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 Detail

      • getBioUnitTransformationList

        java.util.List<BiologicalAssemblyTransformation> getBioUnitTransformationList​(java.lang.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​(java.lang.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​(java.lang.String pdbId)
        Does the PDB ID have biological assembly information?
        Parameters:
        pdbId - the PDB ID. E.g. 1STP
        Returns:
        boolean flag

      • getAsymUnit

        Structure getAsymUnit​(java.lang.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