Bio::Structure::IO::pdb.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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    :