org.openscience.cdk.libio.md

Class ChargeGroup

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.libio.md.ChargeGroup

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener

public class ChargeGroup
extends AtomContainer

A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule. A CG is a small set of atoms with total zero or Integer charge.

Author:

ola

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

libiomd

Field Summary

Fields inherited from class org.openscience.cdk.AtomContainer

atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements

Constructor Summary

Constructors

Constructor and Description
ChargeGroup() Empty constructor.
ChargeGroup(IAtomContainer container, int number, MDMolecule parentMolecule) Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.

Method Summary

Modifier and Type	Method and Description
int	getNumber()
MDMolecule	getParentMolecule()
IAtom	getSwitchingAtom()
void	setNumber(int number)
void	setParentMolecule(MDMolecule parentMolecule)
void	setSwitchingAtom(IAtom switchingAtom)

Methods inherited from class org.openscience.cdk.AtomContainer

add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, clone, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stateChanged, stereoElements, toString

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, compare, 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

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Constructor Detail

ChargeGroup

public ChargeGroup()

Empty constructor.

ChargeGroup

public ChargeGroup(IAtomContainer container,
                   int number,
                   MDMolecule parentMolecule)

Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.

Method Detail

getNumber

public int getNumber()

setNumber

public void setNumber(int number)

getParentMolecule

public MDMolecule getParentMolecule()

setParentMolecule

public void setParentMolecule(MDMolecule parentMolecule)

getSwitchingAtom

public IAtom getSwitchingAtom()

setSwitchingAtom

public void setSwitchingAtom(IAtom switchingAtom)