Package org.openscience.cdk.interfaces

Interface IPDBPolymer

All Superinterfaces:

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

All Known Implementing Classes:

DebugPDBPolymer, PDBPolymer, PDBPolymer

public interface IPDBPolymer
extends IBioPolymer

A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.

Author:

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

Source code:

main

Belongs to CDK module:

interfaces

Keywords:

polymer, biopolymer, pdbpolymer

Created on:

2006-11-20

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

Method Summary

Modifier and Type	Method	Description
void	addAtom(IPDBAtom oAtom)	Adds the atom oAtom without specifying a Monomer or a Strand.
void	addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)	Adds the atom to a specified Strand and a specified Monomer.
void	addStructure(IPDBStructure structure)	Adds the PDBStructure structure a this PDBPolymer.
IPDBPolymer	clone()	Returns a deep clone of this IChemObject.
Collection<IPDBStructure>	getStructures()	Returns a Collection containing the PDBStructure in the PDBPolymer.

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

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

stateChanged

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

addAtom, getMonomer, removeMonomer

Method Detail

addAtom

void addAtom(IPDBAtom oAtom)

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

Parameters:

oAtom - The atom to add

addAtom

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

Adds the atom to a specified Strand and a specified Monomer.

Parameters:

oAtom - The atom to add

oMonomer - The monomer the atom belongs to

oStrand - The strand the atom belongs to

addStructure

void addStructure(IPDBStructure structure)

Adds the PDBStructure structure a this PDBPolymer.

Parameters:

structure - The PDBStructure to add

getStructures

Collection<IPDBStructure> getStructures()

Returns a Collection containing the PDBStructure in the PDBPolymer.

Returns:

Collection containing the PDBStructure in the PDBPolymer

clone

IPDBPolymer clone()
           throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IBioPolymer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IPolymer

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned