Interface IStrand

All Superinterfaces:
Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener
All Known Implementing Classes:
DebugStrand, PDBStrand, Strand, Strand

public interface IStrand extends IAtomContainer
A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
Author:
Martin Eklund <martin.eklund@farmbio.uu.se>
Source code:
main
Belongs to CDK module:
interfaces
Created on:
2004-12-20
  • Method Details

    • getStrandName

      String getStrandName()
      Retrieve the strand name.
      Returns:
      The name of the Strand object
      See Also:
    • getStrandType

      String getStrandType()
      Retrieve the strand type.
      Returns:
      The type of the Strand object
      See Also:
    • setStrandName

      void setStrandName(String cStrandName)
      Set the name of the Strand object.
      Parameters:
      cStrandName - The new name for this strand
      See Also:
    • setStrandType

      void setStrandType(String cStrandType)
      Set the type of the Strand object.
      Parameters:
      cStrandType - The new type for this strand
      See Also:
    • addAtom

      void addAtom(IAtom oAtom)
      Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the atom gets added to a Monomer of type UNKNOWN in a Strand of type UNKNOWN.
      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 specific 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 Strand.
      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 remove
    • getMonomers

      Map<String,IMonomer> getMonomers()
      Returns the monomers in this strand.
      Returns:
      Map containing the monomers in the strand.
    • 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