Package org.openscience.cdk.protein.data
Class PDBMonomer
- 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.protein.data.PDBMonomer
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
,IMonomer
,IPDBMonomer
- Direct Known Subclasses:
DebugPDBMonomer
public class PDBMonomer extends Monomer implements Cloneable, IPDBMonomer
Represents the idea of an monomer as used in PDB files. It contains extra fields normally associated with atoms in such files.- See Also:
PDBAtom
, Serialized Form- Source code:
- main
- Belongs to CDK module:
- data
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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 PDBMonomer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description IPDBMonomer
clone()
Clones thisIChemObject
.String
getChainID()
Gets the Chain ID of this monomer.String
getICode()
Gets the ICode of this monomer.String
getResSeq()
Gets the sequence identifier of this monomer.void
setChainID(String newChainID)
Sets the Chain ID of this monomer.void
setICode(String newICode)
Sets the ICode of this monomer.void
setResSeq(String resSeq)
Sets the sequence identifier of this monomer.String
toString()
Returns a one line string representation of this Atom.-
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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setICode
public void setICode(String newICode)
Description copied from interface:IPDBMonomer
Sets the ICode of this monomer.- Specified by:
setICode
in interfaceIPDBMonomer
- Parameters:
newICode
- the I code of this monomer
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getICode
public String getICode()
Description copied from interface:IPDBMonomer
Gets the ICode of this monomer.- Specified by:
getICode
in interfaceIPDBMonomer
- Returns:
- the ICode of this monomer
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setChainID
public void setChainID(String newChainID)
Description copied from interface:IPDBMonomer
Sets the Chain ID of this monomer.- Specified by:
setChainID
in interfaceIPDBMonomer
- Parameters:
newChainID
- the Chain ID of this monomer
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getChainID
public String getChainID()
Description copied from interface:IPDBMonomer
Gets the Chain ID of this monomer.- Specified by:
getChainID
in interfaceIPDBMonomer
- Returns:
- the Chain ID of this monomer
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toString
public String toString()
Returns a one line string representation of this Atom. Methods is conform RFC #9.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classMonomer
- Returns:
- The string representation of this Atom
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getResSeq
public String getResSeq()
Description copied from interface:IPDBMonomer
Gets the sequence identifier of this monomer.- Specified by:
getResSeq
in interfaceIPDBMonomer
- Returns:
- the sequence identifier of this monomer
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clone
public IPDBMonomer 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
- Specified by:
clone
in interfaceIPDBMonomer
- Overrides:
clone
in classMonomer
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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setResSeq
public void setResSeq(String resSeq)
Description copied from interface:IPDBMonomer
Sets the sequence identifier of this monomer.- Specified by:
setResSeq
in interfaceIPDBMonomer
- Parameters:
resSeq
- the new sequence identifier of this monomer
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