ambit2.core.groups
Class ContainerGroup

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.ContainerGroup

All Implemented Interfaces:

ISGroup, java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<ISGroup>, org.openscience.cdk.interfaces.IAtom, org.openscience.cdk.interfaces.IAtomType, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IElement, org.openscience.cdk.interfaces.IIsotope, org.openscience.cdk.interfaces.IPseudoAtom

public class ContainerGroup
extends AbstractGroup

See Also:

Serialized Form

Nested Class Summary

static class

ContainerGroup.SGROUP_MIXTURE

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

protected java.util.List<ISGroup>	components
protected ContainerGroup.SGROUP_MIXTURE	type

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

ContainerGroup(java.lang.String label, int number)

ContainerGroup(java.lang.String label, int number, ContainerGroup.SGROUP_MIXTURE type)

Method Summary

void	finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol) does nothing
java.util.List<ISGroup>	getComponents()
ContainerGroup.SGROUP_MIXTURE	getType()
void	setComponents(java.util.List<ISGroup> components)
void	setType(ContainerGroup.SGROUP_MIXTURE type)

Methods inherited from class ambit2.core.groups.AbstractGroup

addAtom, addBond, addBondsConnected2Atoms, addBrackets, compareTo, equals, getAtoms, getBonds, getNumber, getSubscript, isExpanded, isGroupVisible, setGroupVisible, setNumber, setSubscript

Methods inherited from class org.openscience.cdk.PseudoAtom

clone, getLabel, setCharge, setExactMass, setFormalCharge, setHydrogenCount, setLabel, setStereoParity, toString

Methods inherited from class org.openscience.cdk.Atom

compare, getCharge, getFractionalPoint3d, getHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setHydrogenCount, setPoint2d, setPoint3d, setStereoParity

Methods inherited from class org.openscience.cdk.AtomType

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, getVanderwaalsRadius, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency, setVanderwaalsRadius

Methods inherited from class org.openscience.cdk.Isotope

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

Methods inherited from class java.lang.Object

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

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

getCharge, getFractionalPoint3d, getHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setHydrogenCount, setPoint2d, setPoint3d, setStereoParity

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

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, getVanderwaalsRadius, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency, setVanderwaalsRadius

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, clone, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

Field Detail

components

protected java.util.List<ISGroup> components

type

protected ContainerGroup.SGROUP_MIXTURE type

Constructor Detail

ContainerGroup

public ContainerGroup(java.lang.String label,
                      int number)

ContainerGroup

public ContainerGroup(java.lang.String label,
                      int number,
                      ContainerGroup.SGROUP_MIXTURE type)

Method Detail

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

getComponents

public java.util.List<ISGroup> getComponents()

setComponents

public void setComponents(java.util.List<ISGroup> components)

getType

public ContainerGroup.SGROUP_MIXTURE getType()

setType

public void setType(ContainerGroup.SGROUP_MIXTURE type)