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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.Chain-module.html">Module Chain</a> ::
Class Chain
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Chain</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.PDB.Entity.Entity-class.html">Entity.Entity</a> --+
|
<strong class="uidshort">Chain</strong>
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<td><span class="summary-sig"><a href="Bio.PDB.Chain.Chain-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
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<span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.Chain.Chain-class.html#_sort" class="summary-sig-name" onclick="show_private();">_sort</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">r1</span>,
<span class="summary-sig-arg">r2</span>)</span><br />
Sort function for residues in a chain</td>
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<span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain._sort">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.Chain.Chain-class.html#_translate_id" class="summary-sig-name" onclick="show_private();">_translate_id</a>(<span class="summary-sig-arg">self</span>,
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A residue id is normally a tuple (hetero flag, sequence identifier,
insertion code).</td>
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<td><span class="summary-sig"><a href="Bio.PDB.Chain.Chain-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
Return the residue with given id.</td>
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<span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.__getitem__">source code</a></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 />
Arguments: o id - (string, int, string) or int</td>
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<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a href="Bio.PDB.Chain.Chain-class.html#get_unpacked_list" class="summary-sig-name">get_unpacked_list</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return a list of undisordered residues.</td>
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<span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.get_unpacked_list">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.Chain.Chain-class.html#has_id" class="summary-sig-name">has_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
Return 1 if a residue with given id is present.</td>
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<span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.has_id">source code</a></span>
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<td><span class="summary-sig"><a name="get_atoms"></a><span class="summary-sig-name">get_atoms</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.get_atoms">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.PDB.Entity.Entity-class.html">Entity.Entity</a></code></b>:
<code><a href="Bio.PDB.Entity.Entity-class.html#__iter__">__iter__</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#__len__">__len__</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#add">add</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#detach_child">detach_child</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#detach_parent">detach_parent</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#get_full_id">get_full_id</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#get_id">get_id</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#get_iterator">get_iterator</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#get_level">get_level</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#get_list">get_list</a></code>,
<code><a href="Bio.PDB.Entity.Entity-class.html#get_parent">get_parent</a></code>,
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<a name="__init__"></a>
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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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><span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.__init__">source code</a></span>
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<dl class="fields">
<dt>Overrides:
<a href="Bio.PDB.Entity.Entity-class.html#__init__">Entity.Entity.__init__</a>
</dt>
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<a name="_sort"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_sort</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">r1</span>,
<span class="sig-arg">r2</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain._sort">source code</a></span>
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<p>Sort function for residues in a chain</p>
<p>Residues are first sorted according to their hetatm records. Protein
and nucleic acid residues first, hetatm residues next, and waters last.
Within each group, the residues are sorted according to their resseq's
(sequence identifiers). Finally, residues with the same resseq's are
sorted according to icode.</p>
<p>Arguments: o r1, r2 - Residue objects</p>
<dl class="fields">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_translate_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain._translate_id">source code</a></span>
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<p>A residue id is normally a tuple (hetero flag, sequence identifier,
insertion code). Since for most residues the hetero flag and the
insertion code are blanc (i.e. " "), you can just use the
sequence identifier to index a residue in a chain. The _translate_id
method translates the sequence identifier to the (" ", sequence
identifier, " ") tuple.</p>
<p>Arguments: o id - int, residue resseq</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.__getitem__">source code</a></span>
</td>
</tr></table>
<p>Return the residue with given id.</p>
<p>The id of a residue is (hetero flag, sequence identifier, insertion
code). If id is an int, it is translated to (" ", id, "
") by the _translate_id method.</p>
<p>Arguments: o id - (string, int, string) or int</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.PDB.Entity.Entity-class.html#__getitem__">Entity.Entity.__getitem__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="get_unpacked_list"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_unpacked_list</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.get_unpacked_list">source code</a></span>
</td>
</tr></table>
<p>Return a list of undisordered residues.</p>
<p>Some Residue objects hide several disordered residues
(DisorderedResidue objects). This method unpacks them, ie. it returns a
list of simple Residue objects.</p>
<dl class="fields">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">has_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Chain-pysrc.html#Chain.has_id">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Return 1 if a residue with given id is present.
The id of a residue is (hetero flag, sequence identifier, insertion code).
If id is an int, it is translated to (" ", id, " ") by the _translate_id
method.
Arguments:
o id - (string, int, string) or int
</pre>
<dl class="fields">
<dt>Overrides:
<a href="Bio.PDB.Entity.Entity-class.html#has_id">Entity.Entity.has_id</a>
</dt>
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