Package org.openscience.cdk.interfaces

Interface IStrand

All Superinterfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener

All Known Implementing Classes:

DebugStrand, PDBStrand, Strand, Strand

public interface IStrand
extends IAtomContainer

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

Author:

Martin Eklund <martin.eklund@farmbio.uu.se>

Source code:

main

Belongs to CDK module:

interfaces

Created on:

2004-12-20

Method Summary

Modifier and Type	Method	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()	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 Strand.
Collection<String>	getMonomerNames()	Returns a collection of the names of all Monomers in this polymer.
Map<String,IMonomer>	getMonomers()	Returns the monomers in this strand.
String	getStrandName()	Retrieve the strand name.
String	getStrandType()	Retrieve the strand type.
void	removeMonomer(String name)	Removes a particular monomer, specified by its name.
void	setStrandName(String cStrandName)	Set the name of the Strand object.
void	setStrandType(String cStrandType)	Set the type of the Strand object.

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.ICDKObject

getBuilder

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, toString

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

stateChanged

Method Detail

getStrandName

String getStrandName()

Retrieve the strand name.

Returns:

The name of the Strand object

See Also:

setStrandName(String)

getStrandType

String getStrandType()

Retrieve the strand type.

Returns:

The type of the Strand object

See Also:

setStrandType(String)

setStrandName

void setStrandName(String cStrandName)

Set the name of the Strand object.

Parameters:

cStrandName - The new name for this strand

See Also:

getStrandName()

setStrandType

void setStrandType(String cStrandType)

Set the type of the Strand object.

Parameters:

cStrandType - The new type for this strand

See Also:

getStrandType()

addAtom

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

Parameters:

oAtom - The atom to add

addAtom

void addAtom(IAtom oAtom,
             IMonomer oMonomer)

Adds the atom oAtom to a specific 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 Strand.

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 remove

getMonomers

Map<String,IMonomer> getMonomers()

Returns the monomers in this strand.

Returns:

Map containing the monomers in the strand.

clone

IStrand 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