ambit2.core.groups
Interface ISGroup

All Superinterfaces:

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

All Known Implementing Classes:

AbstractGroup, ComponentGroup, ContainerGroup, DataGroup, GenericGroup, MonomerGroup, MultipleGroup, StructureRepeatingUnit, SuperAtom

public interface ISGroup
extends java.lang.Comparable<ISGroup>, org.openscience.cdk.interfaces.IAtom

Nested Class Summary

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

org.openscience.cdk.interfaces.IAtomType.Hybridization

Field Summary

static java.lang.String	SGROUP_CONNECTIVITY
static java.lang.String	SGROUP_VISIBLE

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	addBrackets(double x1, double y1, double x2, double y2)
void	finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol)
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()
void	setNumber(int number)
void	setSubscript(java.lang.String subscript) text of Sgroup subscript.

Methods inherited from interface java.lang.Comparable

compareTo

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

SGROUP_VISIBLE

static final java.lang.String SGROUP_VISIBLE

See Also:

Constant Field Values

SGROUP_CONNECTIVITY

static final java.lang.String SGROUP_CONNECTIVITY

See Also:

Constant Field Values

Method Detail

getNumber

int getNumber()

setNumber

void setNumber(int number)

addAtom

org.openscience.cdk.interfaces.IAtom addAtom(org.openscience.cdk.interfaces.IAtom atom)

addBond

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

setSubscript

void setSubscript(java.lang.String subscript)

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

Parameters:

subscript -

getSubscript

java.lang.String getSubscript()

addBrackets

void addBrackets(double x1,
                 double y1,
                 double x2,
                 double y2)

getAtoms

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

getBonds

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

finalizeAtomList

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