Interface PDBInstallation

  • All Known Implementing Classes:
    FlatFileInstallation, MMCIFFileInstallation

    public interface PDBInstallation
    an interface that defines different access methods to PDB installations. Installations can be Flat file based ones, database ones, Installations that download all files from the net, etc.
    Author:
    Andreas Prlic
    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void addPDBFilter​(PDBFilter filter)
      add a filter for PDB files.
      void clearFilters()
      remove all filters, next time getAll is called, it will return all available PDBs
      java.util.List<PDBHeader> getAll()
      get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
      PDBHeader getPDBHeader​(java.lang.String pdbId)
      get the PDB header for a single protein structure
      Structure getStructure​(java.lang.String pdbId)
      request a structure by its PDB identifier
      boolean hasNext()
      return if the iteration over all structures will return another structure
      Structure next()
      iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
    • Method Detail

      • getAll

        java.util.List<PDBHeader> getAll()
        get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
        Returns:
        a list of PDBHeader objects
      • getPDBHeader

        PDBHeader getPDBHeader​(java.lang.String pdbId)
        get the PDB header for a single protein structure
        Parameters:
        pdbId -
        Returns:
        the PDB header object
      • addPDBFilter

        void addPDBFilter​(PDBFilter filter)
        add a filter for PDB files. THis can be used to request, e.g. all X-ray structures, or all structures with a given resolution, all proteins with a certain function, etc.
        Parameters:
        filter - the filter to apply when getAll is being called.
        See Also:
        getAll()
      • clearFilters

        void clearFilters()
        remove all filters, next time getAll is called, it will return all available PDBs
      • getStructure

        Structure getStructure​(java.lang.String pdbId)
        request a structure by its PDB identifier
        Parameters:
        pdbId -
        Returns:
        the structure for the pdbId
      • next

        Structure next()
        iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
        Returns:
        the next structure
      • hasNext

        boolean hasNext()
        return if the iteration over all structures will return another structure
        Returns:
        true if there is another structure that has not been iterated over yet