org.openscience.cdk

Class Strand

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Strand

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IStrand

Direct Known Subclasses:

DebugStrand, PDBStrand

public class Strand
extends AtomContainer
implements Serializable, IStrand

A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.

Author:

Martin Eklund <martin.eklund@farmbio.uu.se>, Ola Spjuth <ola.spjuth@farmbio.uu.se>

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

data

Created on:

2004-12-20

Field Summary

Fields inherited from class org.openscience.cdk.AtomContainer

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

Constructor Summary

Constructors

Constructor and Description
Strand() Constructs a new Strand.

Method Summary

Modifier and Type	Method and Description
void	addAtom(IAtom oAtom) Adds the atom oAtom without specifying a Monomer or a Strand.
void	addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specific Monomer.
IStrand	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 Strand.
Collection<String>	getMonomerNames() Returns a collection of the names of all Monomers in this polymer.
Map<String,IMonomer>	getMonomers() Returns a hashtable containing the monomers in the strand.
String	getStrandName() Retrieves the strand name.
String	getStrandType() Retrieves the strand type.
void	removeMonomer(String name) Removes a particular monomer, specified by its name.
void	setStrandName(String cStrandName) Sets the name of the Strand object.
void	setStrandType(String cStrandType) Sets the type of the Strand object.
String	toString() Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.AtomContainer

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, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stateChanged, stereoElements

Methods inherited from class org.openscience.cdk.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.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, 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.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

Strand

public Strand()

Constructs a new Strand.

Method Detail

getStrandName

public String getStrandName()

Retrieves the strand name.

Specified by:

getStrandName in interface IStrand

Returns:

The name of the Strand object

See Also:

setStrandName(java.lang.String)

getStrandType

public String getStrandType()

Retrieves the strand type.

Specified by:

getStrandType in interface IStrand

Returns:

The type of the Strand object

See Also:

setStrandType(java.lang.String)

setStrandName

public void setStrandName(String cStrandName)

Sets the name of the Strand object.

Specified by:

setStrandName in interface IStrand

Parameters:

cStrandName - The new name for this strand

See Also:

getStrandName()

setStrandType

public void setStrandType(String cStrandType)

Sets the type of the Strand object.

Specified by:

setStrandType in interface IStrand

Parameters:

cStrandType - The new type for this strand

See Also:

getStrandType()

addAtom

public void addAtom(IAtom oAtom)

Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the atom gets added to a Monomer of type UNKNOWN in a Strand of type UNKNOWN.

Specified by:

addAtom in interface IAtomContainer

Specified by:

addAtom in interface IStrand

Overrides:

addAtom in class AtomContainer

Parameters:

oAtom - The atom to add

addAtom

public void addAtom(IAtom oAtom,
                    IMonomer oMonomer)

Adds the atom oAtom to a specific Monomer.

Specified by:

addAtom in interface IStrand

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 Strand.

Specified by:

getMonomerCount in interface IStrand

Returns:

number of monomers

getMonomer

public IMonomer getMonomer(String cName)

Retrieves a Monomer object by specifying its name.

Specified by:

getMonomer in interface IStrand

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 IStrand

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 IStrand

Parameters:

name - The name of the monomer to remove

getMonomers

public Map<String,IMonomer> getMonomers()

Returns a hashtable containing the monomers in the strand.

Specified by:

getMonomers in interface IStrand

Returns:

hashtable containing the monomers in the strand.

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 IStrand 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 IStrand

Overrides:

clone in class AtomContainer

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned