ambit2.core.groups

Class SuperAtom

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

ambit2.core.groups.AbstractGroup

ambit2.core.groups.SuperAtom

All Implemented Interfaces:

IExpandable, ISGroup, Serializable, Cloneable, Comparable<ISGroup>, 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

public class SuperAtom
extends AbstractGroup
implements IExpandable

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ambit2.core.groups.AbstractGroup

AbstractGroup.EmptyIterator<T>, AbstractGroup.SelfIterable<T>

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

org.openscience.cdk.interfaces.IAtomType.Hybridization

Field Summary

Fields

Modifier and Type	Field and Description
protected List<org.openscience.cdk.interfaces.IBond>	contractedBonds

Fields inherited from class ambit2.core.groups.AbstractGroup

atoms, bonds, number

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

Fields inherited from interface ambit2.core.groups.ISGroup

SGROUP_CONNECTIVITY, SGROUP_VISIBLE

Constructor Summary

Constructors

Constructor and Description
SuperAtom(String label, int number)

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.interfaces.IBond	addBond(org.openscience.cdk.interfaces.IBond bond)
void	finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol) does nothing
Iterable<org.openscience.cdk.interfaces.IAtom>	getAtoms(boolean expanded)
Iterable<org.openscience.cdk.interfaces.IBond>	getBonds(boolean expanded)
boolean	isExpanded()
boolean	isExpanded(org.openscience.cdk.interfaces.IBond bond)
void	setExpanded(boolean expanded)
void	setSubscript(String subscript) text of Sgroup subscript.

Methods inherited from class ambit2.core.groups.AbstractGroup

addAtom, addBondsConnected2Atoms, addBrackets, compareTo, equals, getNumber, getSubscript, isGroupVisible, setGroupVisible, setNumber

Methods inherited from class org.openscience.cdk.PseudoAtom

clone, getAttachPointNum, getLabel, setAttachPointNum, setLabel, setStereoParity, toString

Methods inherited from class org.openscience.cdk.Atom

bonds, compare, 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

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, 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.IAtom

bonds, clone, 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

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, 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

contractedBonds

protected List<org.openscience.cdk.interfaces.IBond> contractedBonds

Constructor Detail

SuperAtom

public SuperAtom(String label,
                 int number)

Method Detail

setSubscript

public void setSubscript(String subscript)

Description copied from interface: ISGroup

text of Sgroup subscript. See SGroupMDL2000Helper.SGROUP_LINE.M__SMT.

Specified by:

setSubscript in interface ISGroup

Overrides:

setSubscript in class AbstractGroup

finalizeAtomList

public void finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol)

Description copied from class: AbstractGroup

does nothing

Specified by:

finalizeAtomList in interface ISGroup

Overrides:

finalizeAtomList in class AbstractGroup

addBond

public org.openscience.cdk.interfaces.IBond addBond(org.openscience.cdk.interfaces.IBond bond)

Specified by:

addBond in interface ISGroup

Overrides:

addBond in class AbstractGroup

getBonds

public Iterable<org.openscience.cdk.interfaces.IBond> getBonds(boolean expanded)

Specified by:

getBonds in interface ISGroup

Overrides:

getBonds in class AbstractGroup

getAtoms

public Iterable<org.openscience.cdk.interfaces.IAtom> getAtoms(boolean expanded)

Specified by:

getAtoms in interface ISGroup

Overrides:

getAtoms in class AbstractGroup

isExpanded

public boolean isExpanded(org.openscience.cdk.interfaces.IBond bond)

Overrides:

isExpanded in class AbstractGroup

isExpanded

public boolean isExpanded()

Specified by:

isExpanded in interface IExpandable

setExpanded

public void setExpanded(boolean expanded)

Specified by:

setExpanded in interface IExpandable