Package org.openscience.cdk

Class BioPolymer

java.lang.Object
org.openscience.cdk.ChemObject
org.openscience.cdk.AtomContainer
org.openscience.cdk.Polymer
org.openscience.cdk.BioPolymer
All Implemented Interfaces:
Serializable, Cloneable, IAtomContainer, IBioPolymer, ICDKObject, IChemObject, IChemObjectListener, IPolymer
Direct Known Subclasses:
PDBPolymer
public class BioPolymer extends Polymer implements Serializable, IBioPolymer
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 <[email protected]>, Martin Eklund
See Also:
Keywords:
polymer, biopolymer
Created on:
2001-08-06

  • Constructor Details

    • BioPolymer

      public BioPolymer()
      Constructs a new Polymer to store the Strands.

  • Method Details

    • addAtom

      public 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.
      Specified by:
      addAtom in interface IBioPolymer
      Parameters:
      oAtom - The atom to add
      oStrand - The strand the atom belongs to

    • addAtom

      public void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
      Adds the atom to a specified Strand and a specified Monomer.
      Specified by:
      addAtom in interface IBioPolymer
      Parameters:
      oAtom -
      oMonomer -
      oStrand -

    • getMonomerCount

      public int getMonomerCount()
      Returns the number of monomers present in BioPolymer.
      Specified by:
      getMonomerCount in interface IBioPolymer
      Specified by:
      getMonomerCount in interface IPolymer
      Overrides:
      getMonomerCount in class Polymer
      Returns:
      number of monomers

    • getMonomer

      public IMonomer getMonomer(String monName, String strandName)
      Retrieves 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 "".]
      Specified by:
      getMonomer in interface IBioPolymer
      Parameters:
      monName - The name of the monomer to look for
      Returns:
      The Monomer object which was asked for

    • getMonomerNames

      public Collection<String> getMonomerNames()
      Returns a collection of the names of all Monomers in this BioPolymer.
      Specified by:
      getMonomerNames in interface IBioPolymer
      Specified by:
      getMonomerNames in interface IPolymer
      Overrides:
      getMonomerNames in class Polymer
      Returns:
      a Collection of all the monomer names.

    • getStrandCount

      public int getStrandCount()
      Returns the number of strands present in the BioPolymer.
      Specified by:
      getStrandCount in interface IBioPolymer
      Returns:
      number of strands

    • getStrand

      public IStrand getStrand(String cName)
      Retrieves a Monomer object by specifying its name.
      Specified by:
      getStrand in interface IBioPolymer
      Parameters:
      cName - The name of the monomer to look for
      Returns:
      The Monomer object which was asked for

    • getStrandNames

      public Collection<String> getStrandNames()
      Returns a collection of the names of all Strands in this BioPolymer.
      Specified by:
      getStrandNames in interface IBioPolymer
      Returns:
      a Collection of all the strand names.

    • removeStrand

      public void removeStrand(String name)
      Removes a particular strand, specified by its name.
      Specified by:
      removeStrand in interface IBioPolymer
      Parameters:
      name - name of the strand to remove

    • getStrands

      public Map<String,IStrand> getStrands()
      Specified by:
      getStrands in interface IBioPolymer
      Returns:
      hashtable containing the monomers in the strand.

    • toString

      public String toString()
      Description copied from class: AtomContainer
      Specified by:
      toString in interface IChemObject
      Overrides:
      toString in class Polymer

    • clone

      public IBioPolymer clone() throws CloneNotSupportedException
      Description copied from class: AtomContainer
      Clones this IChemObject. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.
      Specified by:
      clone in interface IAtomContainer
      Specified by:
      clone in interface IBioPolymer
      Specified by:
      clone in interface IChemObject
      Specified by:
      clone in interface IPolymer
      Overrides:
      clone in class Polymer
      Returns:
      The cloned object
      Throws:
      CloneNotSupportedException