Package org.openscience.cdk.interfaces
Interface IAminoAcid
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- All Superinterfaces:
Cloneable
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
,IMonomer
- All Known Implementing Classes:
AminoAcid
,AminoAcid
,DebugAminoAcid
public interface IAminoAcid extends IMonomer
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.- Author:
- Egon Willighagen <e.willighagen@science.ru.nl>
- Source code:
- main
- Belongs to CDK module:
- interfaces
- Keywords:
- amino acid
- Created on:
- 2005-12-05
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Method Summary
All Methods Instance Methods Abstract 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()
Returns a deep clone of this IChemObject.IAtom
getCTerminus()
Retrieves the C-terminus atom.IAtom
getNTerminus()
Retrieves the N-terminus atom.-
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, 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, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
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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
IAtom getNTerminus()
Retrieves the N-terminus atom.- Returns:
- The Atom that is the N-terminus
- See Also:
addNTerminus(IAtom)
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addNTerminus
void addNTerminus(IAtom atom)
Add an Atom and makes it the N-terminus atom.- Parameters:
atom
- The Atom that is the N-terminus- See Also:
getNTerminus()
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getCTerminus
IAtom getCTerminus()
Retrieves the C-terminus atom.- Returns:
- The Atom that is the C-terminus
- See Also:
addCTerminus(IAtom)
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addCTerminus
void addCTerminus(IAtom atom)
Add an Atom and makes it the C-terminus atom.- Parameters:
atom
- The Atom that is the C-terminus- See Also:
getCTerminus()
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clone
IAminoAcid clone() throws CloneNotSupportedException
Returns a deep clone of this IChemObject.- Specified by:
clone
in interfaceIAtomContainer
- Specified by:
clone
in interfaceIChemObject
- Specified by:
clone
in interfaceIMonomer
- Returns:
- Object the clone of this IChemObject.
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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