org.simtk.molecularstructure.nucleicacid
Class NucleicAcid

java.lang.Object
  org.simtk.molecularstructure.MolecularClass
      org.simtk.molecularstructure.MoleculeClass
          org.simtk.molecularstructure.BiopolymerClass
              org.simtk.molecularstructure.nucleicacid.NucleicAcid

All Implemented Interfaces:

MassBody, Biopolymer, Chemical, Molecular, Molecule

Direct Known Subclasses:

DNA, RNA

public class NucleicAcid
extends BiopolymerClass

Field Summary

Fields inherited from class org.simtk.molecularstructure.MoleculeClass

chainId, displaySourceTypes

Constructor Summary

NucleicAcid(char chainId)

Method Summary

protected void	addGenericResidueBonds()
java.util.Collection	computeBaseHydrogenBonds()
java.util.Collection<BasePair>	identifyBasePairs()
java.util.Collection<Duplex>	identifyHairpins()

Methods inherited from class org.simtk.molecularstructure.BiopolymerClass

addGenericResidueBond, addSecondaryStructure, displayableStructures, getResidue, getResidueByNumber, getResidueByNumber, getResidueByNumber, residues, secondaryStructures

Methods inherited from class org.simtk.molecularstructure.MoleculeClass

createFactoryPDBMolecule, createFactoryPDBMolecule, createFactoryPDBMolecule, getDisplaySourceTypes, getPdbChainId, isSolvent, setDisplaySourceTypes, setPdbChainId

Methods inherited from class org.simtk.molecularstructure.MolecularClass

atoms, bestPlane3D, getCenterOfMass, getMass

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.simtk.molecularstructure.Molecule

getDisplaySourceTypes, getPdbChainId, isSolvent, setDisplaySourceTypes

Methods inherited from interface org.simtk.molecularstructure.Molecular

atoms, bestPlane3D

Methods inherited from interface org.simtk.geometry3d.MassBody

getCenterOfMass, getMass

Constructor Detail

NucleicAcid

public NucleicAcid(char chainId)

Method Detail

addGenericResidueBonds

protected void addGenericResidueBonds()

Overrides:

addGenericResidueBonds in class BiopolymerClass

identifyBasePairs

public java.util.Collection<BasePair> identifyBasePairs()

identifyHairpins

public java.util.Collection<Duplex> identifyHairpins()

Returns:

a new created collection of Duplex objects computed from the structure

computeBaseHydrogenBonds

public java.util.Collection computeBaseHydrogenBonds()