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Christopher Fields
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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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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.

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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:


AUTHOR - Kris Boulez

Email kris.boulez@algonomics.com


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    :