Package org.openscience.cdk
Class Monomer
- 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.Monomer
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
,IMonomer
- Direct Known Subclasses:
AminoAcid
,DebugMonomer
,PDBMonomer
public class Monomer extends AtomContainer implements Serializable, IMonomer, Cloneable
A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.- Author:
- Edgar Luttmann <edgar@uni-paderborn.de>
- See Also:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- data
- Keywords:
- monomer
- Created on:
- 2001-08-06
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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 Monomer()
Constructs a new Monomer.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description IMonomer
clone()
Clones thisIChemObject
.String
getMonomerName()
Retrieves the monomer name.String
getMonomerType()
Retrieves the monomer type.void
setMonomerName(String cMonomerName)
Sets the name of the Monomer object.void
setMonomerType(String cMonomerType)
Sets the type of the Monomer object.String
toString()
Returns a one line description of this IChemObject.-
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
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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
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, 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
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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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Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener
stateChanged
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Method Detail
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getMonomerName
public String getMonomerName()
Retrieves the monomer name.- Specified by:
getMonomerName
in interfaceIMonomer
- Returns:
- The name of the Monomer object
- See Also:
setMonomerName(java.lang.String)
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getMonomerType
public String getMonomerType()
Retrieves the monomer type.- Specified by:
getMonomerType
in interfaceIMonomer
- Returns:
- The type of the Monomer object
- See Also:
setMonomerType(java.lang.String)
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setMonomerName
public void setMonomerName(String cMonomerName)
Sets the name of the Monomer object.- Specified by:
setMonomerName
in interfaceIMonomer
- Parameters:
cMonomerName
- The new name for this monomer- See Also:
getMonomerName()
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setMonomerType
public void setMonomerType(String cMonomerType)
Sets the type of the Monomer object.- Specified by:
setMonomerType
in interfaceIMonomer
- Parameters:
cMonomerType
- The new type for this monomer- See Also:
getMonomerType()
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clone
public IMonomer clone() throws CloneNotSupportedException
Clones thisIChemObject
. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.- Specified by:
clone
in interfaceIAtomContainer
- Specified by:
clone
in interfaceIChemObject
- Specified by:
clone
in interfaceIMonomer
- Overrides:
clone
in classAtomContainer
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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toString
public String toString()
Description copied from class:AtomContainer
Returns a one line description of this IChemObject.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classAtomContainer
- Returns:
- a String representation of this object
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