
    
    CDKConstants, Atom.setStereoParity(java.lang.Integer)
  - setAtomTypeName
```
public void setAtomTypeName(String identifier)
```
    Sets the if attribute of the AtomType object.
    
    Specified by:
    
    setAtomTypeName in interface IAtomType
    
    Overrides:
    
    setAtomTypeName in class AtomType
    
    Parameters:
    
    identifier - The new AtomTypeID value. Null if unset.
    
    See Also:
    
    AtomType.getAtomTypeName()
  - setMaxBondOrder
```
public void setMaxBondOrder(IBond.Order maxBondOrder)
```
    Sets the MaxBondOrder attribute of the AtomType object.
    
    Specified by:
    
    setMaxBondOrder in interface IAtomType
    
    Overrides:
    
    setMaxBondOrder in class AtomType
    
    Parameters:
    
    maxBondOrder - The new MaxBondOrder value
    
    See Also:
    
    AtomType.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
    
    Overrides:
    
    setBondOrderSum in class AtomType
    
    Parameters:
    
    bondOrderSum - The new bondOrderSum value
    
    See Also:
    
    AtomType.getBondOrderSum()
  - getAtomTypeName
```
public String getAtomTypeName()
```
    Gets the id attribute of the AtomType object.
    
    Specified by:
    
    getAtomTypeName in interface IAtomType
    
    Overrides:
    
    getAtomTypeName in class AtomType
    
    Returns:
    
    The id value
    
    See Also:
    
    AtomType.setAtomTypeName(java.lang.String)
  - getMaxBondOrder
```
public IBond.Order getMaxBondOrder()
```
    Gets the MaxBondOrder attribute of the AtomType object.
    
    Specified by:
    
    getMaxBondOrder in interface IAtomType
    
    Overrides:
    
    getMaxBondOrder in class AtomType
    
    Returns:
    
    The MaxBondOrder value
    
    See Also:
    
    AtomType.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
    
    Overrides:
    
    getBondOrderSum in class AtomType
    
    Returns:
    
    The bondOrderSum value
    
    See Also:
    
    AtomType.setBondOrderSum(java.lang.Double)
  - setFormalCharge
```
public void setFormalCharge(Integer charge)
```
    Sets the formal charge of this atom.
    
    Specified by:
    
    setFormalCharge in interface IAtomType
    
    Overrides:
    
    setFormalCharge in class AtomType
    
    Parameters:
    
    charge - The formal charge
    
    See Also:
    
    AtomType.getFormalCharge()
  - getFormalCharge
```
public Integer getFormalCharge()
```
    Returns the formal charge of this atom.
    
    Specified by:
    
    getFormalCharge in interface IAtomType
    
    Overrides:
    
    getFormalCharge in class AtomType
    
    Returns:
    
    the formal charge of this atom
    
    See Also:
    
    AtomType.setFormalCharge(java.lang.Integer)
  - setFormalNeighbourCount
```
public void setFormalNeighbourCount(Integer count)
```
    Sets the formal neighbour count of this atom.
    
    Specified by:
    
    setFormalNeighbourCount in interface IAtomType
    
    Overrides:
    
    setFormalNeighbourCount in class AtomType
    
    Parameters:
    
    count - The neighbour count
    
    See Also:
    
    AtomType.getFormalNeighbourCount()
  - getFormalNeighbourCount
```
public Integer getFormalNeighbourCount()
```
    Returns the formal neighbour count of this atom.
    
    Specified by:
    
    getFormalNeighbourCount in interface IAtomType
    
    Overrides:
    
    getFormalNeighbourCount in class AtomType
    
    Returns:
    
    the formal neighbour count of this atom
    
    See Also:
    
    AtomType.setFormalNeighbourCount(java.lang.Integer)
  - setHybridization
```
public void setHybridization(IAtomType.Hybridization hybridization)
```
    Sets the hybridization of this atom.
    
    Specified by:
    
    setHybridization in interface IAtomType
    
    Overrides:
    
    setHybridization in class AtomType
    
    Parameters:
    
    hybridization - The hybridization
    
    See Also:
    
    AtomType.getHybridization()
  - getHybridization
```
public IAtomType.Hybridization getHybridization()
```
    Returns the hybridization of this atom.
    
    Specified by:
    
    getHybridization in interface IAtomType
    
    Overrides:
    
    getHybridization in class AtomType
    
    Returns:
    
    the hybridization of this atom
    
    See Also:
    
    AtomType.setHybridization(org.openscience.cdk.interfaces.IAtomType.Hybridization)
  - setCovalentRadius
```
public void setCovalentRadius(Double radius)
```
    Sets the covalent radius for this AtomType.
    
