Class PDBBioUnitDataProvider

Method Details

• loadPDB

  public PDBHeader loadPDB(String pdbId)

• getAsymUnit

  public Structure getAsymUnit(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

• getBioUnitTransformationList

  public List<BiologicalAssemblyTransformation> getBioUnitTransformationList(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(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(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

• 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