| Bio::Structure::IO::pdb(3pm) | User Contributed Perl Documentation | Bio::Structure::IO::pdb(3pm) |
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.
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
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.
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://github.com/bioperl/bioperl-live/issues
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) Function: Example : Returns : value of _filehandle Args : newvalue (optional)
Title : _noatom Usage : $obj->_noatom($newval) Function: Example : Returns : value of _noatom Args : newvalue (optional)
Title : _noheader Usage : $obj->_noheader($newval) Function: 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 :
| 2018-10-27 | perl v5.26.2 |