ambit2.core.groups

Class AbstractGroup

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

All Implemented Interfaces:

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

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

Nested Classes

Modifier and Type	Class and Description
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

Fields

Modifier and Type	Field and Description
protected List<org.openscience.cdk.interfaces.IAtom>	atoms
protected 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

Constructors

Constructor and Description
AbstractGroup()
AbstractGroup(String label)
AbstractGroup(String label, int number)

Method Summary

Modifier and Type	Method and Description
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, List<org.openscience.cdk.interfaces.IAtom> atoms, List<org.openscience.cdk.interfaces.IBond> bonds)
void	addBrackets(double x1, double y1, double x2, double y2)
int	compareTo(ISGroup o)
boolean	equals(Object obj)
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)
int	getNumber()
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(String subscript) text of Sgroup subscript.

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

atoms

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

bonds

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

number

protected int number

Constructor Detail

AbstractGroup

public AbstractGroup()

AbstractGroup

public AbstractGroup(String label)

AbstractGroup

public AbstractGroup(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 Comparable<ISGroup>

equals

public boolean equals(Object obj)

Overrides:

equals in class org.openscience.cdk.Atom

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

Specified by:

getAtoms in interface ISGroup

getBonds

public 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,
                                    List<org.openscience.cdk.interfaces.IAtom> atoms,
                                    List<org.openscience.cdk.interfaces.IBond> bonds)