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<a href="Scientific-module.html">Package Scientific</a> ::
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Class Group
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Group</h1><p class="nomargin-top"></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Scientific.IO.PDB.Residue-class.html">Residue</a></li><li>, <a href="Scientific.IO.PDB.Molecule-class.html">Molecule</a></li> </ul>
</dd></dl>
<hr />
<p>Atom group (residue or molecule) in a PDB file</p>
<p>This is an abstract base class. Instances can be created using one of
the subclasses (<a href="Scientific.IO.PDB.Molecule-class.html"
class="link">Molecule</a>, <a
href="Scientific.IO.PDB.AminoAcidResidue-class.html"
class="link">AminoAcidResidue</a>, <a
href="Scientific.IO.PDB.NucleotideResidue-class.html"
class="link">NucleotideResidue</a>).</p>
<p>Group objects permit iteration over atoms with for-loops, as well as
extraction of atoms by indexing with the atom name.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Group-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Group-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">atoms</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">number</span>=<span class="summary-sig-default">None</span>)</span></td>
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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></td>
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<span class="summary-type"> </span>
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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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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Group-class.html#addAtom" class="summary-sig-name">addAtom</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">atom</span>)</span><br />
Add an atom to the group</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Group-class.html#changeName" class="summary-sig-name">changeName</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span><br />
Set the PDB residue name</td>
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</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Group-class.html#deleteAtom" class="summary-sig-name">deleteAtom</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">atom</span>)</span><br />
Remove an atom from the group</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<tr>
<td><span class="summary-sig"><a name="deleteHydrogens"></a><span class="summary-sig-name">deleteHydrogens</span>(<span class="summary-sig-arg">self</span>)</span><br />
Remove all hydrogen atoms of the group</td>
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</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="isCompatible"></a><span class="summary-sig-name">isCompatible</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residue_data</span>)</span></td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Group-class.html#writeToFile" class="summary-sig-name">writeToFile</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">file</span>)</span><br />
Write the group to a file</td>
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<!-- ==================== METHOD DETAILS ==================== -->
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<span class="table-header">Method Details</span></td>
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<a name="__getitem__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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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">item</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
>
</td>
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<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>item</code></strong> (<code>int</code> or <code>str</code>) - an integer index or an atom name</li>
</ul></dd>
</dl>
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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">name</span>,
<span class="sig-arg">atoms</span>=<span class="sig-default">None</span>,
<span class="sig-arg">number</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>name</code></strong> (<code>str</code>) - the name of the group</li>
<li><strong class="pname"><code>atoms</code></strong> (<code>list</code> or <code>NoneType</code>) - a list of atoms (or <code>None</code> for no atoms)</li>
<li><strong class="pname"><code>number</code></strong> (<code>int</code> or <code>NoneType</code>) - the PDB residue number (or <code>None</code>)</li>
</ul></dd>
</dl>
</td></tr></table>
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<a name="addAtom"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">addAtom</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">atom</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Add an atom to the group</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>atom</code></strong> (<a href="Scientific.IO.PDB.Atom-class.html" class="link">Atom</a>) - the atom</li>
</ul></dd>
</dl>
</td></tr></table>
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<a name="changeName"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">changeName</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Set the PDB residue name</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>name</code></strong> (<code>str</code>) - the new name</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="deleteAtom"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">deleteAtom</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">atom</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Remove an atom from the group</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>atom</code></strong> (<a href="Scientific.IO.PDB.Atom-class.html" class="link">Atom</a>) - the atom to be removed</li>
</ul></dd>
<dt>Raises:</dt>
<dd><ul class="nomargin-top">
<li><code><strong class='fraise'>KeyError</strong></code> - if the atom is not part of the group</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="writeToFile"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">writeToFile</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">file</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Write the group to a file</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>file</code></strong> (<a href="Scientific.IO.PDB.PDBFile-class.html"
class="link">PDBFile</a> or <code>str</code>) - a PDBFile object or a file name</li>
</ul></dd>
</dl>
</td></tr></table>
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