org.simtk.molecularstructure
Class SecondaryStructureClass

java.lang.Object
  org.simtk.molecularstructure.SecondaryStructureClass

All Implemented Interfaces:

SecondaryStructure

Direct Known Subclasses:

BasePair, BaseStack, BaseTriple, BetaStrand, Duplex, Helix, Pseudoknot

public class SecondaryStructureClass
extends java.lang.Object
implements SecondaryStructure

Nested Class Summary

static class

SecondaryStructureClass.SourceType

Field Summary

protected java.util.Set<Biopolymer>	parentMolecules
protected java.util.Collection<Residue>	residues
protected int	resLimit
protected SecondaryStructureClass.SourceType	sourceType

Constructor Summary

SecondaryStructureClass()

SecondaryStructureClass(java.util.Collection<Residue> residues)

SecondaryStructureClass(java.util.Collection<Residue> residues, int resLimit)

SecondaryStructureClass(java.util.Collection<Residue> residues, int resLimit, java.lang.String source)

SecondaryStructureClass(int resLimit)

Method Summary

boolean	addMolecule(Biopolymer biopolymer)
void	addResidue(Residue residue)
java.util.Collection<Biopolymer>	getMolecules()
java.util.Iterator<Residue>	getResidueIterator()
SecondaryStructureClass.SourceType	getSource()
java.util.Collection<Residue>	residues()
void	setMolecule(Biopolymer biopolymer)
void	setSource(java.lang.String source)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

residues

protected java.util.Collection<Residue> residues

parentMolecules

protected java.util.Set<Biopolymer> parentMolecules

sourceType

protected SecondaryStructureClass.SourceType sourceType

resLimit

protected int resLimit

Constructor Detail

SecondaryStructureClass

public SecondaryStructureClass()

SecondaryStructureClass

public SecondaryStructureClass(int resLimit)

SecondaryStructureClass

public SecondaryStructureClass(java.util.Collection<Residue> residues)

SecondaryStructureClass

public SecondaryStructureClass(java.util.Collection<Residue> residues,
                               int resLimit)

SecondaryStructureClass

public SecondaryStructureClass(java.util.Collection<Residue> residues,
                               int resLimit,
                               java.lang.String source)

Method Detail

getResidueIterator

public java.util.Iterator<Residue> getResidueIterator()

Specified by:

getResidueIterator in interface SecondaryStructure

residues

public java.util.Collection<Residue> residues()

Specified by:

residues in interface SecondaryStructure

addResidue

public void addResidue(Residue residue)

Specified by:

addResidue in interface SecondaryStructure

setMolecule

public void setMolecule(Biopolymer biopolymer)

Specified by:

setMolecule in interface SecondaryStructure

getMolecules

public java.util.Collection<Biopolymer> getMolecules()

Specified by:

getMolecules in interface SecondaryStructure

addMolecule

public boolean addMolecule(Biopolymer biopolymer)

Specified by:

addMolecule in interface SecondaryStructure

getSource

public SecondaryStructureClass.SourceType getSource()

Specified by:

getSource in interface SecondaryStructure

setSource

public void setSource(java.lang.String source)

Specified by:

setSource in interface SecondaryStructure