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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
<a href="Bio.PDB.PDBIO%27-module.html">Module PDBIO'</a> ::
Class PDBIO
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class PDBIO</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.PDBIO%27-pysrc.html#PDBIO">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">PDBIO</strong>
</pre>
<hr />
<p>Write a Structure object (or a subset of a Structure object) as a PDB
file.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>p=PDBParser()
<span class="py-prompt">>>> </span>s=p.get_structure(<span class="py-string">"1fat"</span>, <span class="py-string">"1fat.pdb"</span>)
<span class="py-prompt">>>> </span>io=PDBIO()
<span class="py-prompt">>>> </span>io.set_structure(s)
<span class="py-prompt">>>> </span>io.save(<span class="py-string">"out.pdb"</span>)</pre>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.PDBIO%27.PDBIO-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">use_model_flag</span>=<span class="summary-sig-default">0</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
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<span class="codelink"><a href="Bio.PDB.PDBIO%27-pysrc.html#PDBIO.__init__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_get_atom_line"></a><span class="summary-sig-name">_get_atom_line</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">atom</span>,
<span class="summary-sig-arg">hetfield</span>,
<span class="summary-sig-arg">segid</span>,
<span class="summary-sig-arg">atom_number</span>,
<span class="summary-sig-arg">resname</span>,
<span class="summary-sig-arg">resseq</span>,
<span class="summary-sig-arg">icode</span>,
<span class="summary-sig-arg">chain_id</span>,
<span class="summary-sig-arg">charge</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"> </code><code class="variable-quote">'</code></span>)</span><br />
Returns an ATOM PDB string (PRIVATE).</td>
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<span class="codelink"><a href="Bio.PDB.PDBIO%27-pysrc.html#PDBIO._get_atom_line">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.PDBIO%27.PDBIO-class.html#save" class="summary-sig-name">save</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">file</span>,
<span class="summary-sig-arg">select</span>=<span class="summary-sig-default"><Select all></span>,
<span class="summary-sig-arg">write_end</span>=<span class="summary-sig-default">0</span>)</span></td>
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<span class="codelink"><a href="Bio.PDB.PDBIO%27-pysrc.html#PDBIO.save">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="set_structure"></a><span class="summary-sig-name">set_structure</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">structure</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBIO%27-pysrc.html#PDBIO.set_structure">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">use_model_flag</span>=<span class="sig-default">0</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBIO%27-pysrc.html#PDBIO.__init__">source code</a></span>
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<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>use_model_flag</code></strong> (int) - if 1, force use of the MODEL record in output.</li>
</ul></dd>
<dt>Overrides:
object.__init__
</dt>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">save</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">file</span>,
<span class="sig-arg">select</span>=<span class="sig-default"><Select all></span>,
<span class="sig-arg">write_end</span>=<span class="sig-default">0</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBIO%27-pysrc.html#PDBIO.save">source code</a></span>
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<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>file</code></strong> (string or filehandle) - output file</li>
<li><strong class="pname"><code>select</code></strong> (select hould have the following methods:
<ul>
<li>
accept_model(model)
</li>
<li>
accept_chain(chain)
</li>
<li>
accept_residue(residue)
</li>
<li>
accept_atom(atom)
</li>
</ul>
<p>These methods should return 1 if the entity is to be written
out, 0 otherwise.</p>
<p>Typically select is a subclass of <a
href="Bio.PDB.PDBIO%27.Select-class.html"
class="link">Select</a>.</p>) - selects which entities will be written.</li>
</ul></dd>
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