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)

_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    :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq