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

NAME

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

SYNOPSIS

       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
           }

DESCRIPTION

       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.

FEEDBACK

   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.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

       bioperl-l@bioperl.org

       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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Kris Boulez

       Email kris.boulez@algonomics.com

APPENDIX

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

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

   write_structure
        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

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

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

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

   _read_PDB_singlecontline
        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

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

   _read_PDB_remark_1
        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    :

   _read_PDB_coordinate_section
        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    :