Package 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

Direct Known Subclasses:

DebugFragmentAtom

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

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, MARKUSH, 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
FragmentAtom()

Method Summary

Modifier and Type	Method	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()	Returns the fully expended form of the IFragmentAtom.
boolean	isExpanded()	Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.
void	setExactMass(Double mass)	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	setFragment(IAtomContainer fragment)	Sets the fully expended form of the IFragmentAtom.
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, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, hashCode, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setMapIdx, 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, clear, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, 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.IAtom

bonds, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, getTotalHydrogenCount, isAromatic, isInRing, neighbors, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, 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.ICDKObject

getBuilder

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

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

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

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

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

getMassNumber, getNaturalAbundance, setMassNumber, setNaturalAbundance

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

getAttachPointNum, getLabel, setAttachPointNum, setLabel

Constructor Details

FragmentAtom

public FragmentAtom()

Method Details

isExpanded

public boolean isExpanded()

Description copied from interface: IFragmentAtom

Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.

Specified by:

isExpanded in interface IFragmentAtom

Returns:

true, if it should be considered in expended form

setExpanded

public void setExpanded(boolean bool)

Description copied from interface: IFragmentAtom

Sets whether this atom is to be fully drawn and not just in the abbreviated form.

Specified by:

setExpanded in interface IFragmentAtom

Parameters:

bool - true if the full structure should be drawn

getFragment

public IAtomContainer getFragment()

Description copied from interface: IFragmentAtom

Returns the fully expended form of the IFragmentAtom.

Specified by:

getFragment in interface IFragmentAtom

Returns:

the fully expanded form as an IAtomContainer object

setFragment

public void setFragment(IAtomContainer fragment)

Description copied from interface: IFragmentAtom

Sets the fully expended form of the IFragmentAtom.

Specified by:

setFragment in interface IFragmentAtom

Parameters:

fragment - The fragment

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 - if the IChemObject cannot be cloned