Package org.openscience.cdk.protein.data

Class PDBPolymer

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Polymer

org.openscience.cdk.BioPolymer

org.openscience.cdk.protein.data.PDBPolymer

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, IBioPolymer, ICDKObject, IChemObject, IChemObjectListener, IPDBPolymer, IPolymer

Direct Known Subclasses:

DebugPDBPolymer

public class PDBPolymer
extends BioPolymer
implements Cloneable, IPDBPolymer

An entry in the PDB database. It is not just a regular protein, but the regular PDB mix of protein or protein complexes, ligands, water molecules and other species.

Author:

Egon Willighagen

See Also:

Serialized Form

Source code:

main

Belongs to CDK module:

data

Keywords:

polymer

Created on:

2006-04-19

Field Summary

Fields inherited from class org.openscience.cdk.AtomContainer

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

Constructor Summary

Constructors

Constructor	Description
PDBPolymer()	Constructs a new Polymer to store the IMonomers.

Method Summary

Modifier and Type	Method	Description
void	addAtom(IPDBAtom oAtom)	Adds the atom oAtom without specifying a IMonomer or a Strand.
void	addAtom(IPDBAtom oAtom, IMonomer oMonomer)	Adds the atom oAtom to a specified Monomer.
void	addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
void	addStructure(IPDBStructure structure)	Adds the PDBStructure structure a this PDBPolymer.
IPDBPolymer	clone()	Clones this IChemObject.
Collection<String>	getMonomerNamesInSequentialOrder()	Returns the monomer names in the order in which they were added.
Collection<IPDBStructure>	getStructures()	Returns a Collection containing the PDBStructure in the PDBPolymer.
String	toString()	Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.BioPolymer

addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand

Methods inherited from class org.openscience.cdk.Polymer

addAtom, getMonomer, removeMonomer

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, 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.IBioPolymer

addAtom, addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand

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

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

stateChanged

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

addAtom, getMonomer, removeMonomer

Constructor Detail

PDBPolymer

public PDBPolymer()

Constructs a new Polymer to store the IMonomers.

Method Detail

addStructure

public void addStructure(IPDBStructure structure)

Description copied from interface: IPDBPolymer

Adds the PDBStructure structure a this PDBPolymer.

Specified by:

addStructure in interface IPDBPolymer

Parameters:

structure - The PDBStructure to add

getStructures

public Collection<IPDBStructure> getStructures()

Description copied from interface: IPDBPolymer

Returns a Collection containing the PDBStructure in the PDBPolymer.

Specified by:

getStructures in interface IPDBPolymer

Returns:

Collection containing the PDBStructure in the PDBPolymer

addAtom

public void addAtom(IPDBAtom oAtom)

Adds the atom oAtom without specifying a IMonomer or a Strand. Therefore the atom to this AtomContainer, but not to a certain Strand or IMonomer (intended e.g. for HETATMs).

Specified by:

addAtom in interface IPDBPolymer

Parameters:

oAtom - The IPDBAtom to add

addAtom

public void addAtom(IPDBAtom oAtom,
                    IMonomer oMonomer)

Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.

Parameters:

oAtom - The IPDBAtom to add

oMonomer - The monomer the atom belongs to

addAtom

public void addAtom(IPDBAtom oAtom,
                    IMonomer oMonomer,
                    IStrand oStrand)

Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand. Additionally, it keeps record of the iCode.

Specified by:

addAtom in interface IPDBPolymer

Parameters:

oAtom - The IPDBAtom to add

oMonomer - The monomer the atom belongs to

oStrand - The strand the atom belongs to

getMonomerNamesInSequentialOrder

public Collection<String> getMonomerNamesInSequentialOrder()

Returns the monomer names in the order in which they were added.

See Also:

IPolymer.getMonomerNames()

clone

public IPDBPolymer 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 IBioPolymer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IPDBPolymer

Specified by:

clone in interface IPolymer

Overrides:

clone in class BioPolymer

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

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 BioPolymer

Returns:

a String representation of this object