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mjames-upc ae6bbbc780 python updates: cartopy, cycler, cython, h5py, nose, pil, pyparsing, pygtk, pycairo, pint, python-dateutil, scientific 
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<?xml version="1.0" encoding="ascii"?>
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Class&nbsp;NucleotideResidue
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class NucleotideResidue</h1><p class="nomargin-top"></p>
<pre class="base-tree">
<a href="Scientific.IO.PDB.Group-class.html">Group</a> --+
|
<a href="Scientific.IO.PDB.Residue-class.html">Residue</a> --+
|
<strong class="uidshort">NucleotideResidue</strong>
</pre>
<hr />
<p>Nucleotide residue in a PDB file</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Instance Methods</span></td>
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-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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</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-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>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>bool</code></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-class.html#hasDesoxyribose" class="summary-sig-name">hasDesoxyribose</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
<code>True</code> if the residue has no atom named O2*</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>bool</code></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-class.html#hasPhosphate" class="summary-sig-name">hasPhosphate</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
<code>True</code> if the residue has a phosphate group</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>bool</code></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-class.html#hasRibose" class="summary-sig-name">hasRibose</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
<code>True</code> if the residue has an atom named O2*</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>bool</code></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-class.html#hasTerminalH" class="summary-sig-name">hasTerminalH</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
<code>True</code> if the residue has a 3-terminal H atom</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-class.html#isCompatible" class="summary-sig-name">isCompatible</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residue_data</span>)</span></td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.NucleotideResidue-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>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Scientific.IO.PDB.Group-class.html">Group</a></code></b>:
<code><a href="Scientific.IO.PDB.Group-class.html#__getitem__">__getitem__</a></code>,
<code><a href="Scientific.IO.PDB.Group-class.html#__len__">__len__</a></code>,
<code><a href="Scientific.IO.PDB.Group-class.html#__repr__">__repr__</a></code>,
<code><a href="Scientific.IO.PDB.Group-class.html#__str__">__str__</a></code>,
<code><a href="Scientific.IO.PDB.Group-class.html#changeName">changeName</a></code>,
<code><a href="Scientific.IO.PDB.Group-class.html#deleteAtom">deleteAtom</a></code>,
<code><a href="Scientific.IO.PDB.Group-class.html#deleteHydrogens">deleteHydrogens</a></code>
</p>
</td>
</tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
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cellspacing="0" width="100%" bgcolor="white">
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<span class="table-header">Class Variables</span></td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="is_nucleotide"></a><span class="summary-name">is_nucleotide</span> = <code title="1">1</code>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
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<span class="table-header">Method Details</span></td>
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<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<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"
>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>name</code></strong> - the name of the group</li>
<li><strong class="pname"><code>atoms</code></strong> - a list of atoms (or <code>None</code> for no atoms)</li>
<li><strong class="pname"><code>number</code></strong> - the PDB residue number (or <code>None</code>)</li>
</ul></dd>
<dt>Overrides:
<a href="Scientific.IO.PDB.Group-class.html#__init__">Group.__init__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="addAtom"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<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"
>&nbsp;
</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> - the atom</li>
</ul></dd>
<dt>Overrides:
<a href="Scientific.IO.PDB.Group-class.html#addAtom">Group.addAtom</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="hasDesoxyribose"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">hasDesoxyribose</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Returns: <code>bool</code></dt>
<dd><code>True</code> if the residue has no atom named O2*</dd>
</dl>
</td></tr></table>
</div>
<a name="hasPhosphate"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">hasPhosphate</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Returns: <code>bool</code></dt>
<dd><code>True</code> if the residue has a phosphate group</dd>
</dl>
</td></tr></table>
</div>
<a name="hasRibose"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">hasRibose</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Returns: <code>bool</code></dt>
<dd><code>True</code> if the residue has an atom named O2*</dd>
</dl>
</td></tr></table>
</div>
<a name="hasTerminalH"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">hasTerminalH</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Returns: <code>bool</code></dt>
<dd><code>True</code> if the residue has a 3-terminal H atom</dd>
</dl>
</td></tr></table>
</div>
<a name="isCompatible"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">isCompatible</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">residue_data</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="Scientific.IO.PDB.Group-class.html#isCompatible">Group.isCompatible</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="writeToFile"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<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"
>&nbsp;
</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 PDBFile object or a file name</li>
</ul></dd>
<dt>Overrides:
<a href="Scientific.IO.PDB.Group-class.html#writeToFile">Group.writeToFile</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
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