ambit2.core.groups

Interface ISGroup

All Superinterfaces:

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

All Known Implementing Classes:

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

public interface ISGroup
extends 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

Fields

Modifier and Type	Field and Description
static String	SGROUP_CONNECTIVITY
static String	SGROUP_VISIBLE

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	addBrackets(double x1, double y1, double x2, double y2)
void	finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol)
Iterable<org.openscience.cdk.interfaces.IAtom>	getAtoms(boolean expanded)
Iterable<org.openscience.cdk.interfaces.IBond>	getBonds(boolean expanded)
int	getNumber()
String	getSubscript()
void	setNumber(int number)
void	setSubscript(String subscript) text of Sgroup subscript.

Methods inherited from interface java.lang.Comparable

compareTo

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

SGROUP_VISIBLE

static final String SGROUP_VISIBLE

See Also:

Constant Field Values

SGROUP_CONNECTIVITY

static final 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(String subscript)

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

Parameters:

subscript -

getSubscript

String getSubscript()

addBrackets

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

getAtoms

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

getBonds

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

finalizeAtomList

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