org.openscience.cdk.silent

Class PDBMonomer

java.lang.Object

org.openscience.cdk.silent.ChemObject

org.openscience.cdk.silent.AtomContainer

org.openscience.cdk.silent.Monomer

org.openscience.cdk.silent.PDBMonomer

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IMonomer, IPDBMonomer

public class PDBMonomer
extends Monomer
implements Cloneable, IPDBMonomer

Represents the idea of an monomer as used in PDB files. It contains extra fields normally associated with atoms in such files.

See Also:

PDBAtom, Serialized Form

Source code:

master

Belongs to CDK module:

silent

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
PDBMonomer()

Method Summary

Modifier and Type	Method and Description
IPDBMonomer	clone() Clones this IChemObject.
String	getChainID()
String	getICode()
String	getResSeq()
void	setChainID(String newChainID)
void	setICode(String newICode)
void	setResSeq(String resSeq)
String	toString() Returns a one line string representation of this Atom.

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

getMonomerName, getMonomerType, setMonomerName, setMonomerType

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, 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.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.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

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

getBuilder

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

stateChanged

Constructor Detail

PDBMonomer

public PDBMonomer()

Method Detail

setICode

public void setICode(String newICode)

Specified by:

setICode in interface IPDBMonomer

getICode

public String getICode()

Specified by:

getICode in interface IPDBMonomer

setChainID

public void setChainID(String newChainID)

Specified by:

setChainID in interface IPDBMonomer

getChainID

public String getChainID()

Specified by:

getChainID in interface IPDBMonomer

toString

public String toString()

Returns a one line string representation of this Atom. Methods is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Monomer

Returns:

The string representation of this Atom

getResSeq

public String getResSeq()

Specified by:

getResSeq in interface IPDBMonomer

clone

public IPDBMonomer clone()
                  throws CloneNotSupportedException

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 IMonomer

Specified by:

clone in interface IPDBMonomer

Overrides:

clone in class Monomer

Returns:

The cloned object

Throws:

CloneNotSupportedException

setResSeq

public void setResSeq(String resSeq)

Specified by:

setResSeq in interface IPDBMonomer