Interface IBioPolymer

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

public interface IBioPolymer extends IPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
Author:
Edgar Luttmann <edgar@uni-paderborn.de>
Source code:
main
Belongs to CDK module:
interfaces
Keywords:
polymer, biopolymer
Created on:
2001-08-06
  • Method Details

    • addAtom

      void addAtom(IAtom 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).
      Specified by:
      addAtom in interface IAtomContainer
      Specified by:
      addAtom in interface IPolymer
      Parameters:
      oAtom - The atom to add
    • addAtom

      void addAtom(IAtom oAtom, IStrand oStrand)
      Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence the atom will be added to a Monomer of type UNKNOWN in the specified Strand.
      Parameters:
      oAtom - The atom to add
      oStrand - The strand the atom belongs to
    • addAtom

      void addAtom(IAtom 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
    • getMonomerCount

      int getMonomerCount()
      Return the number of monomers present in BioPolymer.
      Specified by:
      getMonomerCount in interface IPolymer
      Returns:
      number of monomers
    • getMonomer

      IMonomer getMonomer(String monName, String strandName)
      Retrieve a Monomer object by specifying its name.

      You have to specify the strand to enable monomers with the same name in different strands. There is at least one such case: every strand contains a monomer called "".

      Parameters:
      monName - The name of the monomer to look for
      strandName - The name of the strand 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 BioPolymer.
      Specified by:
      getMonomerNames in interface IPolymer
      Returns:
      a Collection of all the monomer names.
    • getStrandCount

      int getStrandCount()
      Return the number of strands present in the BioPolymer.
      Returns:
      number of strands
    • getStrand

      IStrand getStrand(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
    • getStrandNames

      Collection<String> getStrandNames()
      Returns a collection of the names of all Strands in this BioPolymer.
      Returns:
      a Collection of all the strand names.
    • removeStrand

      void removeStrand(String name)
      Removes a particular strand, specified by its name.
      Parameters:
      name - The name of the strand to remove
    • getStrands

      Map<String,IStrand> getStrands()
      Returns a Map containing the strands in the Polymer.
      Returns:
      hashtable containing the strands in the Polymer
    • clone

      Returns a deep clone of this IChemObject.
      Specified by:
      clone in interface IAtomContainer
      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