ambit2.core.groups
Class AbstractGroup

Package class diagram package AbstractGroup
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
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
Direct Known Subclasses:
ComponentGroup, ContainerGroup, DataGroup, GenericGroup, MonomerGroup, MultipleGroup, StructureRepeatingUnit, SuperAtom

public abstract class AbstractGroup
extends org.openscience.cdk.PseudoAtom
implements ISGroup

See Also:
Serialized Form

Nested Class Summary
protected  class AbstractGroup.EmptyIterator<T>
           
protected  class 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.IAtom> atoms
           
protected  java.util.List<org.openscience.cdk.interfaces.IBond> bonds
           
protected  int 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
AbstractGroup()
           
AbstractGroup(java.lang.String label)
           
AbstractGroup(java.lang.String label, int number)
           
 
Method Summary
 org.openscience.cdk.interfaces.IAtom addAtom(org.openscience.cdk.interfaces.IAtom atom)
           
 org.openscience.cdk.interfaces.IBond addBond(org.openscience.cdk.interfaces.IBond bond)
           
 void addBondsConnected2Atoms(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.List<org.openscience.cdk.interfaces.IAtom> atoms, java.util.List<org.openscience.cdk.interfaces.IBond> bonds)
           
 void addBrackets(double x1, double y1, double x2, double y2)
           
 int compareTo(ISGroup o)
           
 boolean equals(java.lang.Object obj)
           
 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)
           
 int getNumber()
           
 java.lang.String getSubscript()
           
 boolean isExpanded(org.openscience.cdk.interfaces.IBond bond)
           
static boolean isGroupVisible(org.openscience.cdk.interfaces.IChemObject c)
           
static void setGroupVisible(org.openscience.cdk.interfaces.IChemObject c, boolean visible)
           
 void setNumber(int number)
           
 void setSubscript(java.lang.String subscript)
          text of Sgroup subscript.
 
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

atoms

protected java.util.List<org.openscience.cdk.interfaces.IAtom> atoms

bonds

protected java.util.List<org.openscience.cdk.interfaces.IBond> bonds

number

protected int number
Constructor Detail

AbstractGroup

public AbstractGroup()

AbstractGroup

public AbstractGroup(java.lang.String label)

AbstractGroup

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

getNumber

public int getNumber()
Specified by:
getNumber in interface ISGroup

setNumber

public void setNumber(int number)
Specified by:
setNumber in interface ISGroup

compareTo

public int compareTo(ISGroup o)
Specified by:
compareTo in interface java.lang.Comparable<ISGroup>

equals

public boolean equals(java.lang.Object obj)
Overrides:
equals in class java.lang.Object

addAtom

public org.openscience.cdk.interfaces.IAtom addAtom(org.openscience.cdk.interfaces.IAtom atom)
Specified by:
addAtom in interface ISGroup

addBond

public org.openscience.cdk.interfaces.IBond addBond(org.openscience.cdk.interfaces.IBond bond)
Specified by:
addBond in interface ISGroup

finalizeAtomList

public void finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol)
does nothing

Specified by:
finalizeAtomList in interface ISGroup

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

getSubscript

public java.lang.String getSubscript()
Specified by:
getSubscript in interface ISGroup

addBrackets

public void addBrackets(double x1,
                        double y1,
                        double x2,
                        double y2)
Specified by:
addBrackets in interface ISGroup

getAtoms

public java.lang.Iterable<org.openscience.cdk.interfaces.IAtom> getAtoms(boolean expanded)
Specified by:
getAtoms in interface ISGroup

getBonds

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

isExpanded

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

setGroupVisible

public static void setGroupVisible(org.openscience.cdk.interfaces.IChemObject c,
                                   boolean visible)

isGroupVisible

public static boolean isGroupVisible(org.openscience.cdk.interfaces.IChemObject c)

addBondsConnected2Atoms

public void addBondsConnected2Atoms(org.openscience.cdk.interfaces.IAtomContainer mol,
                                    java.util.List<org.openscience.cdk.interfaces.IAtom> atoms,
                                    java.util.List<org.openscience.cdk.interfaces.IBond> bonds)