Package org.openscience.cdk.libio.md
Class ChargeGroup
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.AtomContainer
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- org.openscience.cdk.libio.md.ChargeGroup
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- 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:
- main
- Belongs to CDK module:
- libiomd
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Field Summary
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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Constructor Summary
Constructors Constructor 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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getNumber()
MDMolecule
getParentMolecule()
IAtom
getSwitchingAtom()
void
setNumber(int number)
void
setParentMolecule(MDMolecule parentMolecule)
void
setSwitchingAtom(IAtom switchingAtom)
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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, newAtom, newAtom, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, shallowCopy, singleElectrons, stateChanged, stereoElements, toString
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Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer
newAtom, newAtom, newBond
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Constructor Detail
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ChargeGroup
public ChargeGroup()
Empty constructor.
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ChargeGroup
public ChargeGroup(IAtomContainer container, int number, MDMolecule parentMolecule)
Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
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Method Detail
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getNumber
public int getNumber()
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setNumber
public void setNumber(int number)
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getParentMolecule
public MDMolecule getParentMolecule()
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setParentMolecule
public void setParentMolecule(MDMolecule parentMolecule)
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getSwitchingAtom
public IAtom getSwitchingAtom()
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setSwitchingAtom
public void setSwitchingAtom(IAtom switchingAtom)
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