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Bio::Structure::IO::pdUser Contributed Perl DocumentBio::Structure::IO::pdb(3)

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:

	 http://bugzilla.open-bio.org/

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	:

perl v5.14.1			  2011-07-22	    Bio::Structure::IO::pdb(3)
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