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

Interface RawBioUnitDataProvider

  • All Known Implementing Classes:
    MmCifPDBBiolAssemblyProvider, RemoteRawBioUnitDataProvider
    public interface RawBioUnitDataProvider
    Defines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein. This is very close to the way PDB is representing biological assemblies. For the outside it is probably easier to use the other way of accessing the data as defined in BioUnitDataProvider
    Since:
    3.0.5
    Author:
    Andreas Prlic

    • Method Detail

      • setPdbId

        void setPdbId​(java.lang.String pdbId)
        Tell the provider for which PDB ID the quaternary structure should be returned.
        Parameters:
        pdbId -

      • getPdbxStructAssemblies

        java.util.List<PdbxStructAssembly> getPdbxStructAssemblies()
        Data access method for list describing all assemblies
        Returns:

      • getPdbxStructAssemblyGens

        java.util.List<PdbxStructAssemblyGen> getPdbxStructAssemblyGens()
        Data access method for list describing all assemblies
        Returns:

      • getPdbxStructOperList

        java.util.List<PdbxStructOperList> getPdbxStructOperList()
        Get all the possible operators
        Returns:

      • getNrBiolAssemblies

        int getNrBiolAssemblies()
        Returns the number of available biological assemblies.
        Returns:

      • hasBiolAssembly

        boolean hasBiolAssembly()
        Does the PDB ID have biological assembly information?
        Returns:
        boolean flag

      • getPdbxStructAssembly

        PdbxStructAssembly getPdbxStructAssembly​(int biolAssemblyNr)
        get the data for a particular pdbxStructAssembly. We start counting at 0.
        Parameters:
        biolAssemblyNr -
        Returns:

      • getPdbxStructAssemblyGen

        java.util.List<PdbxStructAssemblyGen> getPdbxStructAssemblyGen​(int biolAssemblyNr)
        get the data for a particular pdbxStructAssemblyGen. We start counting at 0.
        Parameters:
        biolAssemblyNr -
        Returns: