Package org.openscience.cdk.interfaces
Interface IStrand
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- All Superinterfaces:
Cloneable
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
- All Known Implementing Classes:
DebugStrand
,PDBStrand
,Strand
,Strand
public interface IStrand extends IAtomContainer
A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.- Author:
- Martin Eklund <martin.eklund@farmbio.uu.se>
- Source code:
- main
- Belongs to CDK module:
- interfaces
- Created on:
- 2004-12-20
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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)
Adds the atom oAtom to a specific Monomer.IStrand
clone()
Returns a deep clone of this IChemObject.IMonomer
getMonomer(String cName)
Retrieve a Monomer object by specifying its name.int
getMonomerCount()
Return the number of monomers present in the Strand.Collection<String>
getMonomerNames()
Returns a collection of the names of allMonomer
s in this polymer.Map<String,IMonomer>
getMonomers()
Returns the monomers in this strand.String
getStrandName()
Retrieve the strand name.String
getStrandType()
Retrieve the strand type.void
removeMonomer(String name)
Removes a particular monomer, specified by its name.void
setStrandName(String cStrandName)
Set the name of the Strand object.void
setStrandType(String cStrandType)
Set the type of the Strand object.-
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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Method Detail
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getStrandName
String getStrandName()
Retrieve the strand name.- Returns:
- The name of the Strand object
- See Also:
setStrandName(String)
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getStrandType
String getStrandType()
Retrieve the strand type.- Returns:
- The type of the Strand object
- See Also:
setStrandType(String)
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setStrandName
void setStrandName(String cStrandName)
Set the name of the Strand object.- Parameters:
cStrandName
- The new name for this strand- See Also:
getStrandName()
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setStrandType
void setStrandType(String cStrandType)
Set the type of the Strand object.- Parameters:
cStrandType
- The new type for this strand- See Also:
getStrandType()
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addAtom
void addAtom(IAtom oAtom)
Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the atom gets added to a Monomer of type UNKNOWN in a Strand of type UNKNOWN.- Specified by:
addAtom
in interfaceIAtomContainer
- Parameters:
oAtom
- The atom to add
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addAtom
void addAtom(IAtom oAtom, IMonomer oMonomer)
Adds the atom oAtom to a specific Monomer.- Parameters:
oAtom
- The atom to addoMonomer
- The monomer the atom belongs to
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getMonomerCount
int getMonomerCount()
Return the number of monomers present in the Strand.- Returns:
- number of monomers
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getMonomer
IMonomer getMonomer(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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getMonomerNames
Collection<String> getMonomerNames()
Returns a collection of the names of allMonomer
s in this polymer.- Returns:
- a
Collection
of all the monomer names.
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removeMonomer
void removeMonomer(String name)
Removes a particular monomer, specified by its name.- Parameters:
name
- The name of the monomer to remove
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getMonomers
Map<String,IMonomer> getMonomers()
Returns the monomers in this strand.- Returns:
- Map containing the monomers in the strand.
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clone
IStrand clone() throws CloneNotSupportedException
Returns a deep clone of this IChemObject.- Specified by:
clone
in interfaceIAtomContainer
- Specified by:
clone
in interfaceIChemObject
- Returns:
- Object the clone of this IChemObject.
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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