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.\" ========================================================================
.\"
.IX Title "Bio::Structure::IO::pdb 3pm"
.TH Bio::Structure::IO::pdb 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Structure::IO::pdb \- PDB input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
It is probably best not to use this object directly, but
rather go through the Bio::Structure::IO handler system. Go:
.PP
.Vb 2
\&    $stream = Bio::Structure::IO\->new(\-file => $filename,
\&                                      \-format => \*(AqPDB\*(Aq);
\&
\&    while (my $structure = $stream\->next_structure) {
\&            # do something with $structure
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::Structure objects to and from \s-1PDB\s0 flat
file databases. The working is similar to that of the Bio::SeqIO handlers.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Kris Boulez"
.IX Header "AUTHOR - Kris Boulez"
Email kris.boulez@algonomics.com
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "next_structure;"
.IX Subsection "next_structure;"
.Vb 5
\& Title   : next_structure
\& Usage   : $struc = $stream\->next_structure()
\& Function: returns the next structure in the stream
\& Returns : Bio::Structure object
\& Args    :
.Ve
.SS "write_structure"
.IX Subsection "write_structure"
.Vb 5
\& 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
.Ve
.SS "_filehandle"
.IX Subsection "_filehandle"
.Vb 6
\& Title   : _filehandle
\& Usage   : $obj\->_filehandle($newval)
\& Function:
\& Example :
\& Returns : value of _filehandle
\& Args    : newvalue (optional)
.Ve
.SS "_noatom"
.IX Subsection "_noatom"
.Vb 6
\& Title   : _noatom
\& Usage   : $obj\->_noatom($newval)
\& Function:
\& Example :
\& Returns : value of _noatom
\& Args    : newvalue (optional)
.Ve
.SS "_noheader"
.IX Subsection "_noheader"
.Vb 6
\& Title   : _noheader
\& Usage   : $obj\->_noheader($newval)
\& Function:
\& Example :
\& Returns : value of _noheader
\& Args    : newvalue (optional)
.Ve
.SS "_read_PDB_singlecontline"
.IX Subsection "_read_PDB_singlecontline"
.Vb 5
\& 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
.Ve
.SS "_read_PDB_jrnl"
.IX Subsection "_read_PDB_jrnl"
.Vb 5
\& Title   : _read_PDB_jrnl
\& Usage   : $obj\->_read_PDB_jrnl($\ebuffer))
\& Function: read jrnl record from PDB
\& Returns : Bio::Annotation::Reference object
\& Args    :
.Ve
.SS "_read_PDB_remark_1"
.IX Subsection "_read_PDB_remark_1"
.Vb 5
\& Title   : _read_PDB_remark_1
\& Usage   : $obj\->_read_PDB_remark_1($\ebuffer))
\& Function: read "remark 1"  record from PDB
\& Returns : array of Bio::Annotation::Reference objects
\& Args    :
.Ve
.SS "_read_PDB_coordinate_section"
.IX Subsection "_read_PDB_coordinate_section"
.Vb 5
\& Title   : _read_PDB_coordinate_section
\& Usage   : $obj\->_read_PDB_coordinate_section($\ebuffer))
\& Function: read one model from a PDB
\& Returns : Bio::Structure::Model object
\& Args    :
.Ve