Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Structure::IO - Handler for Structure Formats


           use Bio::Structure::IO;

           $in  = Bio::Structure::IO->new(-file => "inputfilename",
                                          -format => 'pdb');

           while ( my $struc = $in->next_structure() ) {
              print "Structure ", $struc->id, " number of models: ",
                    scalar $struc->model,"\n";


       Bio::Structure::IO is a handler module for the formats in the Structure::IO set (e.g.
       Bio::Structure::IO::pdb). It is the officially sanctioned way of getting at the format
       objects, which most people should use.

       The Bio::Structure::IO system can be thought of like biological file handles.  They are
       attached to filehandles with smart formatting rules (e.g. PDB format) and can either read
       or write structure objects (Bio::Structure objects, or more correctly,
       Bio::Structure::StructureI implementing objects, of which Bio::Structure is one such
       object). If you want to know what to do with a Bio::Structure object, read Bio::Structure.

       The idea is that you request a stream object for a particular format.  All the stream
       objects have a notion of an internal file that is read from or written to. A particular
       Structure::IO object instance is configured for either input or output. A specific example
       of a stream object is the Bio::Structure::IO::pdb object.

       Each stream object has functions





          $stream->type() # returns 'INPUT' or 'OUTPUT'

       As an added bonus, you can recover a filehandle that is tied to the Structure::IOIO
       object, allowing you to use the standard <> and print operations to read and write
       structure::IOuence objects:

           use Bio::Structure::IO;

           $stream = Bio::Structure::IO->newFh(-format => 'pdb'); # read from standard input

           while ( $structure = <$stream> ) {
               # do something with $structure


           print $stream $structure; # when stream is in output mode


          $stream = Bio::Structure::IO->new(-file => 'filename',   -format=>$format);
          $stream = Bio::Structure::IO->new(-fh   => \*FILEHANDLE, -format=>$format);
          $stream = Bio::Structure::IO->new(-format => $format);

       The new() class method constructs a new Bio::Structure::IO object. The returned object can
       be used to retrieve or print Bio::Structure objects.  new() accepts the following

           A file path to be opened for reading or writing.  The usual Perl conventions apply:

              'file'       # open file for reading
              '>file'      # open file for writing
              '>>file'     # open file for appending
              '+<file'     # open file read/write
              'command |'  # open a pipe from the command
              '| command'  # open a pipe to the command

       -fh You may provide new() with a previously-opened filehandle.  For example, to read from

              $strucIO = Bio::Structure::IO->new(-fh => \*STDIN);

           Note that you must pass filehandles as references to globs.

           If neither a filehandle nor a filename is specified, then the module will read from
           the @ARGV array or STDIN, using the familiar <> semantics.

           Specify the format of the file.  Supported formats include:

              pdb         Protein Data Bank format

           If no format is specified and a filename is given, then the module will attempt to
           deduce it from the filename.  If this is unsuccessful, PDB format is assumed.

           The format name is case insensitive.  'PDB', 'Pdb' and 'pdb' are all supported.

          $fh = Bio::Structure::IO->newFh(-fh   => \*FILEHANDLE, -format=>$format);
          $fh = Bio::Structure::IO->newFh(-format => $format);
          # etc.

       This constructor behaves like new(), but returns a tied filehandle rather than a
       Bio::Structure::IO object.  You can read structures from this object using the familiar <>
       operator, and write to it using print().  The usual array and $_ semantics work.  For
       example, you can read all structure objects into an array like this:

         @structures = <$fh>;

       Other operations, such as read(), sysread(), write(), close(), and printf() are not


       See below for more detailed summaries.  The main methods are:

   $structure = $structIO->next_structure()
       Fetch the next structure from the stream.

   $structIO->write_structure($struc [,$another_struc,...])
       Write the specified structure(s) to the stream.

       These provide the tie interface.  See perltie for more details.


   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

AUTHORS - Ewan Birney, Lincoln Stein, Kris Boulez



       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : $stream = Bio::Structure::IO->new(-file => $filename, -format => 'Format')
        Function: Returns a new structIOstream
        Returns : A Bio::Structure::IO handler initialised with the appropriate format
        Args    : -file => $filename
                  -format => format
                  -fh => filehandle to attach to

        Title   : newFh
        Usage   : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format')
        Function: does a new() followed by an fh()
        Example : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format')
                  $structure = <$fh>;   # read a structure object
                  print $fh $structure; # write a structure object
        Returns : filehandle tied to the Bio::Structure::IO::Fh class
        Args    :

        Title   : fh
        Usage   : $obj->fh
        Example : $fh = $obj->fh;      # make a tied filehandle
                  $structure = <$fh>;   # read a structure object
                  print $fh $structure; # write a structure object
        Returns : filehandle tied to the Bio::Structure::IO::Fh class
        Args    :

        Title   : format
        Usage   : $format = $obj->format()
        Function: Get the structure format
        Returns : structure format
        Args    : none

        Title   : next_structure
        Usage   : $structure = stream->next_structure
        Function: Reads the next structure object from the stream and returns a
                  Bio::Structure::Entry object.

                  Certain driver modules may encounter entries in the stream that
                  are either misformatted or that use syntax not yet understood
                  by the driver. If such an incident is recoverable, e.g., by
                  dismissing a feature of a feature table or some other non-mandatory
                  part of an entry, the driver will issue a warning. In the case
                  of a non-recoverable situation an exception will be thrown.
                  Do not assume that you can resume parsing the same stream after
                  catching the exception. Note that you can always turn recoverable
                  errors into exceptions by calling $stream->verbose(2) (see
                  Bio::RootI POD page).
        Returns : a Bio::Structure::Entry object
        Args    : none

        Title   : write_structure
        Usage   : $stream->write_structure($structure)
        Function: writes the $structure object into the stream
        Returns : 1 for success and 0 for error
        Args    : Bio::Structure object

        Title   : _load_format_module
        Usage   : *INTERNAL Structure::IO stuff*
        Function: Loads up (like use) a module at run time on demand
        Example :
        Returns :
        Args    :

        Title   : _concatenate_lines
        Usage   : $s = _concatenate_lines($line, $continuation_line)
        Function: Private. Concatenates two strings assuming that the second stems
                  from a continuation line of the first. Adds a space between both
                  unless the first ends with a dash.

                  Takes care of either arg being empty.
        Example :
        Returns : A string.
        Args    :

        Title   : _filehandle
        Usage   : $obj->_filehandle($newval)
        Function: This method is deprecated. Call _fh() instead.
        Example :
        Returns : value of _filehandle
        Args    : newvalue (optional)

        Title   : _guess_format
        Usage   : $obj->_guess_format($filename)
        Example :
        Returns : guessed format of filename (lower case)
        Args    :