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:
https://github.com/bioperl/bioperl-live/issues
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)
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 :
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 :