Package org.openscience.cdk

Class Polymer

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Polymer

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IPolymer

Direct Known Subclasses:

BioPolymer, DebugPolymer

public class Polymer
extends AtomContainer
implements Serializable, IPolymer

Subclass of Molecule to store Polymer specific attributes that a Polymer has.

Author:

Edgar Luttmann <edgar@uni-paderborn.de>, Martin Eklund <martin.eklund@farmbio.uu.se>

See Also:

Serialized Form

Source code:

main

Belongs to CDK module:

data

Keywords:

polymer

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, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
Polymer()	Constructs a new Polymer to store the Monomers.

Method Summary

Modifier and Type	Method	Description
void	addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
IPolymer	clone()	Clones this IChemObject.
IMonomer	getMonomer(String cName)	Retrieves a Monomer object by specifying its name.
int	getMonomerCount()	Returns the number of monomers present in the Polymer.
Collection<String>	getMonomerNames()	Returns a collection of the names of all Monomers in this polymer.
void	removeMonomer(String name)	Removes a particular monomer, specified by its name.
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, 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

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

addAtom

Constructor Detail

Polymer

public Polymer()

Constructs a new Polymer to store the Monomers.

Method Detail

addAtom

public void addAtom(IAtom oAtom,
                    IMonomer oMonomer)

Adds the atom oAtom to a specified Monomer.

Specified by:

addAtom in interface IPolymer

Parameters:

oAtom - The atom to add

oMonomer - The monomer the atom belongs to

getMonomerCount

public int getMonomerCount()

Returns the number of monomers present in the Polymer.

Specified by:

getMonomerCount in interface IPolymer

Returns:

number of monomers

getMonomer

public IMonomer getMonomer(String cName)

Retrieves a Monomer object by specifying its name.

Specified by:

getMonomer in interface IPolymer

Parameters:

cName - The name of the monomer to look for

Returns:

The Monomer object which was asked for

getMonomerNames

public Collection<String> getMonomerNames()

Returns a collection of the names of all Monomers in this polymer.

Specified by:

getMonomerNames in interface IPolymer

Returns:

a Collection of all the monomer names.

removeMonomer

public void removeMonomer(String name)

Removes a particular monomer, specified by its name.

Specified by:

removeMonomer in interface IPolymer

Parameters:

name - The name of the monomer to remove

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

clone

public IPolymer clone()
               throws CloneNotSupportedException

Description copied from class: AtomContainer

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 IPolymer

Overrides:

clone in class AtomContainer

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned