Package org.biojava.bio.structure.server

Class FlatFileInstallation

  • All Implemented Interfaces:
    PDBInstallation
    public class FlatFileInstallation
extends java.lang.Object
implements PDBInstallation
    a PDB installation that reads all files from one directory in the file system. and keeps several files with the information parsed from the PDB headers for easier data access.
    In particular these files are:
    • pdbinfo.txt - contains resolution, experimetnal technique, deposition and modification date, biological description of the structure
    • chaininfo.txt - contains information about every chain, like the compound information from the header, the nr of amino acids in chain, The alignment to the SEQRES residues
    In order to create these index files for this PDB installation, please see the PrepareIndexFile class.
    Author:
    Andreas Prlic
    See Also:
    PrepareIndexFile

    • Constructor Summary

      Constructors 
      Constructor Description
      FlatFileInstallation​(java.io.File filePath)
      create a new FlatFile Installation and point it to the directory that contains all PDB files

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addPDBFilter​(PDBFilter filter)
      add a filter for PDB files.
      void applyFilters()  
      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
      java.io.File getChainInfoFile()  
      java.io.File getFilePath()  
      PDBHeader getPDBHeader​(java.lang.String pdbId)
      get the PDB header for a single protein structure
      java.io.File getPDBInfoFile()  
      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.
      void setChainInfoFile​(java.io.File chainInfoFile)  
      void setFilePath​(java.io.File filePath)  
      void setPDBInfoFile​(java.io.File indexFile)  

      • 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

      • DEFAULT_INDEX_FILE

        public static final java.lang.String DEFAULT_INDEX_FILE
        See Also:
        Constant Field Values

      • DEFAUL_CHAIN_FILE

        public static final java.lang.String DEFAUL_CHAIN_FILE
        See Also:
        Constant Field Values

      • dateFormat

        public static java.text.SimpleDateFormat dateFormat

    • Constructor Detail

      • FlatFileInstallation

        public FlatFileInstallation​(java.io.File filePath)
        create a new FlatFile Installation and point it to the directory that contains all PDB files
        Parameters:
        filePath -

    • Method Detail

      • getPDBInfoFile

        public java.io.File getPDBInfoFile()

      • setPDBInfoFile

        public void setPDBInfoFile​(java.io.File indexFile)

      • getChainInfoFile

        public java.io.File getChainInfoFile()

      • setChainInfoFile

        public void setChainInfoFile​(java.io.File chainInfoFile)

      • getFilePath

        public java.io.File getFilePath()

      • setFilePath

        public void setFilePath​(java.io.File filePath)

      • 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

      • applyFilters

        public void applyFilters()

      • 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