399 lines
14 KiB
HTML
Executable file
399 lines
14 KiB
HTML
Executable file
<?xml version="1.0" encoding="ascii"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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"DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<title>Scientific.IO.PDB.Atom</title>
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<link rel="stylesheet" href="epydoc.css" type="text/css" />
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<body bgcolor="white" text="black" link="blue" vlink="#204080"
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alink="#204080">
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<!-- ==================== NAVIGATION BAR ==================== -->
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><a class="navbar" target="_top" href="http://dirac.cnrs-orleans.fr/ScientificPython/">Scientific Python</a></th>
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<span class="breadcrumbs">
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<a href="Scientific-module.html">Package Scientific</a> ::
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<a href="Scientific.IO-module.html">Package IO</a> ::
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<a href="Scientific.IO.PDB-module.html">Module PDB</a> ::
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Class Atom
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</span>
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</td>
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<td>
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<table cellpadding="0" cellspacing="0">
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<!-- hide/show private -->
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<tr><td align="right"><span class="options"
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>[<a href="frames.html" target="_top">frames</a
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>] | <a href="Scientific.IO.PDB.Atom-class.html"
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target="_top">no frames</a>]</span></td></tr>
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</table>
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</td>
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</table>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
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<h1 class="epydoc">Class Atom</h1><p class="nomargin-top"></p>
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<dl><dt>Known Subclasses:</dt>
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<dd>
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<ul class="subclass-list">
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<li><a href="Scientific.IO.PDB.HetAtom-class.html">HetAtom</a></li> </ul>
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</dd></dl>
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<hr />
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<p>Atom in a PDB structure</p>
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<!-- ==================== INSTANCE METHODS ==================== -->
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<a name="section-InstanceMethods"></a>
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<table class="summary" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr bgcolor="#70b0f0" class="table-header">
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<td align="left" colspan="2" class="table-header">
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<span class="table-header">Instance Methods</span></td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Atom-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
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<span class="summary-sig-arg">item</span>)</span><br />
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Returns:
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the property value</td>
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<td align="right" valign="top">
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Atom-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
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<span class="summary-sig-arg">name</span>,
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<span class="summary-sig-arg">position</span>,
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<span class="summary-sig-arg">**properties</span>)</span></td>
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<span class="summary-type"> </span>
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</td><td class="summary">
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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><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Atom-class.html#__setitem__" class="summary-sig-name">__setitem__</a>(<span class="summary-sig-arg">self</span>,
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<span class="summary-sig-arg">item</span>,
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<span class="summary-sig-arg">value</span>)</span></td>
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<td align="right" valign="top">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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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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<td align="right" valign="top">
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</td>
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</table>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"><code>str</code></span>
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Atom-class.html#type" class="summary-sig-name">type</a>(<span class="summary-sig-arg">self</span>)</span><br />
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Returns:
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the six-letter record type, ATOM or HETATM</td>
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<td align="right" valign="top">
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</td>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.Atom-class.html#writeToFile" class="summary-sig-name">writeToFile</a>(<span class="summary-sig-arg">self</span>,
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<span class="summary-sig-arg">file</span>)</span><br />
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Write an atom record to a file</td>
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<td align="right" valign="top">
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</td>
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</tr>
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</table>
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</td>
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</table>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="section-MethodDetails"></a>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr bgcolor="#70b0f0" class="table-header">
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<td align="left" colspan="2" class="table-header">
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<span class="table-header">Method Details</span></td>
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</tr>
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</table>
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<a name="__getitem__"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr><td>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
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<span class="sig-arg">item</span>)</span>
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<br /><em class="fname">(Indexing operator)</em>
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</h3>
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</td><td align="right" valign="top"
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>
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</td>
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</tr></table>
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>item</code></strong> (<code>str</code>) - the name of a property, including "name" or
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"position"</li>
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</ul></dd>
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<dt>Returns:</dt>
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<dd>the property value</dd>
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</dl>
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</td></tr></table>
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</div>
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<a name="__init__"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr><td>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
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<span class="sig-arg">name</span>,
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<span class="sig-arg">position</span>,
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<span class="sig-arg">**properties</span>)</span>
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<br /><em class="fname">(Constructor)</em>
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</h3>
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</td><td align="right" valign="top"
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>
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</td>
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</tr></table>
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>name</code></strong> (<code>str</code>) - the atom name</li>
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<li><strong class="pname"><code>position</code></strong> (<a href="Scientific.Geometry.Vector-class.html"
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class="link">Scientific.Geometry.Vector</a>) - the atom position</li>
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<li><strong class="pname"><code>properties</code></strong> - any other atom properties as keyword parameters. These properties
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are stored in the atom object and can be accessed by indexing, as
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for dictionaries.</li>
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</ul></dd>
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</dl>
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</td></tr></table>
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</div>
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<a name="__setitem__"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr><td>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__setitem__</span>(<span class="sig-arg">self</span>,
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<span class="sig-arg">item</span>,
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<span class="sig-arg">value</span>)</span>
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<br /><em class="fname">(Index assignment operator)</em>
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</h3>
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</td><td align="right" valign="top"
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>
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</td>
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</tr></table>
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>item</code></strong> (<code>str</code>) - the name of an existing or to be defined property</li>
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<li><strong class="pname"><code>value</code></strong> - the new value for the property</li>
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</ul></dd>
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</dl>
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</td></tr></table>
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</div>
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<a name="type"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr><td>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">type</span>(<span class="sig-arg">self</span>)</span>
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</h3>
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</td><td align="right" valign="top"
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>
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</td>
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</tr></table>
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<dl class="fields">
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<dt>Returns: <code>str</code></dt>
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<dd>the six-letter record type, ATOM or HETATM</dd>
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</dl>
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</td></tr></table>
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</div>
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<a name="writeToFile"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr><td>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">writeToFile</span>(<span class="sig-arg">self</span>,
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<span class="sig-arg">file</span>)</span>
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</h3>
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</td><td align="right" valign="top"
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>
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</td>
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</tr></table>
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<p>Write an atom record to a file</p>
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>file</code></strong> (<a href="Scientific.IO.PDB.PDBFile-class.html"
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class="link">PDBFile</a> or <code>str</code>) - a PDB file object or a filename</li>
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</ul></dd>
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</dl>
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</td></tr></table>
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</div>
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<br />
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