Package org.biojava.nbio.structure.quaternary.io

Interface BioUnitDataProvider

All Known Implementing Classes:
MmCifBiolAssemblyProvider, PDBBioUnitDataProvider, RemoteBioUnitDataProvider
public interface BioUnitDataProvider
Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein. This is probably the simpler approach of accessing the necessary information. There is a second access layer, which is closer to the way the PDB is representing the files, it is defined by the interface RawBioUnitDataProvider.
Author:
Andreas Prlic

  • Method Details

    • getBioUnitTransformationList

      List<BiologicalAssemblyTransformation> getBioUnitTransformationList(String pdbId, int biolAssemblyNr)
      get the data for a particular assembly, counting starts at 1...
      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

      int getNrBiolAssemblies(String pdbId)
      Returns the number of available biological assemblies.
      Parameters:
      pdbId - the PDB ID. E.g. 1STP
      Returns:
      nr of available assemblies.

    • hasBiolAssembly

      boolean hasBiolAssembly(String pdbId)
      Does the PDB ID have biological assembly information?
      Parameters:
      pdbId - the PDB ID. E.g. 1STP
      Returns:
      boolean flag

    • getAsymUnit

      Structure getAsymUnit(String pdbId)
      load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object
      Parameters:
      pdbId -
      Returns:

    • setAsymUnit

      void setAsymUnit(Structure asymUnit)

    • setAtomCache

      void setAtomCache(AtomCache cache)
      Set an AtomCache to use when fetching asymmetric units. If null, a new cache will be created with default parameters.
      Parameters:
      cache -

    • getAtomCache

      AtomCache getAtomCache()
      Returns:
      The current cache, or null if no cache has been initialized