Package org.openscience.cdk.libio.md
Class Residue
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.AtomContainer
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- org.openscience.cdk.libio.md.Residue
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- 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:
- main
- Belongs to CDK module:
- libiomd
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description Residue()
Empty constructorResidue(IAtomContainer container, int number, MDMolecule parentMolecule)
Constructor to create a Residue based on an AC, a number, and a MDMolecule.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getName()
int
getNumber()
MDMolecule
getParentMolecule()
void
setName(String name)
void
setNumber(int number)
void
setParentMolecule(MDMolecule parentMolecule)
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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
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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
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer
newAtom, newAtom, newBond
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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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
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Constructor Detail
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Residue
public Residue()
Empty constructor
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Residue
public Residue(IAtomContainer container, int number, MDMolecule parentMolecule)
Constructor to create a Residue based on an AC, a number, and a MDMolecule.
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Method Detail
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getName
public String getName()
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setName
public void setName(String name)
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getNumber
public int getNumber()
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setNumber
public void setNumber(int number)
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getParentMolecule
public MDMolecule getParentMolecule()
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setParentMolecule
public void setParentMolecule(MDMolecule parentMolecule)
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