Package 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

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
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

Modifier and Type	Method	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, 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, toString

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

addBond, newAtom, newAtom, newBond

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

Constructor Details

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 Details

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)