Package org.biojava.bio.structure.server

Class MMCIFFileInstallation

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.util.logging.Logger logger  

    • Constructor Summary

      Constructors 
      Constructor Description
      MMCIFFileInstallation​(java.io.File filePath)  

    • Method Summary

      All Methods Instance Methods Concrete 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.io.File downloadCIF​(java.lang.String pdbId)  
      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
      boolean isAutoFetch()
      should the parser to fetch missing mmCif files from the RCSB FTP server automatically? default is false
      Structure next()
      iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
      void setAutoFetch​(boolean autoFetch)
      tell the parser to fetch missing mmCif files from the RCSB FTP server automatically.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • logger

        public static final java.util.logging.Logger logger

    • Constructor Detail

      • MMCIFFileInstallation

        public MMCIFFileInstallation​(java.io.File filePath)

    • Method Detail

      • isAutoFetch

        public boolean isAutoFetch()
        should the parser to fetch missing mmCif files from the RCSB FTP server automatically? default is false
        Returns:
        flag

      • setAutoFetch

        public void setAutoFetch​(boolean autoFetch)
        tell the parser to fetch missing mmCif files from the RCSB FTP server automatically. default is false. If true, new PDB files will be automatically stored in the Path and gzip compressed.
        Parameters:
        autoFetch -

      • downloadCIF

        public java.io.File downloadCIF​(java.lang.String pdbId)

      • addPDBFilter

        public void addPDBFilter​(PDBFilter filter)
        Description copied from interface: PDBInstallation
        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.
        Specified by:
        addPDBFilter in interface PDBInstallation
        Parameters:
        filter - the filter to apply when getAll is being called.
        See Also:
        PDBInstallation.getAll()

      • clearFilters

        public void clearFilters()
        Description copied from interface: PDBInstallation
        remove all filters, next time getAll is called, it will return all available PDBs
        Specified by:
        clearFilters in interface PDBInstallation

      • getAll

        public java.util.List<PDBHeader> getAll()
        Description copied from interface: PDBInstallation
        get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
        Specified by:
        getAll in interface PDBInstallation
        Returns:
        a list of PDBHeader objects

      • getPDBHeader

        public PDBHeader getPDBHeader​(java.lang.String pdbId)
        Description copied from interface: PDBInstallation
        get the PDB header for a single protein structure
        Specified by:
        getPDBHeader in interface PDBInstallation
        Returns:
        the PDB header object

      • getStructure

        public Structure getStructure​(java.lang.String pdbId)
        Description copied from interface: PDBInstallation
        request a structure by its PDB identifier
        Specified by:
        getStructure in interface PDBInstallation
        Returns:
        the structure for the pdbId

      • hasNext

        public boolean hasNext()
        Description copied from interface: PDBInstallation
        return if the iteration over all structures will return another structure
        Specified by:
        hasNext in interface PDBInstallation
        Returns:
        true if there is another structure that has not been iterated over yet

      • next

        public Structure next()
        Description copied from interface: PDBInstallation
        iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
        Specified by:
        next in interface PDBInstallation
        Returns:
        the next structure