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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.Entity-module.html">Module Entity</a> ::
Class Entity
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Entity</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Entity</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.PDB.Structure.Structure-class.html">Structure.Structure</a></li><li>, <a href="Bio.PDB.Residue.Residue-class.html">Residue.Residue</a></li><li>, <a href="Bio.PDB.Model.Model-class.html">Model.Model</a></li><li>, <a href="Bio.PDB.Chain.Chain-class.html">Chain.Chain</a></li> </ul>
</dd></dl>
<hr />
<p>Basic container object. Structure, Model, Chain and Residue are
subclasses of Entity. It deals with storage and lookup.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.PDB.Entity.Entity-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</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.Entity-pysrc.html#Entity.__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="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the number of children.</td>
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<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__len__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
Return the child with given id.</td>
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<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__getitem__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__delitem__"></a><span class="summary-sig-name">__delitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
Remove a child.</td>
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<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__delitem__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__iter__"></a><span class="summary-sig-name">__iter__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over children.</td>
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<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.__iter__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.Entity.Entity-class.html#get_level" class="summary-sig-name">get_level</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return level in hierarchy.</td>
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<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_level">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_parent"></a><span class="summary-sig-name">set_parent</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">entity</span>)</span><br />
Set the parent Entity object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.set_parent">source code</a></span>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="detach_parent"></a><span class="summary-sig-name">detach_parent</span>(<span class="summary-sig-arg">self</span>)</span><br />
Detach the parent.</td>
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<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.detach_parent">source code</a></span>
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<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="detach_child"></a><span class="summary-sig-name">detach_child</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
Remove a child.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.detach_child">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="add"></a><span class="summary-sig-name">add</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">entity</span>)</span><br />
Add a child to the Entity.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.add">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="get_iterator"></a><span class="summary-sig-name">get_iterator</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return iterator over children.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_iterator">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_list"></a><span class="summary-sig-name">get_list</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return a copy of the list of children.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_list">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="has_id"></a><span class="summary-sig-name">has_id</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
True if a child with given id exists.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.has_id">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_parent"></a><span class="summary-sig-name">get_parent</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the parent Entity object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_parent">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_id"></a><span class="summary-sig-name">get_id</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the id.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_id">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.Entity.Entity-class.html#get_full_id" class="summary-sig-name">get_full_id</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the full id.</td>
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<span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_full_id">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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<!-- ==================== PROPERTIES ==================== -->
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
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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">id</span>)</span>
<br /><em class="fname">(Constructor)</em>
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<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
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</h3>
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<p>Return level in hierarchy.</p>
<p>A - atom R - residue C - chain M - model S - structure</p>
<dl class="fields">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_full_id</span>(<span class="sig-arg">self</span>)</span>
</h3>
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><span class="codelink"><a href="Bio.PDB.Entity-pysrc.html#Entity.get_full_id">source code</a></span>
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<p>Return the full id.</p>
<p>The full id is a tuple containing all id's starting from the top
object (Structure) down to the current object. A full id for a Residue
object e.g. is something like:</p>
<p>("1abc", 0, "A", (" ", 10,
"A"))</p>
<p>This corresponds to:</p>
<p>Structure with id "1abc" Model with id 0 Chain with id
"A" Residue with id (" ", 10, "A")</p>
<p>The Residue id indicates that the residue is not a hetero-residue (or
a water) beacuse it has a blank hetero field, that its sequence
identifier is 10 and its insertion code "A".</p>
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