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<a href="Bio-module.html">Package Bio</a> ::
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Module PSEA
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module PSEA</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.PSEA-pysrc.html">source code</a></span></p>
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<span class="summary-type"> </span>
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<a href="Bio.PDB.PSEA.PSEA-class.html" class="summary-name">PSEA</a>
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<!-- ==================== FUNCTIONS ==================== -->
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<td><span class="summary-sig"><a name="run_psea"></a><span class="summary-sig-name">run_psea</span>(<span class="summary-sig-arg">fname</span>)</span><br />
Run PSEA and return output filename.</td>
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<td><span class="summary-sig"><a name="psea"></a><span class="summary-sig-name">psea</span>(<span class="summary-sig-arg">pname</span>)</span><br />
Parse PSEA output file.</td>
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<td><span class="summary-sig"><a name="psea2HEC"></a><span class="summary-sig-name">psea2HEC</span>(<span class="summary-sig-arg">pseq</span>)</span><br />
Translate PSEA secondary structure string into HEC.</td>
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<td><span class="summary-sig"><a name="annotate"></a><span class="summary-sig-name">annotate</span>(<span class="summary-sig-arg">m</span>,
<span class="summary-sig-arg">ss_seq</span>)</span></td>
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<span class="codelink"><a href="Bio.PDB.PSEA-pysrc.html#annotate">source code</a></span>
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<span class="summary-type"> </span>
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<a href="Bio.PDB.PSEA-module.html#standard_aa_names" class="summary-name">standard_aa_names</a> = <code title="['ALA',
'CYS',
'ASP',
'GLU',
'PHE',
'GLY',
'HIS',
'ILE',
..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">CYS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code><code class="variable-ellipsis">...</code></code>
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<a href="Bio.PDB.PSEA-module.html#to_one_letter_code" class="summary-name">to_one_letter_code</a> = <code title="{'2AS': 'D',
'3AH': 'H',
'5HP': 'E',
'ACL': 'R',
'AGM': 'R',
'AIB': 'A',
'ALA': 'A',
'ALM': 'A',
..."><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">2AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">3AH</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">5HP</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ACL</code><code class="variable-ellipsis">...</code></code>
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<h3 class="epydoc">standard_aa_names</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">CYS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">HIS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ILE</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
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<h3 class="epydoc">to_one_letter_code</h3>
<dl class="fields">
</dl>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">2AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">3AH</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">5HP</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ACL</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">AGM</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">AIB</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ALM</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
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