Interface IPolymer

All Superinterfaces:
Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener
All Known Subinterfaces:
IBioPolymer, IPDBPolymer
All Known Implementing Classes:
BioPolymer, BioPolymer, DebugBioPolymer, DebugPDBPolymer, DebugPolymer, PDBPolymer, PDBPolymer, Polymer, Polymer

public interface IPolymer extends IAtomContainer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
Author:
Edgar Luttmann <edgar@uni-paderborn.de>, Martin Eklund <martin.eklund@farmbio.uu.se>
Source code:
main
Belongs to CDK module:
interfaces
Keywords:
polymer
Created on:
2001-08-06
  • Method Details

    • addAtom

      void addAtom(IAtom oAtom)
      Adds the atom oAtom without specifying a Monomer. Therefore the atom to this AtomContainer, but not to a certain Monomer (intended e.g. for HETATMs).
      Specified by:
      addAtom in interface IAtomContainer
      Parameters:
      oAtom - The atom to add
    • addAtom

      void addAtom(IAtom oAtom, IMonomer oMonomer)
      Adds the atom oAtom to a specified Monomer.
      Parameters:
      oAtom - The atom to add
      oMonomer - The monomer the atom belongs to
    • getMonomerCount

      int getMonomerCount()
      Return the number of monomers present in the Polymer.
      Returns:
      number of monomers
    • 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
    • getMonomerNames

      Collection<String> getMonomerNames()
      Returns a collection of the names of all Monomers in this polymer.
      Returns:
      a Collection of all the monomer names.
    • removeMonomer

      void removeMonomer(String name)
      Removes a particular monomer, specified by its name.
      Parameters:
      name - The name of the monomer to be removed
    • clone

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