Package org.openscience.cdk.protein.data
Class PDBPolymer
- 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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- org.openscience.cdk.protein.data.PDBPolymer
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomContainer
,IBioPolymer
,ICDKObject
,IChemObject
,IChemObjectListener
,IPDBPolymer
,IPolymer
- Direct Known Subclasses:
DebugPDBPolymer
public class PDBPolymer extends BioPolymer implements Cloneable, IPDBPolymer
An entry in the PDB database. It is not just a regular protein, but the regular PDB mix of protein or protein complexes, ligands, water molecules and other species.- Author:
- Egon Willighagen
- See Also:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- data
- Keywords:
- polymer
- Created on:
- 2006-04-19
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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 PDBPolymer()
Constructs a new Polymer to store theIMonomer
s.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addAtom(IPDBAtom oAtom)
Adds the atom oAtom without specifying aIMonomer
or a Strand.void
addAtom(IPDBAtom oAtom, IMonomer oMonomer)
Adds the atom oAtom to a specified Monomer.void
addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.void
addStructure(IPDBStructure structure)
Adds the PDBStructure structure a this PDBPolymer.IPDBPolymer
clone()
Clones thisIChemObject
.Collection<String>
getMonomerNamesInSequentialOrder()
Returns the monomer names in the order in which they were added.Collection<IPDBStructure>
getStructures()
Returns a Collection containing the PDBStructure in the PDBPolymer.String
toString()
Returns a one line description of this IChemObject.-
Methods inherited from class org.openscience.cdk.BioPolymer
addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand
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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, addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand
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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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Constructor Detail
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PDBPolymer
public PDBPolymer()
Constructs a new Polymer to store theIMonomer
s.
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Method Detail
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addStructure
public void addStructure(IPDBStructure structure)
Description copied from interface:IPDBPolymer
Adds the PDBStructure structure a this PDBPolymer.- Specified by:
addStructure
in interfaceIPDBPolymer
- Parameters:
structure
- The PDBStructure to add
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getStructures
public Collection<IPDBStructure> getStructures()
Description copied from interface:IPDBPolymer
Returns a Collection containing the PDBStructure in the PDBPolymer.- Specified by:
getStructures
in interfaceIPDBPolymer
- Returns:
- Collection containing the PDBStructure in the PDBPolymer
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addAtom
public void addAtom(IPDBAtom oAtom)
Adds the atom oAtom without specifying aIMonomer
or a Strand. Therefore the atom to this AtomContainer, but not to a certain Strand orIMonomer
(intended e.g. for HETATMs).- Specified by:
addAtom
in interfaceIPDBPolymer
- Parameters:
oAtom
- TheIPDBAtom
to add
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addAtom
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer)
Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.- Parameters:
oAtom
- The IPDBAtom to addoMonomer
- The monomer the atom belongs to
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addAtom
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand. Additionally, it keeps record of the iCode.- Specified by:
addAtom
in interfaceIPDBPolymer
- Parameters:
oAtom
- The IPDBAtom to addoMonomer
- The monomer the atom belongs tooStrand
- The strand the atom belongs to
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getMonomerNamesInSequentialOrder
public Collection<String> getMonomerNamesInSequentialOrder()
Returns the monomer names in the order in which they were added.- See Also:
IPolymer.getMonomerNames()
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clone
public IPDBPolymer 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 interfaceIBioPolymer
- Specified by:
clone
in interfaceIChemObject
- Specified by:
clone
in interfaceIPDBPolymer
- Specified by:
clone
in interfaceIPolymer
- Overrides:
clone
in classBioPolymer
- 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 classBioPolymer
- Returns:
- a String representation of this object
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