org.openscience.cdk.silent

Class BioPolymer

java.lang.Object

org.openscience.cdk.silent.ChemObject

org.openscience.cdk.silent.AtomContainer

org.openscience.cdk.silent.Polymer

org.openscience.cdk.silent.BioPolymer

All Implemented Interfaces:

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

Direct Known Subclasses:

PDBPolymer

public class BioPolymer
extends Polymer
implements Serializable, IBioPolymer

A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.

Author:

Edgar Luttmann <edgar@uni-paderborn.de>, Martin Eklund

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

silent

Keywords:

polymer, biopolymer

Created on:

2001-08-06

Field Summary

Fields inherited from class org.openscience.cdk.silent.AtomContainer

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

Constructor Summary

Constructors

Constructor and Description
BioPolymer() Constructs a new Polymer to store the Strands.

Method Summary

Methods

Modifier and Type	Method and Description
void	addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand) Adds the atom to a specified Strand and a specified Monomer.
void	addAtom(IAtom oAtom, IStrand oStrand) Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
IBioPolymer	clone() Clones this AtomContainer object and its content.
IMonomer	getMonomer(String monName, String strandName) Retrieves a Monomer object by specifying its name.
int	getMonomerCount() Returns the number of monomers present in BioPolymer.
Collection<String>	getMonomerNames() Returns a collection of the names of all Monomers in this BioPolymer.
IStrand	getStrand(String cName) Retrieves a Monomer object by specifying its name.
int	getStrandCount() Returns the number of strands present in the BioPolymer.
Collection<String>	getStrandNames() Returns a collection of the names of all Strands in this BioPolymer.
Map<String,IStrand>	getStrands() Returns a Map containing the strands in the Polymer.
void	removeStrand(String name) Removes a particular strand, specified by its name.
String	toString() Returns a one line string representation of this Container.

Methods inherited from class org.openscience.cdk.silent.Polymer

addAtom, getMonomer, removeMonomer

Methods inherited from class org.openscience.cdk.silent.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, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, singleElectrons, stateChanged, stereoElements

Methods inherited from class org.openscience.cdk.silent.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.IBioPolymer

addAtom

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

addAtom, getMonomer, removeMonomer

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, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, singleElectrons, stereoElements

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

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

stateChanged

Constructor Detail

BioPolymer

public BioPolymer()

Constructs a new Polymer to store the Strands.

Method Detail

addAtom

public void addAtom(IAtom oAtom,
           IStrand oStrand)

Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence the atom will be added to a Monomer of type UNKNOWN in the specified Strand.

Specified by:

addAtom in interface IBioPolymer

Parameters:

oAtom - The atom to add

oStrand - The strand the atom belongs to

addAtom

public void addAtom(IAtom oAtom,
           IMonomer oMonomer,
           IStrand oStrand)

Adds the atom to a specified Strand and a specified Monomer.

Specified by:

addAtom in interface IBioPolymer

Parameters:

oAtom -

oMonomer -

oStrand -

getMonomerCount

public int getMonomerCount()

Returns the number of monomers present in BioPolymer.

Specified by:

getMonomerCount in interface IBioPolymer

Specified by:

getMonomerCount in interface IPolymer

Overrides:

getMonomerCount in class Polymer

Returns:

number of monomers

getMonomer

public IMonomer getMonomer(String monName,
                  String strandName)

Retrieves a Monomer object by specifying its name. [You have to specify the strand to enable monomers with the same name in different strands. There is at least one such case: every strand contains a monomer called "".]

Specified by:

getMonomer in interface IBioPolymer

Parameters:

monName - The name of the monomer to look for

strandName - The name of the strand 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 BioPolymer.

Specified by:

getMonomerNames in interface IBioPolymer

Specified by:

getMonomerNames in interface IPolymer

Overrides:

getMonomerNames in class Polymer

Returns:

a Collection of all the monomer names.

getStrandCount

public int getStrandCount()

Returns the number of strands present in the BioPolymer.

Specified by:

getStrandCount in interface IBioPolymer

Returns:

number of strands

getStrand

public IStrand getStrand(String cName)

Retrieves a Monomer object by specifying its name.

Specified by:

getStrand in interface IBioPolymer

Parameters:

cName - The name of the monomer to look for

Returns:

The Monomer object which was asked for

getStrandNames

public Collection<String> getStrandNames()

Returns a collection of the names of all Strands in this BioPolymer.

Specified by:

getStrandNames in interface IBioPolymer

Returns:

a Collection of all the strand names.

removeStrand

public void removeStrand(String name)

Removes a particular strand, specified by its name.

Specified by:

removeStrand in interface IBioPolymer

Parameters:

name - name of the strand to remove

getStrands

public Map<String,IStrand> getStrands()

Description copied from interface: IBioPolymer

Returns a Map containing the strands in the Polymer.

Specified by:

getStrands in interface IBioPolymer

Returns:

hashtable containing the monomers in the strand.

toString

public String toString()

Description copied from class: AtomContainer

Returns a one line string representation of this Container. This method is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Polymer

Returns:

The string representation of this Container

clone

public IBioPolymer clone()
                  throws CloneNotSupportedException

Description copied from class: AtomContainer

Clones this AtomContainer object and its content.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IBioPolymer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IPolymer

Overrides:

clone in class Polymer

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

See Also:

ChemObject.shallowCopy()