ambit2.core.groups
Class SuperAtom

Package class diagram package SuperAtom
java.lang.Object
  extended by org.openscience.cdk.ChemObject
      extended by org.openscience.cdk.Element
          extended by org.openscience.cdk.Isotope
              extended by org.openscience.cdk.AtomType
                  extended by org.openscience.cdk.Atom
                      extended by org.openscience.cdk.PseudoAtom
                          extended by ambit2.core.groups.AbstractGroup
                              extended by ambit2.core.groups.SuperAtom
All Implemented Interfaces:
IExpandable, 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 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
protected  java.util.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
SuperAtom(java.lang.String label, int number)
           
 
Method Summary
 org.openscience.cdk.interfaces.IBond addBond(org.openscience.cdk.interfaces.IBond bond)
           
 void finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol)
          does nothing
 java.lang.Iterable<org.openscience.cdk.interfaces.IAtom> getAtoms(boolean expanded)
           
 java.lang.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(java.lang.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, 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

contractedBonds

protected java.util.List<org.openscience.cdk.interfaces.IBond> contractedBonds
Constructor Detail

SuperAtom

public SuperAtom(java.lang.String label,
                 int number)
Method Detail

setSubscript

public void setSubscript(java.lang.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 java.lang.Iterable<org.openscience.cdk.interfaces.IBond> getBonds(boolean expanded)
Specified by:
getBonds in interface ISGroup
Overrides:
getBonds in class AbstractGroup

getAtoms

public java.lang.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