Package org.openscience.cdk.protein.data

Class PDBPolymer

java.lang.Object
org.openscience.cdk.ChemObject
org.openscience.cdk.AtomContainer
org.openscience.cdk.Polymer
org.openscience.cdk.BioPolymer
org.openscience.cdk.protein.data.PDBPolymer
All Implemented Interfaces:
Serializable, Cloneable, IAtomContainer, IBioPolymer, ICDKObject, IChemObject, IChemObjectListener, IPDBPolymer, IPolymer
Direct Known Subclasses:
DebugPDBPolymer
public class PDBPolymer extends BioPolymer implements Cloneable, IPDBPolymer
An entry in the PDB database. It is not just a regular protein, but the regular PDB mix of protein or protein complexes, ligands, water molecules and other species.
Author:
Egon Willighagen
See Also:
Keywords:
polymer
Created on:
2006-04-19

  • Constructor Details

    • PDBPolymer

      public PDBPolymer()
      Constructs a new Polymer to store the IMonomers.

  • Method Details

    • addStructure

      public void addStructure(IPDBStructure structure)
      Description copied from interface: IPDBPolymer
      Adds the PDBStructure structure a this PDBPolymer.
      Specified by:
      addStructure in interface IPDBPolymer
      Parameters:
      structure - The PDBStructure to add

    • getStructures

      public Collection<IPDBStructure> getStructures()
      Description copied from interface: IPDBPolymer
      Returns a Collection containing the PDBStructure in the PDBPolymer.
      Specified by:
      getStructures in interface IPDBPolymer
      Returns:
      Collection containing the PDBStructure in the PDBPolymer

    • addAtom

      public void addAtom(IPDBAtom oAtom)
      Adds the atom oAtom without specifying a IMonomer or a Strand. Therefore the atom to this AtomContainer, but not to a certain Strand or IMonomer (intended e.g. for HETATMs).
      Specified by:
      addAtom in interface IPDBPolymer
      Parameters:
      oAtom - The IPDBAtom to add

    • addAtom

      public void addAtom(IPDBAtom oAtom, IMonomer oMonomer)
      Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.
      Parameters:
      oAtom - The IPDBAtom to add
      oMonomer - The monomer the atom belongs to

    • addAtom

      public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
      Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand. Additionally, it keeps record of the iCode.
      Specified by:
      addAtom in interface IPDBPolymer
      Parameters:
      oAtom - The IPDBAtom to add
      oMonomer - The monomer the atom belongs to
      oStrand - The strand the atom belongs to

    • getMonomerNamesInSequentialOrder

      public Collection<String> getMonomerNamesInSequentialOrder()
      Returns the monomer names in the order in which they were added.
      See Also:

    • clone

      public IPDBPolymer clone() throws CloneNotSupportedException
      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 IPDBPolymer
      Specified by:
      clone in interface IPolymer
      Overrides:
      clone in class BioPolymer
      Returns:
      The cloned object
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned

    • toString

      public String toString()
      Description copied from class: AtomContainer
      Returns a one line description of this IChemObject.
      Specified by:
      toString in interface IChemObject
      Overrides:
      toString in class BioPolymer
      Returns:
      a String representation of this object