Package org.openscience.cdk.debug

Class DebugPDBPolymer

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

org.openscience.cdk.debug.DebugPDBPolymer

All Implemented Interfaces:

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

public class DebugPDBPolymer
extends PDBPolymer
implements IBioPolymer

Debugging data class.

Author:

Miguel Rojas

See Also:

• Serialized Form

Field Summary

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

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

Constructor Summary

Constructors

Constructor	Description
DebugPDBPolymer()

Method Summary

Modifier and Type	Method	Description
void	addStructure(IPDBStructure structure)	Adds the PDBStructure structure a this PDBPolymer.
Collection<IPDBStructure>	getStructures()	Returns a Collection containing the PDBStructure in the PDBPolymer.

Methods inherited from class org.openscience.cdk.protein.data.PDBPolymer

addAtom, addAtom, addAtom, clone, getMonomerNamesInSequentialOrder, toString

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, 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, addBond, 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

Constructor Details

DebugPDBPolymer

public DebugPDBPolymer()

Method Details

getStructures

public Collection<IPDBStructure> getStructures()

Returns a Collection containing the PDBStructure in the PDBPolymer.

Specified by:

getStructures in interface IPDBPolymer

Overrides:

getStructures in class PDBPolymer

Returns:

Collection containing the PDBStructure in the PDBPolymer

addStructure

public void addStructure(IPDBStructure structure)

Adds the PDBStructure structure a this PDBPolymer.

Specified by:

addStructure in interface IPDBPolymer

Overrides:

addStructure in class PDBPolymer

Parameters:

structure - The PDBStructure to add