Ewan Birney


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

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    :