Package org.openscience.cdk.interfaces
Interface IBioPolymer
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- All Superinterfaces:
Cloneable
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
,IPolymer
- All Known Subinterfaces:
IPDBPolymer
- All Known Implementing Classes:
BioPolymer
,BioPolymer
,DebugBioPolymer
,DebugPDBPolymer
,PDBPolymer
,PDBPolymer
public interface IBioPolymer extends IPolymer
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>
- Source code:
- main
- Belongs to CDK module:
- interfaces
- 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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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
addAtom(IAtom oAtom)
Adds the atom oAtom without specifying a Monomer or a Strand.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()
Returns a deep clone of this IChemObject.IMonomer
getMonomer(String monName, String strandName)
Retrieve aMonomer
object by specifying its name.int
getMonomerCount()
Return 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)
Retrieve a Monomer object by specifying its name.int
getStrandCount()
Return 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.-
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.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, 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.IPolymer
addAtom, getMonomer, removeMonomer
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Method Detail
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addAtom
void addAtom(IAtom oAtom)
Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the atom to this AtomContainer, but not to a certain Strand or Monomer (intended e.g. for HETATMs).- Specified by:
addAtom
in interfaceIAtomContainer
- Specified by:
addAtom
in interfaceIPolymer
- Parameters:
oAtom
- The atom to add
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addAtom
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.- Parameters:
oAtom
- The atom to addoStrand
- The strand the atom belongs to
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addAtom
void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.- Parameters:
oAtom
- The atom to addoMonomer
- The monomer the atom belongs tooStrand
- The strand the atom belongs to
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getMonomerCount
int getMonomerCount()
Return the number of monomers present in BioPolymer.- Specified by:
getMonomerCount
in interfaceIPolymer
- Returns:
- number of monomers
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getMonomer
IMonomer getMonomer(String monName, String strandName)
Retrieve aMonomer
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 "".
- 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
Collection<String> getMonomerNames()
Returns a collection of the names of allMonomer
s in this BioPolymer.- Specified by:
getMonomerNames
in interfaceIPolymer
- Returns:
- a
Collection
of all the monomer names.
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getStrandCount
int getStrandCount()
Return the number of strands present in the BioPolymer.- Returns:
- number of strands
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getStrand
IStrand getStrand(String cName)
Retrieve a Monomer object by specifying its name.- Parameters:
cName
- The name of the monomer to look for- Returns:
- The Monomer object which was asked for
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getStrandNames
Collection<String> getStrandNames()
Returns a collection of the names of allStrand
s in this BioPolymer.- Returns:
- a
Collection
of all the strand names.
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removeStrand
void removeStrand(String name)
Removes a particular strand, specified by its name.- Parameters:
name
- The name of the strand to remove
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getStrands
Map<String,IStrand> getStrands()
Returns a Map containing the strands in the Polymer.- Returns:
- hashtable containing the strands in the Polymer
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clone
IBioPolymer clone() throws CloneNotSupportedException
Returns a deep clone of this IChemObject.- Specified by:
clone
in interfaceIAtomContainer
- Specified by:
clone
in interfaceIChemObject
- Specified by:
clone
in interfaceIPolymer
- Returns:
- Object the clone of this IChemObject.
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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