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awips2/pythonPackages/scientific/Doc/Reference/Scientific.IO.PDB.Chain-class.html
root a02aeb236c Initial revision of AWIPS2 11.9.0-7p5 
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<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>Scientific.IO.PDB.Chain</title>
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<a href="Scientific-module.html">Package&nbsp;Scientific</a> ::
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<a href="Scientific.IO.PDB-module.html">Module&nbsp;PDB</a> ::
Class&nbsp;Chain
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Chain</h1><p class="nomargin-top"></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li>DummyChain</li><li>, <a href="Scientific.IO.PDB.NucleotideChain-class.html">NucleotideChain</a></li><li>, <a href="Scientific.IO.PDB.PeptideChain-class.html">PeptideChain</a></li> </ul>
</dd></dl>
<hr />
<p>Chain of PDB residues</p>
<p>This is an abstract base class. Instances can be created using one of
the subclasses (<a href="Scientific.IO.PDB.PeptideChain-class.html"
class="link">PeptideChain</a>, <a
href="Scientific.IO.PDB.NucleotideChain-class.html"
class="link">NucleotideChain</a>).</p>
<p>Chain objects respond to len() and return their residues by indexing
with integers.</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>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><a href="Scientific.IO.PDB.AminoAcidResidue-class.html"
class="link">AminoAcidResidue</a> or <a
href="Scientific.IO.PDB.NucleotideResidue-class.html"
class="link">NucleotideResidue</a></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.Chain-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">index</span>)</span><br />
Returns:
the residue corresponding to the index</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"><a href="Scientific.IO.PDB.PeptideChain-class.html"
class="link">PeptideChain</a> or <a
href="Scientific.IO.PDB.NucleotideChain-class.html"
class="link">NucleotideChain</a></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.Chain-class.html#__getslice__" class="summary-sig-name">__getslice__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">i1</span>,
<span class="summary-sig-arg">i2</span>)</span><br />
Returns:
the subchain from i1 to i2</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.Chain-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residues</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">chain_id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">segment_id</span>=<span class="summary-sig-default">None</span>)</span></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>int</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.Chain-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
the number of residues in the chain</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.Chain-class.html#addResidue" class="summary-sig-name">addResidue</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residue</span>)</span><br />
Add a residue at the end of the chain</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 name="deleteHydrogens"></a><span class="summary-sig-name">deleteHydrogens</span>(<span class="summary-sig-arg">self</span>)</span><br />
Remove all hydrogen atoms in the chain</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.Chain-class.html#removeResidues" class="summary-sig-name">removeResidues</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">first</span>,
<span class="summary-sig-arg">last</span>)</span><br />
Remove residues in a given index range.</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>list</code> of <code>str</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.Chain-class.html#sequence" class="summary-sig-name">sequence</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
the list of residue names</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.Chain-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 chain to a file</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" 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">Method Details</span></td>
</tr>
</table>
<a name="__getitem__"></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">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">index</span>)</span>
<br /><em class="fname">(Indexing operator)</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>index</code></strong> (<code>int</code>) - an index into the chain</li>
</ul></dd>
<dt>Returns: <a href="Scientific.IO.PDB.AminoAcidResidue-class.html"
class="link">AminoAcidResidue</a> or <a
href="Scientific.IO.PDB.NucleotideResidue-class.html"
class="link">NucleotideResidue</a></dt>
<dd>the residue corresponding to the index</dd>
<dt>Raises:</dt>
<dd><ul class="nomargin-top">
<li><code><strong class='fraise'>IndexError</strong></code> - if index exceeds the chain length</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="__getslice__"></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">__getslice__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">i1</span>,
<span class="sig-arg">i2</span>)</span>
<br /><em class="fname">(Slicling operator)</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>i1</code></strong> (<code>int</code>) - in index into the chain</li>
<li><strong class="pname"><code>i2</code></strong> - in index into the chain @type i12 <code>int</code></li>
</ul></dd>
<dt>Returns: <a href="Scientific.IO.PDB.PeptideChain-class.html"
class="link">PeptideChain</a> or <a
href="Scientific.IO.PDB.NucleotideChain-class.html"
class="link">NucleotideChain</a></dt>
<dd>the subchain from i1 to i2</dd>
</dl>
</td></tr></table>
</div>
<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">residues</span>=<span class="sig-default">None</span>,
<span class="sig-arg">chain_id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">segment_id</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>residues</code></strong> (<code>list</code> or <code>NoneType</code>) - a list of residue objects, or <code>None</code> meaning that the
chain is initially empty</li>
<li><strong class="pname"><code>chain_id</code></strong> (<code>str</code> or <code>NoneType</code>) - a one-letter chain identifier or <code>None</code></li>
<li><strong class="pname"><code>segment_id</code></strong> (<code>str</code> or <code>NoneType</code>) - a multi-character segment identifier or <code>None</code></li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="__len__"></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">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Returns: <code>int</code></dt>
<dd>the number of residues in the chain</dd>
</dl>
</td></tr></table>
</div>
<a name="addResidue"></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">addResidue</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">residue</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<p>Add a residue at the end of the chain</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>residue</code></strong> (<a href="Scientific.IO.PDB.AminoAcidResidue-class.html"
class="link">AminoAcidResidue</a> or <a
href="Scientific.IO.PDB.NucleotideResidue-class.html"
class="link">NucleotideResidue</a>) - the residue to be added</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="removeResidues"></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">removeResidues</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">first</span>,
<span class="sig-arg">last</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<p>Remove residues in a given index range.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>first</code></strong> (<code>int</code>) - the index of the first residue to be removed</li>
<li><strong class="pname"><code>last</code></strong> (<code>int</code> or <code>NoneType</code>) - the index of the first residue to be kept, or <code>None</code>
meaning remove everything to the end of the chain.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="sequence"></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">sequence</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>list</code> of <code>str</code></dt>
<dd>the list of residue names</dd>
</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 chain 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>
</div>
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