Package org.openscience.cdk
Class BioPolymer
- 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.Polymer
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- org.openscience.cdk.BioPolymer
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomContainer
,IBioPolymer
,ICDKObject
,IChemObject
,IChemObjectListener
,IPolymer
- Direct Known Subclasses:
DebugBioPolymer
,PDBPolymer
public class BioPolymer extends Polymer implements Serializable, IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.- Author:
- Edgar Luttmann <edgar@uni-paderborn.de>, Martin Eklund
- See Also:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- data
- Keywords:
- polymer, biopolymer
- 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 BioPolymer()
Constructs a new Polymer to store the Strands.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.void
addAtom(IAtom oAtom, IStrand oStrand)
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.IBioPolymer
clone()
Clones thisIChemObject
.IMonomer
getMonomer(String monName, String strandName)
Retrieves a Monomer object by specifying its name.int
getMonomerCount()
Returns the number of monomers present in BioPolymer.Collection<String>
getMonomerNames()
Returns a collection of the names of allMonomer
s in this BioPolymer.IStrand
getStrand(String cName)
Retrieves a Monomer object by specifying its name.int
getStrandCount()
Returns the number of strands present in the BioPolymer.Collection<String>
getStrandNames()
Returns a collection of the names of allStrand
s in this BioPolymer.Map<String,IStrand>
getStrands()
Returns a Map containing the strands in the Polymer.void
removeStrand(String name)
Removes a particular strand, specified by its name.String
toString()
Returns a one line description of this IChemObject.-
Methods inherited from class org.openscience.cdk.Polymer
addAtom, getMonomer, removeMonomer
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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, 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.IBioPolymer
addAtom
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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.IPolymer
addAtom, getMonomer, removeMonomer
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Method Detail
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addAtom
public void addAtom(IAtom oAtom, IStrand oStrand)
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence the atom will be added to a Monomer of type UNKNOWN in the specified Strand.- Specified by:
addAtom
in interfaceIBioPolymer
- Parameters:
oAtom
- The atom to addoStrand
- The strand the atom belongs to
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addAtom
public void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.- Specified by:
addAtom
in interfaceIBioPolymer
- Parameters:
oAtom
-oMonomer
-oStrand
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getMonomerCount
public int getMonomerCount()
Returns the number of monomers present in BioPolymer.- Specified by:
getMonomerCount
in interfaceIBioPolymer
- Specified by:
getMonomerCount
in interfaceIPolymer
- Overrides:
getMonomerCount
in classPolymer
- Returns:
- number of monomers
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getMonomer
public IMonomer getMonomer(String monName, String strandName)
Retrieves a Monomer object by specifying its name. [You have to specify the strand to enable monomers with the same name in different strands. There is at least one such case: every strand contains a monomer called "".]- Specified by:
getMonomer
in interfaceIBioPolymer
- Parameters:
monName
- The name of the monomer to look forstrandName
- The name of the strand to look for- Returns:
- The Monomer object which was asked for
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getMonomerNames
public Collection<String> getMonomerNames()
Returns a collection of the names of allMonomer
s in this BioPolymer.- Specified by:
getMonomerNames
in interfaceIBioPolymer
- Specified by:
getMonomerNames
in interfaceIPolymer
- Overrides:
getMonomerNames
in classPolymer
- Returns:
- a
Collection
of all the monomer names.
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getStrandCount
public int getStrandCount()
Returns the number of strands present in the BioPolymer.- Specified by:
getStrandCount
in interfaceIBioPolymer
- Returns:
- number of strands
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getStrand
public IStrand getStrand(String cName)
Retrieves a Monomer object by specifying its name.- Specified by:
getStrand
in interfaceIBioPolymer
- Parameters:
cName
- The name of the monomer to look for- Returns:
- The Monomer object which was asked for
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getStrandNames
public Collection<String> getStrandNames()
Returns a collection of the names of allStrand
s in this BioPolymer.- Specified by:
getStrandNames
in interfaceIBioPolymer
- Returns:
- a
Collection
of all the strand names.
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removeStrand
public void removeStrand(String name)
Removes a particular strand, specified by its name.- Specified by:
removeStrand
in interfaceIBioPolymer
- Parameters:
name
- name of the strand to remove
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getStrands
public Map<String,IStrand> getStrands()
Description copied from interface:IBioPolymer
Returns a Map containing the strands in the Polymer.- Specified by:
getStrands
in interfaceIBioPolymer
- Returns:
- hashtable containing the monomers in the strand.
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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 classPolymer
- Returns:
- a String representation of this object
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clone
public IBioPolymer clone() throws CloneNotSupportedException
Description copied from class:AtomContainer
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 interfaceIBioPolymer
- Specified by:
clone
in interfaceIChemObject
- Specified by:
clone
in interfaceIPolymer
- Overrides:
clone
in classPolymer
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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