org.openscience.cdk.libio.md

Class Residue

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.libio.md.Residue

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener

public class Residue
extends AtomContainer

A residue is a named, numbered collection of atoms in an MDMolecule. Residues are used to partition molecules in distinct pieces.

Author:

ola

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

libiomd

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
Residue() Empty constructor
Residue(IAtomContainer container, int number, MDMolecule parentMolecule) Constructor to create a Residue based on an AC, a number, and a MDMolecule.

Method Summary

Methods

Modifier and Type	Method and Description
String	getName()
int	getNumber()
MDMolecule	getParentMolecule()
void	setName(String name)
void	setNumber(int number)
void	setParentMolecule(MDMolecule parentMolecule)

Methods inherited from class org.openscience.cdk.AtomContainer

add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, clone, 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, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, singleElectrons, stateChanged, stereoElements, toString

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.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

Constructor Detail

Residue

public Residue()

Empty constructor

Residue

public Residue(IAtomContainer container,
       int number,
       MDMolecule parentMolecule)

Constructor to create a Residue based on an AC, a number, and a MDMolecule.

Method Detail

getName

public String getName()

setName

public void setName(String name)

getNumber

public int getNumber()

setNumber

public void setNumber(int number)

getParentMolecule

public MDMolecule getParentMolecule()

setParentMolecule

public void setParentMolecule(MDMolecule parentMolecule)