org.simtk.molecularstructure
Class BiopolymerClass

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

All Implemented Interfaces:

MassBody, Biopolymer, Chemical, Molecular, Molecule

Direct Known Subclasses:

NucleicAcid, PDBProteinClass

public class BiopolymerClass
extends MoleculeClass
implements Biopolymer

Author:

Christopher Bruns \brief A macromolecular heteropolymer, such as protein or DNA

Field Summary

Fields inherited from class org.simtk.molecularstructure.MoleculeClass

chainId, displaySourceTypes

Constructor Summary

BiopolymerClass(char chainId)

Method Summary

protected void	addGenericResidueBond(java.lang.String atom1, java.lang.String atom2)
protected void	addGenericResidueBonds()
void	addSecondaryStructure(SecondaryStructure ss)
java.util.Set<SecondaryStructure>	displayableStructures()
Residue	getResidue(int i)
Residue	getResidueByNumber(int i)
Residue	getResidueByNumber(int i, char insertionCode)
Residue	getResidueByNumber(java.lang.String n)
java.util.List<Residue>	residues()
java.util.Set<SecondaryStructure>	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

BiopolymerClass

public BiopolymerClass(char chainId)

Method Detail

residues

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

Specified by:

residues in interface Biopolymer

getResidue

public Residue getResidue(int i)

Specified by:

getResidue in interface Biopolymer

getResidueByNumber

public Residue getResidueByNumber(int i)

Specified by:

getResidueByNumber in interface Biopolymer

getResidueByNumber

public Residue getResidueByNumber(int i,
                                  char insertionCode)

getResidueByNumber

public Residue getResidueByNumber(java.lang.String n)

addSecondaryStructure

public void addSecondaryStructure(SecondaryStructure ss)

secondaryStructures

public java.util.Set<SecondaryStructure> secondaryStructures()

Specified by:

secondaryStructures in interface Biopolymer

displayableStructures

public java.util.Set<SecondaryStructure> displayableStructures()

addGenericResidueBond

protected void addGenericResidueBond(java.lang.String atom1,
                                     java.lang.String atom2)

addGenericResidueBonds

protected void addGenericResidueBonds()