Package org.openscience.cdk

Class Monomer

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Monomer

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IMonomer

Direct Known Subclasses:

AminoAcid, DebugMonomer, PDBMonomer

public class Monomer
extends AtomContainer
implements Serializable, IMonomer, Cloneable

A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.

Author:

Edgar Luttmann <edgar@uni-paderborn.de>

See Also:

• Serialized Form

Keywords:

monomer

Created on:

2001-08-06

Field Summary

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
Monomer()	Constructs a new Monomer.

Method Summary

Modifier and Type	Method	Description
IMonomer	clone()	Clones this IChemObject.
String	getMonomerName()	Retrieves the monomer name.
String	getMonomerType()	Retrieves the monomer type.
void	setMonomerName(String cMonomerName)	Sets the name of the Monomer object.
void	setMonomerType(String cMonomerType)	Sets the type of the Monomer object.
String	toString()	Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.AtomContainer

add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, 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

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

Methods inherited from class java.lang.Object

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

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

add, addAtom, addBond, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, 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, newAtom, newAtom, newBond, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stereoElements

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

getBuilder

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

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

stateChanged

Constructor Details

Monomer

public Monomer()

Constructs a new Monomer.

Method Details

getMonomerName

public String getMonomerName()

Retrieves the monomer name.

Specified by:

getMonomerName in interface IMonomer

Returns:

The name of the Monomer object

See Also:

• setMonomerName(java.lang.String)

getMonomerType

public String getMonomerType()

Retrieves the monomer type.

Specified by:

getMonomerType in interface IMonomer

Returns:

The type of the Monomer object

See Also:

• setMonomerType(java.lang.String)

setMonomerName

public void setMonomerName(String cMonomerName)

Sets the name of the Monomer object.

Specified by:

setMonomerName in interface IMonomer

Parameters:

cMonomerName - The new name for this monomer

See Also:

• getMonomerName()

setMonomerType

public void setMonomerType(String cMonomerType)

Sets the type of the Monomer object.

Specified by:

setMonomerType in interface IMonomer

Parameters:

cMonomerType - The new type for this monomer

See Also:

• getMonomerType()

clone

public IMonomer clone()
               throws CloneNotSupportedException

Clones this IChemObject. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IMonomer

Overrides:

clone in class AtomContainer

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

toString

public String toString()

Description copied from class: AtomContainer

Returns a one line description of this IChemObject.

Specified by:

toString in interface IChemObject

Overrides:

toString in class AtomContainer

Returns:

a String representation of this object