Interface IPDBPolymer

All Superinterfaces:
Cloneable, IAtomContainer, IBioPolymer, ICDKObject, IChemObject, IChemObjectListener, IPolymer
All Known Implementing Classes:
DebugPDBPolymer, PDBPolymer, PDBPolymer

public interface IPDBPolymer extends IBioPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.
Author:
Miguel Rojas <miguel.rojas@uni-koeln.de>
Source code:
main
Belongs to CDK module:
interfaces
Keywords:
polymer, biopolymer, pdbpolymer
Created on:
2006-11-20
  • Method Details

    • addAtom

      void addAtom(IPDBAtom 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).
      Parameters:
      oAtom - The atom to add
    • addAtom

      void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
      Adds the atom to a specified Strand and a specified Monomer.
      Parameters:
      oAtom - The atom to add
      oMonomer - The monomer the atom belongs to
      oStrand - The strand the atom belongs to
    • addStructure

      void addStructure(IPDBStructure structure)
      Adds the PDBStructure structure a this PDBPolymer.
      Parameters:
      structure - The PDBStructure to add
    • getStructures

      Collection<IPDBStructure> getStructures()
      Returns a Collection containing the PDBStructure in the PDBPolymer.
      Returns:
      Collection containing the PDBStructure in the PDBPolymer
    • clone

      Returns a deep clone of this IChemObject.
      Specified by:
      clone in interface IAtomContainer
      Specified by:
      clone in interface IBioPolymer
      Specified by:
      clone in interface IChemObject
      Specified by:
      clone in interface IPolymer
      Returns:
      Object the clone of this IChemObject.
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned