org.openscience.cdk.interfaces

Interface IPDBMonomer

All Superinterfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IMonomer

All Known Implementing Classes:

DebugPDBMonomer, PDBMonomer, PDBMonomer

public interface IPDBMonomer
extends IMonomer

Represents the idea of an protein monomer as found in PDB files.

Author:

Miguel Rojas <miguel.rojas@uni-koeln.de>

Source code:

master

Belongs to CDK module:

interfaces

Keywords:

pdbpolymer

Created on:

2006-11-20

Method Summary

Modifier and Type	Method and Description
IPDBMonomer	clone() Returns a deep clone of this IChemObject.
String	getChainID() Gets the Chain ID of this monomer.
String	getICode() Gets the ICode of this monomer.
String	getResSeq() Gets the sequence identifier of this monomer.
void	setChainID(String newChainID) Sets the Chain ID of this monomer.
void	setICode(String newICode) Sets the ICode of this monomer.
void	setResSeq(String newResSeq) Sets the sequence identifier of this monomer.

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

getMonomerName, getMonomerType, setMonomerName, setMonomerType

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

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, 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, toString

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

getBuilder

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

stateChanged

Method Detail

setICode

void setICode(String newICode)

Sets the ICode of this monomer.

Parameters:

newICode - the I code of this monomer

getICode

String getICode()

Gets the ICode of this monomer.

Returns:

the ICode of this monomer

setChainID

void setChainID(String newChainID)

Sets the Chain ID of this monomer.

Parameters:

newChainID - the Chain ID of this monomer

getChainID

String getChainID()

Gets the Chain ID of this monomer.

Returns:

the Chain ID of this monomer

getResSeq

String getResSeq()

Gets the sequence identifier of this monomer.

Returns:

the sequence identifier of this monomer

setResSeq

void setResSeq(String newResSeq)

Sets the sequence identifier of this monomer.

Parameters:

newResSeq - the new sequence identifier of this monomer

clone

IPDBMonomer clone()
           throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IMonomer

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned