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root 2c3569dd39 Initial revision of AWIPS2 11.9.0-7p5 
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<?xml version="1.0" encoding="ascii"?>
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<title>Scientific.IO.PDB.Structure</title>
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<a href="Scientific-module.html">Package&nbsp;Scientific</a> ::
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Class&nbsp;Structure
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Structure</h1><p class="nomargin-top"></p>
<p>A high-level representation of the contents of a PDB file</p>
<p>The components of a structure can be accessed in several ways ('s' is
an instance of this class):</p>
<ul>
<li>
's.residues' is a list of all PDB residues, in the order in which
they occurred in the file.
</li>
<li>
's.peptide_chains' is a list of PeptideChain objects, containing all
peptide chains in the file in their original order.
</li>
<li>
's.nucleotide_chains' is a list of NucleotideChain objects,
containing all nucleotide chains in the file in their original order.
</li>
<li>
's.molecules' is a list of all PDB residues that are neither amino
acid residues nor nucleotide residues, in their original order.
</li>
<li>
's.objects' is a list of all high-level objects (peptide chains,
nucleotide chains, and molecules) in their original order.
</li>
<li>
's.to_fractional' is the transformation from real-space coordinates
to fractional coordinates, as read from the SCALEn records.
</li>
<li>
's.from_fractional' is the transformation from fractional coordinates
to real-space coordinates, the inverse of s.to_fractional.
</li>
<li>
's.ncs_transformations' is a list of transformations that describe
non-crystallographic symmetries, as read from the MTRIXn records.
</li>
<li>
if a CRYST1 record exists, 's.a', 's.b', 's.c', 's.alpha', 's.beta',
's.gamma' are the parameters of the unit cell and 's.space_group' is
a string indicating the space group. If no CRYST1 record exists, all
those values are None. Furthermore, 's.cs_transformations' is a list
of transformations that describe crystallographic symmetries. If no
CRYST1 record exists, the list is empty.
</li>
</ul>
<p>An iteration over a Structure instance by a for-loop is equivalent to
an iteration over the residue list.</p>
<!-- ==================== NESTED CLASSES ==================== -->
<a name="section-NestedClasses"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<span class="table-header">Nested Classes</span></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">
<a href="Scientific.IO.PDB.Molecule-class.html" class="summary-name">molecule_constructor</a><br />
Molecule in a PDB file
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="Scientific.IO.PDB.NucleotideChain-class.html" class="summary-name">nucleotide_chain_constructor</a><br />
Nucleotide chain in a PDB file
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="Scientific.IO.PDB.PeptideChain-class.html" class="summary-name">peptide_chain_constructor</a><br />
Peptide chain in a PDB file
</td>
</tr>
</table>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<span class="table-header">Instance Methods</span></td>
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<span class="summary-type">&nbsp;</span>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">item</span>)</span></td>
<td align="right" valign="top">
</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.Structure-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">file_or_filename</span>,
<span class="summary-sig-arg">model</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">alternate_code</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code></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">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<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>
<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="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</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">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="addMolecule"></a><span class="summary-sig-name">addMolecule</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">molecule</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">&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</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="deleteResidue"></a><span class="summary-sig-name">deleteResidue</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residue</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">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="extractData"></a><span class="summary-sig-name">extractData</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</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">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="findSpaceGroupTransformations"></a><span class="summary-sig-name">findSpaceGroupTransformations</span>(<span class="summary-sig-arg">self</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">&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.Structure-class.html#joinNucleotideChains" class="summary-sig-name">joinNucleotideChains</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">first</span>,
<span class="summary-sig-arg">second</span>)</span><br />
Join two nucleotide chains into a single one.</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.Structure-class.html#joinPeptideChains" class="summary-sig-name">joinPeptideChains</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">first</span>,
<span class="summary-sig-arg">second</span>)</span><br />
Join two peptide chains into a single one.</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="newChain"></a><span class="summary-sig-name">newChain</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residue</span>,
<span class="summary-sig-arg">chain_data</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">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="newResidue"></a><span class="summary-sig-name">newResidue</span>(<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>
</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="parseFile"></a><span class="summary-sig-name">parseFile</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">file</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">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="renumberAtoms"></a><span class="summary-sig-name">renumberAtoms</span>(<span class="summary-sig-arg">self</span>)</span><br />
Renumber all atoms sequentially starting with 1</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.Structure-class.html#splitNucleotideChain" class="summary-sig-name">splitNucleotideChain</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">number</span>,
<span class="summary-sig-arg">position</span>)</span><br />
Split a nucleotide chain into two chains</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.Structure-class.html#splitPeptideChain" class="summary-sig-name">splitPeptideChain</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">number</span>,
<span class="summary-sig-arg">position</span>)</span><br />
Split a peptide chain into two chains</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.Structure-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 everything 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="__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">file_or_filename</span>,
<span class="sig-arg">model</span>=<span class="sig-default">0</span>,
<span class="sig-arg">alternate_code</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code></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>file_or_filename</code></strong> (<code>str</code> or <code>file</code>) - the name of the PDB file, or a file object. Compressed files and
URLs are accepted, as for class <a
href="Scientific.IO.PDB.PDBFile-class.html"
class="link">PDBFile</a>.</li>
<li><strong class="pname"><code>model</code></strong> (<code>int</code>) - the number of the model to read from a multiple-model file. Only
one model can be treated at a time.</li>
<li><strong class="pname"><code>alternate_code</code></strong> (single-letter <code>str</code>) - the version of the positions to be read from a file with
alternate positions.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="joinNucleotideChains"></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">joinNucleotideChains</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">first</span>,
<span class="sig-arg">second</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<p>Join two nucleotide chains into a single one. The new chain occupies
the position of the first chain, the second one is removed from the
nucleotide chain list.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>first</code></strong> (<code>int</code>) - the number of the first chain</li>
<li><strong class="pname"><code>second</code></strong> (<code>int</code>) - the number of the second chain</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="joinPeptideChains"></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">joinPeptideChains</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">first</span>,
<span class="sig-arg">second</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<p>Join two peptide chains into a single one. The new chain occupies the
position of the first chain, the second one is removed from the peptide
chain list.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>first</code></strong> (<code>int</code>) - the number of the first chain</li>
<li><strong class="pname"><code>second</code></strong> (<code>int</code>) - the number of the second chain</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="splitNucleotideChain"></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">splitNucleotideChain</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">number</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<p>Split a nucleotide chain into two chains</p>
<p>The two chain fragments remain adjacent in the nucleotide chain list,
i.e. the numbers of all following chains increase by one.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>number</code></strong> (<code>int</code>) - the number of the nucleotide chain to be split</li>
<li><strong class="pname"><code>position</code></strong> (<code>int</code>) - the residue index at which the chain is split.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="splitPeptideChain"></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">splitPeptideChain</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">number</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<p>Split a peptide chain into two chains</p>
<p>The two chain fragments remain adjacent in the peptide chain list,
i.e. the numbers of all following chains increase by one.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>number</code></strong> (<code>int</code>) - the number of the peptide chain to be split</li>
<li><strong class="pname"><code>position</code></strong> (<code>int</code>) - the residue index at which the chain is split.</li>
</ul></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;
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<p>Write everything 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 PDB file object or a filename</li>
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