    Specified by:
    
    setCovalentRadius in interface IAtomType
    
    Overrides:
    
    setCovalentRadius in class AtomType
    
    Parameters:
    
    radius - The covalent radius for this AtomType
    
    See Also:
    
    AtomType.getCovalentRadius()
  - getCovalentRadius
```
public Double getCovalentRadius()
```
    Returns the covalent radius for this AtomType.
    
    Specified by:
    
    getCovalentRadius in interface IAtomType
    
    Overrides:
    
    getCovalentRadius in class AtomType
    
    Returns:
    
    The covalent radius for this AtomType
    
    See Also:
    
    AtomType.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
    
    Overrides:
    
    setValency in class AtomType
    
    Parameters:
    
    valency - The new valency value
    
    See Also:
    
    AtomType.getValency()
  - getValency
```
public Integer getValency()
```
    Gets the the exact electron valency of the AtomType object.
    
    Specified by:
    
    getValency in interface IAtomType
    
    Overrides:
    
    getValency in class AtomType
    
    Returns:
    
    The valency value
    
    See Also:
    
    AtomType.setValency(java.lang.Integer)
  - setNaturalAbundance
```
public void setNaturalAbundance(Double naturalAbundance)
```
    Sets the NaturalAbundance attribute of the Isotope object.
    
    Specified by:
    
    setNaturalAbundance in interface IIsotope
    
    Overrides:
    
    setNaturalAbundance in class Isotope
    
    Parameters:
    
    naturalAbundance - The new NaturalAbundance value
    
    See Also:
    
    Isotope.getNaturalAbundance()
  - setExactMass
```
public void setExactMass(Double exactMass)
```
    Sets the ExactMass attribute of the Isotope object.
    
    Specified by:
    
    setExactMass in interface IIsotope
    
    Overrides:
    
    setExactMass in class FragmentAtom
    
    Parameters:
    
    exactMass - The new ExactMass value
    
    See Also:
    
    Isotope.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
    
    Overrides:
    
    getNaturalAbundance in class Isotope
    
    Returns:
    
    The NaturalAbundance value
    
    See Also:
    
    Isotope.setNaturalAbundance(java.lang.Double)
  - getExactMass
```
public Double getExactMass()
```
    The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
    
    Specified by:
    
    getExactMass in interface IIsotope
    
    Overrides:
    
    getExactMass in class FragmentAtom
    
    Returns:
    
    The ExactMass value
    
    See Also:
    
    Isotope.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
    
    Overrides:
    
    getMassNumber in class Isotope
    
    Returns:
    
    The atomic mass of this element
    
    See Also:
    
    Isotope.setMassNumber(Integer)
  - setMassNumber
```
public void setMassNumber(Integer massNumber)
```
    Sets the atomic mass of this element.
    
    Specified by:
    
    setMassNumber in interface IIsotope
    
    Overrides:
    
    setMassNumber in class Isotope
    
    Parameters:
    
    massNumber - The atomic mass to be assigned to this element
    
    See Also:
    
    Isotope.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
    
    Overrides:
    
    getAtomicNumber in class Element
    
    Returns:
    
    The atomic number of this element
    
    See Also:
    
    Element.setAtomicNumber(java.lang.Integer)
  - setAtomicNumber
```
public void setAtomicNumber(Integer atomicNumber)
```
    Sets the atomic number of this element.
    
    Specified by:
    
    setAtomicNumber in interface IElement
    
    Overrides:
    
    setAtomicNumber in class Element
    
    Parameters:
    
    atomicNumber - The atomic mass to be assigned to this element
    
    See Also:
    
    Element.getAtomicNumber()
  - getSymbol
```
public String getSymbol()
```
    Returns the element symbol of this element.
    
    Specified by:
    
    getSymbol in interface IElement
    
    Overrides:
    
    getSymbol in class Element
    
    Returns:
    
    The element symbol of this element. Null if unset.
    
    See Also:
    
    Element.setSymbol(java.lang.String)
  - setSymbol
```
public void setSymbol(String symbol)
```
    Sets the element symbol of this element.
    
    Specified by:
    
    setSymbol in interface IElement
    
    Overrides:
    
    setSymbol in class Element
    
    Parameters:
    
    symbol - The element symbol to be assigned to this atom
    
    See Also:
    
    Element.getSymbol()
  - addListener
```
public void addListener(IChemObjectListener col)
```
    Use this to add yourself to this IChemObject as a listener. In order to do so, you must implement the ChemObjectListener Interface.
    
    Specified by:
    
    addListener in interface IChemObject
    
    Overrides:
    
    addListener in class ChemObject
    
    Parameters:
    
    col - the ChemObjectListener
    
    See Also:
    
    ChemObject.removeListener(org.openscience.cdk.interfaces.IChemObjectListener)
  - getListenerCount
```
public int getListenerCount()
```
    Returns the number of ChemObjectListeners registered with this object.
    
    Specified by:
    
    getListenerCount in interface IChemObject
    
    Overrides:
    
    getListenerCount in class ChemObject
    
    Returns:
    
    the number of registered listeners.
  - removeListener
```
public void removeListener(IChemObjectListener col)
```
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject. It will then not be notified of change in this object anymore.
    
    Specified by:
    
    removeListener in interface IChemObject
    
    Overrides:
    
    removeListener in class ChemObject
    
    Parameters:
    
    col - The ChemObjectListener to be removed
    
    See Also:
    
    ChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)
  - notifyChanged
```
public void notifyChanged()
```
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    
    Specified by:
    
    notifyChanged in interface IChemObject
    
    Overrides:
    
    notifyChanged in class ChemObject
  - notifyChanged
```
public void notifyChanged(IChemObjectChangeEvent evt)
```
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.
    
    Specified by:
    
    notifyChanged in interface IChemObject
    
    Overrides:
    
    notifyChanged in class ChemObject
    
    Parameters:
    
    evt - A ChemObjectChangeEvent pointing to the source of where the change happened
  - setProperty
```
public void setProperty(Object description,
                        Object property)
```
    Sets a property for a IChemObject.
    
    Specified by:
    
    setProperty in interface IChemObject
    
    Overrides:
    
    setProperty in class ChemObject
    
    Parameters:
    
    description - An object description of the property (most likely a unique string)
    
    property - An object with the property itself
    
    See Also:
    
    ChemObject.getProperty(java.lang.Object), ChemObject.removeProperty(java.lang.Object)
  - removeProperty
```
public void removeProperty(Object description)
```
    Removes a property for a IChemObject.
    
    Specified by:
    
    removeProperty in interface IChemObject
    
    Overrides:
    
    removeProperty in class ChemObject
    
    Parameters:
    
    description - The object description of the property (most likely a unique string)
    
    See Also:
    
    ChemObject.setProperty(java.lang.Object, java.lang.Object), ChemObject.getProperty(java.lang.Object)
  - getProperty
```
public <T> T getProperty(Object description)
```
    Returns a property for the IChemObject.
    
    Specified by:
    
    getProperty in interface IChemObject
    
    Overrides:
    
    getProperty in class ChemObject
    
    Type Parameters:
    
    T - generic return type
    
    Parameters:
    
    description - An object description of the property (most likely a unique string)
    
    Returns:
    
    The object containing the property. Returns null if propert is not set.
    
    See Also:
    
    ChemObject.setProperty(java.lang.Object, java.lang.Object), ChemObject.removeProperty(java.lang.Object)
  - getProperties
```
public Map<Object,Object> getProperties()
```
    Returns a Map with the IChemObject's properties.
    
    Specified by:
    
    getProperties in interface IChemObject
    
    Overrides:
    
    getProperties in class ChemObject
    
    Returns:
    
    The object's properties as an Hashtable
    
    See Also:
    
    ChemObject.addProperties(java.util.Map<java.lang.Object, java.lang.Object>)
  - getID
```
public String getID()
```
    Returns the identifier (ID) of this object.
    
    Specified by:
    
    getID in interface IChemObject
    
    Overrides:
    
    getID in class ChemObject
    
    Returns:
    
    a String representing the ID value
    
    See Also:
    
    ChemObject.setID(java.lang.String)
  - setID
```
public void setID(String identifier)
```
    Sets the identifier (ID) of this object.
    
    Specified by:
    
    setID in interface IChemObject
    
    Overrides:
    
    setID in class ChemObject
    
    Parameters:
    
    identifier - a String representing the ID value
    
    See Also:
    
    ChemObject.getID()
  - setFlag
```
public void setFlag(int flagType,
                    boolean flagValue)
```
    Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC or IChemObject.VISITED). The flags are intrinsic internal properties and should not be used to store custom values, please use IChemObject.setProperty(Object, Object).
    // set this chem object to be aromatic chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE); // ... // indicate we have visited this chem object chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
    Specified by:
    
    setFlag in interface IChemObject
    
    Overrides:
    
    setFlag in class ChemObject
    
    Parameters:
    
    flagType - flag to set the value for
    
    flagValue - value to assign to flag
    
    See Also:
    
    IChemObject.getFlag(int)
  - getFlag
```
public boolean getFlag(int flagType)
```
    Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC).
    if(chemObject.getFlag(CDKConstants.ISAROMATIC)){ // handle aromatic flag on this chem object }
    Specified by:
    
    getFlag in interface IChemObject
    
    Overrides:
    
    getFlag in class ChemObject
    
    Parameters:
    
    flagType - flag to retrieve the value of
    
    Returns:
    
    true if the flag flag_type is set
    
    See Also:
    
    IChemObject.setFlag(int, boolean)
  - addProperties
```
public void addProperties(Map<Object,Object> properties)
```
    Sets the properties of this object.
    
