Package org.openscience.cdk.protein.data

Class PDBMonomer

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Monomer

org.openscience.cdk.protein.data.PDBMonomer

All Implemented Interfaces:

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

Direct Known Subclasses:

DebugPDBMonomer

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:

main

Belongs to CDK module:

data

Field Summary

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
PDBMonomer()

Method Summary

Modifier and Type	Method	Description
IPDBMonomer	clone()	Clones 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 resSeq)	Sets the sequence identifier of this monomer.
String	toString()	Returns a one line string representation of this Atom.

Methods inherited from class org.openscience.cdk.Monomer

getMonomerName, getMonomerType, setMonomerName, setMonomerType

Methods inherited from class org.openscience.cdk.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, newAtom, newAtom, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, shallowCopy, singleElectrons, stateChanged, stereoElements

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

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, 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, newAtom, newAtom, newAtom, newAtom, newBond, newBond, 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, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

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

stateChanged

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

getMonomerName, getMonomerType, setMonomerName, setMonomerType

Constructor Detail

PDBMonomer

public PDBMonomer()

Method Detail

setICode

public void setICode(String newICode)

Description copied from interface: IPDBMonomer

Sets the ICode of this monomer.

Specified by:

setICode in interface IPDBMonomer

Parameters:

newICode - the I code of this monomer

getICode

public String getICode()

Description copied from interface: IPDBMonomer

Gets the ICode of this monomer.

Specified by:

getICode in interface IPDBMonomer

Returns:

the ICode of this monomer

setChainID

public void setChainID(String newChainID)

Description copied from interface: IPDBMonomer

Sets the Chain ID of this monomer.

Specified by:

setChainID in interface IPDBMonomer

Parameters:

newChainID - the Chain ID of this monomer

getChainID

public String getChainID()

Description copied from interface: IPDBMonomer

Gets the Chain ID of this monomer.

Specified by:

getChainID in interface IPDBMonomer

Returns:

the Chain ID of this monomer

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()

Description copied from interface: IPDBMonomer

Gets the sequence identifier of this monomer.

Specified by:

getResSeq in interface IPDBMonomer

Returns:

the sequence identifier of this monomer

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 - if the IChemObject cannot be cloned

setResSeq

public void setResSeq(String resSeq)

Description copied from interface: IPDBMonomer

Sets the sequence identifier of this monomer.

Specified by:

setResSeq in interface IPDBMonomer

Parameters:

resSeq - the new sequence identifier of this monomer