Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::Structure::IO::pdb - PDB input/output stream


       It is probably best not to use this object directly, but rather go through the
       Bio::Structure::IO handler system. Go:

           $stream = Bio::Structure::IO->new(-file => $filename,
                                             -format => 'PDB');

           while (my $structure = $stream->next_structure) {
                   # do something with $structure


       This object can transform Bio::Structure objects to and from PDB flat file databases. The
       working is similar to that of the Bio::SeqIO handlers.


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AUTHOR - Kris Boulez



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

        Title   : next_structure
        Usage   : $struc = $stream->next_structure()
        Function: returns the next structure in the stream
        Returns : Bio::Structure object
        Args    :

        Title   : write_structure
        Usage   : $stream->write_structure($struc)
        Function: writes the $struc object (must be a Bio::Structure) to the stream
        Returns : 1 for success and 0 for error
        Args    : Bio::Structure object

        Title   : _filehandle
        Usage   : $obj->_filehandle($newval)
        Example :
        Returns : value of _filehandle
        Args    : newvalue (optional)

        Title   : _noatom
        Usage   : $obj->_noatom($newval)
        Example :
        Returns : value of _noatom
        Args    : newvalue (optional)

        Title   : _noheader
        Usage   : $obj->_noheader($newval)
        Example :
        Returns : value of _noheader
        Args    : newvalue (optional)

        Title   : _read_PDB_singlecontline
        Usage   : $obj->_read_PDB_singlecontline($record, $fromto, $buffer))
        Function: read single continued record from PDB
        Returns : concatenated record entry (between $fromto columns)
        Args    : record, colunm delimiters, buffer

        Title   : _read_PDB_jrnl
        Usage   : $obj->_read_PDB_jrnl($\buffer))
        Function: read jrnl record from PDB
        Returns : Bio::Annotation::Reference object
        Args    :

        Title   : _read_PDB_remark_1
        Usage   : $obj->_read_PDB_remark_1($\buffer))
        Function: read "remark 1"  record from PDB
        Returns : array of Bio::Annotation::Reference objects
        Args    :

        Title   : _read_PDB_coordinate_section
        Usage   : $obj->_read_PDB_coordinate_section($\buffer))
        Function: read one model from a PDB
        Returns : Bio::Structure::Model object
        Args    :