Class PDBFileReader

    • Field Detail

      • PDB_SPLIT_DIR

        public static final java.lang.String[] PDB_SPLIT_DIR
      • PDB_OBSOLETE_DIR

        public static final java.lang.String[] PDB_OBSOLETE_DIR
    • Constructor Detail

      • PDBFileReader

        public PDBFileReader()
        Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized in the same way as UserConfiguration, i.e. to system property/environment variable UserConfiguration.PDB_DIR. Both autoFetch and splitDir are initialized to false
      • PDBFileReader

        public PDBFileReader​(java.lang.String path)
        Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized to the given path, both autoFetch and splitDir are initialized to false.

        If path is null, initialize using the system property/environment variable UserConfiguration.PDB_DIR.

        Parameters:
        path - Path to the PDB file directory
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
      • downloadPDB

        @Deprecated
        public void downloadPDB​(java.lang.String pdbId)
                         throws java.io.IOException
        Deprecated.
        Throws:
        java.io.IOException
      • setFetchFileEvenIfObsolete

        @Deprecated
        public void setFetchFileEvenIfObsolete​(boolean fetchFileEvenIfObsolete)
        Deprecated.
        Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
        N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
        Parameters:
        fetchFileEvenIfObsolete - the fetchFileEvenIfObsolete to set
      • isFetchFileEvenIfObsolete

        @Deprecated
        public boolean isFetchFileEvenIfObsolete()
        Deprecated.
        Use FileParsingParameters#getObsoleteBehavior()
        forces the reader to fetch the file if its status is OBSOLETE. This feature has a higher priority than setFetchCurrent(boolean).
        N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
        Returns:
        the fetchFileEvenIfObsolete
        Since:
        3.0.2
        See Also:
        #fetchCurrent
      • setFetchCurrent

        @Deprecated
        public void setFetchCurrent​(boolean fetchNewestCurrent)
        Deprecated.
        Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
        if enabled, the reader searches for the newest possible PDB ID, if not present in he local installation. The setFetchFileEvenIfObsolete(boolean) function has a higher priority than this function.
        N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
        Parameters:
        fetchCurrent - the fetchCurrent to set
        Since:
        3.0.2
        See Also:
        setFetchFileEvenIfObsolete(boolean)
      • isFetchCurrent

        @Deprecated
        public boolean isFetchCurrent()
        Deprecated.
        Use FileParsingParameters#getObsoleteBehavior()
        N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
        Returns:
        the fetchCurrent
      • getFilename

        protected java.lang.String getFilename​(java.lang.String pdbId)
        Description copied from class: LocalPDBDirectory
        Converts a PDB ID into a filename with the proper extension
        Specified by:
        getFilename in class LocalPDBDirectory
        Returns:
        The filename, e.g. "4hhb.pdb.gz"
      • getStructure

        public Structure getStructure​(java.io.InputStream inStream)
                               throws java.io.IOException
        Description copied from class: LocalPDBDirectory
        Handles the actual parsing of the file into a Structure object.
        Specified by:
        getStructure in class LocalPDBDirectory
        Returns:
        Throws:
        java.io.IOException
      • getSplitDirPath

        protected java.lang.String[] getSplitDirPath()
        Description copied from class: LocalPDBDirectory
        Location of split files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.
        Specified by:
        getSplitDirPath in class LocalPDBDirectory
        Returns:
        A list of directories, relative to the /pub/pdb directory on the server
      • getObsoleteDirPath

        protected java.lang.String[] getObsoleteDirPath()
        Description copied from class: LocalPDBDirectory
        Location of obsolete files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.
        Specified by:
        getObsoleteDirPath in class LocalPDBDirectory
        Returns:
        A list of directories, relative to the /pub/pdb directory on the server