Field Detail

• DEFAULT_SERVERNAME

  public static final java.lang.String DEFAULT_SERVERNAME

  See Also:

  Constant Field Values

• NR_BIOL_APPEND

  public static final java.lang.String NR_BIOL_APPEND

  See Also:

  Constant Field Values

• BIO_ASSEMBLY

  public static final java.lang.String BIO_ASSEMBLY

  See Also:

  Constant Field Values

Constructor Detail

• RemoteBioUnitDataProvider

  public RemoteBioUnitDataProvider()

Method Detail

• getBioUnitTransformationList

  public java.util.List<BiologicalAssemblyTransformation> getBioUnitTransformationList​(java.lang.String pdbId,
                                                                                       int biolAssemblyNr)

  Description copied from interface: BioUnitDataProvider
  get the data for a particular assembly, counting starts at 1...

  Specified by:

  getBioUnitTransformationList in interface BioUnitDataProvider

  Parameters:

  pdbId - the PDB ID. E.g. 1STP

  biolAssemblyNr - the number of the assembly, the first one is nr 1. 0 refers to the asym unit

  Returns:

  list of transformations.

• getNrBiolAssemblies

  public int getNrBiolAssemblies​(java.lang.String pdbId)

  Description copied from interface: BioUnitDataProvider
  Returns the number of available biological assemblies.

  Specified by:

  getNrBiolAssemblies in interface BioUnitDataProvider

  Parameters:

  pdbId - the PDB ID. E.g. 1STP

  Returns:

  nr of available assemblies.

• hasBiolAssembly

  public boolean hasBiolAssembly​(java.lang.String pdbId)

  Description copied from interface: BioUnitDataProvider
  Does the PDB ID have biological assembly information?

  Specified by:

  hasBiolAssembly in interface BioUnitDataProvider

  Parameters:

  pdbId - the PDB ID. E.g. 1STP

  Returns:

  boolean flag

• getAsymUnit

  public Structure getAsymUnit​(java.lang.String pdbId)

  Description copied from interface: BioUnitDataProvider
  load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object

  Specified by:

  getAsymUnit in interface BioUnitDataProvider

  Returns:

• setAsymUnit

  public void setAsymUnit​(Structure s)

  Specified by:

  setAsymUnit in interface BioUnitDataProvider

• setAtomCache

  public void setAtomCache​(AtomCache cache)

  Description copied from interface: BioUnitDataProvider
  Set an AtomCache to use when fetching asymmetric units. If null, a new cache will be created with default parameters.

  Specified by:

  setAtomCache in interface BioUnitDataProvider

• getAtomCache

  public AtomCache getAtomCache()

  Specified by:

  getAtomCache in interface BioUnitDataProvider

  Returns:

  The current cache, or null if no cache has been initialized