Package org.openscience.cdk.interfaces

Interface IPolymer

All Superinterfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener

All Known Subinterfaces:

IBioPolymer, IPDBPolymer

All Known Implementing Classes:

BioPolymer, BioPolymer, DebugBioPolymer, DebugPDBPolymer, DebugPolymer, PDBPolymer, PDBPolymer, Polymer, Polymer

public interface IPolymer
extends IAtomContainer

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>

Source code:

main

Belongs to CDK module:

interfaces

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

Method Summary

Modifier and Type	Method	Description
void	addAtom(IAtom oAtom)	Adds the atom oAtom without specifying a Monomer.
void	addAtom(IAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
IPolymer	clone()	Returns a deep clone of this IChemObject.
IMonomer	getMonomer(String cName)	Retrieve a Monomer object by specifying its name.
int	getMonomerCount()	Return 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.

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, toString

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

stateChanged

Method Detail

addAtom

void addAtom(IAtom oAtom)

Adds the atom oAtom without specifying a Monomer. Therefore the atom to this AtomContainer, but not to a certain Monomer (intended e.g. for HETATMs).

Specified by:

addAtom in interface IAtomContainer

Parameters:

oAtom - The atom to add

addAtom

void addAtom(IAtom oAtom,
             IMonomer oMonomer)

Adds the atom oAtom to a specified Monomer.

Parameters:

oAtom - The atom to add

oMonomer - The monomer the atom belongs to

getMonomerCount

int getMonomerCount()

Return the number of monomers present in the Polymer.

Returns:

number of monomers

getMonomer

IMonomer getMonomer(String cName)

Retrieve a Monomer object by specifying its name.

Parameters:

cName - The name of the monomer to look for

Returns:

The Monomer object which was asked for

getMonomerNames

Collection<String> getMonomerNames()

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

Returns:

a Collection of all the monomer names.

removeMonomer

void removeMonomer(String name)

Removes a particular monomer, specified by its name.

Parameters:

name - The name of the monomer to be removed

clone

IPolymer clone()
        throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned