org.openscience.cdk

Class FragmentAtom

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

All Implemented Interfaces:

Serializable, Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IFragmentAtom, IIsotope, IPseudoAtom

public class FragmentAtom
extends PseudoAtom
implements IFragmentAtom

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:

master

Belongs to CDK module:

data

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, symbol

Constructor Summary

Constructors

Constructor and Description
FragmentAtom()

Method Summary

Modifier and Type	Method and Description
IFragmentAtom	clone() Clones this atom object and its content.
Double	getExactMass() The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
IAtomContainer	getFragment()
boolean	isExpanded()
void	setExactMass(Double mass) Sets the ExactMass attribute of the Isotope object.
void	setExpanded(boolean bool)
void	setFragment(IAtomContainer fragment)
String	toString() Returns a one line string representation of this Atom.

Methods inherited from class org.openscience.cdk.PseudoAtom

getAttachPointNum, getLabel, setAttachPointNum, setLabel, setStereoParity

Methods inherited from class org.openscience.cdk.Atom

bonds, compare, equals, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getPoint2d, getPoint3d, getStereoParity, hashCode, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, 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

getMassNumber, getNaturalAbundance, setMassNumber, setNaturalAbundance

Methods inherited from class org.openscience.cdk.Element

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from class org.openscience.cdk.ChemObject

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

Methods inherited from class java.lang.Object

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

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

getAttachPointNum, getLabel, setAttachPointNum, setLabel

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

getMassNumber, getNaturalAbundance, 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

FragmentAtom

public FragmentAtom()

Method Detail

isExpanded

public boolean isExpanded()

Specified by:

isExpanded in interface IFragmentAtom

setExpanded

public void setExpanded(boolean bool)

Specified by:

setExpanded in interface IFragmentAtom

getFragment

public IAtomContainer getFragment()

Specified by:

getFragment in interface IFragmentAtom

setFragment

public void setFragment(IAtomContainer fragment)

Specified by:

setFragment in interface IFragmentAtom

setExactMass

public void setExactMass(Double mass)

Description copied from class: Isotope

Sets the ExactMass attribute of the Isotope object.

Specified by:

setExactMass in interface IIsotope

Overrides:

setExactMass in class Isotope

Parameters:

mass - The new ExactMass value

See Also:

Isotope.getExactMass()

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 Isotope

Returns:

The ExactMass value

See Also:

Isotope.setExactMass(java.lang.Double)

toString

public String toString()

Description copied from class: PseudoAtom

Returns a one line string representation of this Atom. Methods is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class PseudoAtom

Returns:

The string representation of this Atom

clone

public IFragmentAtom clone()
                    throws CloneNotSupportedException

Description copied from class: Atom

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 PseudoAtom

Returns:

The cloned object

Throws:

CloneNotSupportedException