org.openscience.cdk.protein.data

Class PDBStrand

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Strand

org.openscience.cdk.protein.data.PDBStrand

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IStrand

public class PDBStrand
extends Strand

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:

master

Belongs to CDK module:

pdb

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 and Description
PDBStrand() Constructs a new Polymer to store the Monomers.

Method Summary

Modifier and Type	Method and Description
void	addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specified Monomer.
Collection<String>	getMonomerNamesInSequentialOrder() Returns the monomer names in the order in which they were added.
String	toString() Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.Strand

addAtom, clone, getMonomer, getMonomerCount, getMonomerNames, getMonomers, getStrandName, getStrandType, removeMonomer, setStrandName, setStrandType

Methods inherited from class org.openscience.cdk.AtomContainer

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, 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.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

PDBStrand

public PDBStrand()

Constructs a new Polymer to store the Monomers.

Method Detail

addAtom

public void addAtom(IAtom oAtom,
                    IMonomer oMonomer)

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

Specified by:

addAtom in interface IStrand

Overrides:

addAtom in class Strand

Parameters:

oAtom - The atom to add

oMonomer - The monomer 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()

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 Strand

Returns:

a String representation of this object