    Specified by:
    
    addProperties in interface IChemObject
    
    Overrides:
    
    addProperties in class ChemObject
    
    Parameters:
    
    properties - a Hashtable specifying the property values
    
    See Also:
    
    ChemObject.getProperties()
  - setFlags
```
public void setFlags(boolean[] flagsNew)
```
    Sets the whole set of flags.
    
    Specified by:
    
    setFlags in interface IChemObject
    
    Overrides:
    
    setFlags in class ChemObject
    
    Parameters:
    
    flagsNew - the new flags.
    
    See Also:
    
    ChemObject.getFlags()
  - getFlags
```
public boolean[] getFlags()
```
    Returns the whole set of flags.
    
    Specified by:
    
    getFlags in interface IChemObject
    
    Overrides:
    
    getFlags in class ChemObject
    
    Returns:
    
    the flags.
    
    See Also:
    
    ChemObject.setFlags(boolean[])
  - clone
```
public IFragmentAtom clone()
                    throws CloneNotSupportedException
```
    Clones this atom object and its content.
    
    Specified by:
    
    clone in interface IAtom
    
    Specified by:
    
    clone in interface IChemObject
    
    Specified by:
    
    clone in interface IPseudoAtom
    
    Overrides:
    
    clone in class FragmentAtom
    
    Returns:
    
    The cloned object
    
    Throws:
    
    CloneNotSupportedException - if the IChemObject cannot be cloned
  - getBuilder
```
public IChemObjectBuilder getBuilder()
```
    Returns a IChemObjectBuilder for the data classes that extend this class.
    
    Specified by:
    
    getBuilder in interface ICDKObject
    
    Overrides:
    
    getBuilder in class ChemObject
    
    Returns:
    
    The IChemObjectBuilder matching this ICDKObject
  - getLabel
```
public String getLabel()
```
    Returns the label of this PseudoAtom.
    
    Specified by:
    
    getLabel in interface IPseudoAtom
    
    Overrides:
    
    getLabel in class PseudoAtom
    
    Returns:
    
    The label for this PseudoAtom
    
    See Also:
    
    PseudoAtom.setLabel(java.lang.String)
  - setLabel
```
public void setLabel(String label)
```
    Sets the label of this PseudoAtom.
    
    Specified by:
    
    setLabel in interface IPseudoAtom
    
    Overrides:
    
    setLabel in class PseudoAtom
    
    Parameters:
    
    label - The new label for this PseudoAtom
    
    See Also:
    
    PseudoAtom.getLabel()

Class DebugFragmentAtom

Nested Class Summary

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

Field Summary

Fields inherited from class org.openscience.cdk.Atom

Fields inherited from class org.openscience.cdk.AtomType

Fields inherited from class org.openscience.cdk.Isotope

Fields inherited from class org.openscience.cdk.Element

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

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

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.FragmentAtom

Methods inherited from class org.openscience.cdk.PseudoAtom

Methods inherited from class org.openscience.cdk.Atom

Methods inherited from class org.openscience.cdk.ChemObject

Methods inherited from class java.lang.Object

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

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

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

Constructor Detail

DebugFragmentAtom

Method Detail

isExpanded

setExpanded

getFragment

setFragment

setCharge

getCharge

setImplicitHydrogenCount

getImplicitHydrogenCount

setPoint2d

setPoint3d

setFractionalPoint3d

setStereoParity

getPoint2d

getPoint3d

getFractionalPoint3d

getStereoParity

setAtomTypeName

setMaxBondOrder

setBondOrderSum

getAtomTypeName

getMaxBondOrder

getBondOrderSum

setFormalCharge

getFormalCharge

setFormalNeighbourCount

getFormalNeighbourCount

setHybridization

getHybridization

setCovalentRadius

getCovalentRadius

setValency

getValency

setNaturalAbundance

setExactMass

getNaturalAbundance

getExactMass

getMassNumber

setMassNumber

getAtomicNumber

setAtomicNumber

getSymbol

setSymbol

addListener

getListenerCount

removeListener

notifyChanged

notifyChanged

setProperty

removeProperty

getProperty

getProperties

getID

setID

setFlag

getFlag

addProperties

setFlags