Package org.openscience.cdk
Class AminoAcid
- 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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- org.openscience.cdk.AminoAcid
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAminoAcid
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
,IMonomer
- Direct Known Subclasses:
DebugAminoAcid
public class AminoAcid extends Monomer implements IAminoAcid, Serializable, Cloneable
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.- Author:
- Egon Willighagen <e.willighagen@science.ru.nl>
- See Also:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- data
- Keywords:
- amino acid
- Created on:
- 2005-08-11
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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 AminoAcid()
Constructs a new AminoAcid.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCTerminus(IAtom atom)
Add an Atom and makes it the C-terminus atom.void
addNTerminus(IAtom atom)
Add an Atom and makes it the N-terminus atom.IAminoAcid
clone()
Clones this AminoAcid object.IAtom
getCTerminus()
Retrieves the C-terminus atom.IAtom
getNTerminus()
Retrieves the N-terminus atom.String
toString()
Returns a one line description of this IChemObject.-
Methods inherited from class org.openscience.cdk.Monomer
getMonomerName, getMonomerType, setMonomerName, setMonomerType
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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, 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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Methods inherited from interface org.openscience.cdk.interfaces.IMonomer
getMonomerName, getMonomerType, setMonomerName, setMonomerType
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Method Detail
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getNTerminus
public IAtom getNTerminus()
Retrieves the N-terminus atom.- Specified by:
getNTerminus
in interfaceIAminoAcid
- Returns:
- The Atom that is the N-terminus
- See Also:
addNTerminus(IAtom)
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addNTerminus
public void addNTerminus(IAtom atom)
Add an Atom and makes it the N-terminus atom.- Specified by:
addNTerminus
in interfaceIAminoAcid
- Parameters:
atom
- The Atom that is the N-terminus- See Also:
getNTerminus()
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getCTerminus
public IAtom getCTerminus()
Retrieves the C-terminus atom.- Specified by:
getCTerminus
in interfaceIAminoAcid
- Returns:
- The Atom that is the C-terminus
- See Also:
addCTerminus(IAtom)
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addCTerminus
public void addCTerminus(IAtom atom)
Add an Atom and makes it the C-terminus atom.- Specified by:
addCTerminus
in interfaceIAminoAcid
- Parameters:
atom
- The Atom that is the C-terminus- See Also:
getCTerminus()
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clone
public IAminoAcid clone() throws CloneNotSupportedException
Clones this AminoAcid object.- Specified by:
clone
in interfaceIAminoAcid
- Specified by:
clone
in interfaceIAtomContainer
- Specified by:
clone
in interfaceIChemObject
- Specified by:
clone
in interfaceIMonomer
- Overrides:
clone
in classMonomer
- 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 classMonomer
- Returns:
- a String representation of this object
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