public class PDBPolymer extends BioPolymer implements Cloneable, IPDBPolymer
atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements
Constructor and Description |
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PDBPolymer()
Constructs a new Polymer to store the
IMonomer s. |
Modifier and Type | Method and Description |
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void |
addAtom(IPDBAtom oAtom)
Adds the atom oAtom without specifying a
IMonomer 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 this AtomContainer object and its content.
|
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 string representation of this Container.
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addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand
addAtom, getMonomer, removeMonomer
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, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, singleElectrons, stateChanged, stereoElements
addListener, addProperties, compare, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
addAtom, addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand
addAtom, getMonomer, removeMonomer
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, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, singleElectrons, stereoElements
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
getBuilder
stateChanged
public PDBPolymer()
IMonomer
s.public void addStructure(IPDBStructure structure)
IPDBPolymer
addStructure
in interface IPDBPolymer
structure
- The PDBStructure to addpublic Collection<IPDBStructure> getStructures()
IPDBPolymer
getStructures
in interface IPDBPolymer
public void addAtom(IPDBAtom oAtom)
IMonomer
or a Strand. Therefore the
atom to this AtomContainer, but not to a certain Strand or IMonomer
(intended
e.g. for HETATMs).addAtom
in interface IPDBPolymer
oAtom
- The IPDBAtom
to addpublic void addAtom(IPDBAtom oAtom, IMonomer oMonomer)
oAtom
- The IPDBAtom to addoMonomer
- The monomer the atom belongs topublic void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
addAtom
in interface IPDBPolymer
oAtom
- The IPDBAtom to addoMonomer
- The monomer the atom belongs tooStrand
- The strand the atom belongs topublic Collection<String> getMonomerNamesInSequentialOrder()
IPolymer.getMonomerNames()
public IPDBPolymer clone() throws CloneNotSupportedException
clone
in interface IAtomContainer
clone
in interface IBioPolymer
clone
in interface IChemObject
clone
in interface IPDBPolymer
clone
in interface IPolymer
clone
in class BioPolymer
CloneNotSupportedException
- if the IChemObject cannot be clonedChemObject.shallowCopy()
public String toString()
AtomContainer
toString
in interface IChemObject
toString
in class BioPolymer
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