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.

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://www.bioperl.org/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email kris.boulez@algonomics.com 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 :