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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Alphabet-module.html">Package Alphabet</a> ::
Module Reduced
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<h1 class="epydoc">Source Code for <a href="Bio.Alphabet.Reduced-module.html">Module Bio.Alphabet.Reduced</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-1');">Alphabet</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-string">Reduced (redundant or simplified) alphabets are used to represent protein sequences using an</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-string">alternative alphabet which lumps together several amino-acids into one letter, based</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-string">on physico-chemical traits. For example, all the aliphatics (I,L,V) are usually</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-string">quite interchangeable, so many sequence studies group them into one letter</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-string">Examples of reduced alphabets are available in:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-string">http://viscose.ifg.uni-muenster.de/html/alphabets.html</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-string">Bio.utils.reduce_sequence is used to take a Protein alphabet, and reduce it using one of</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-string">the tables here, or a user-defined table.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"># The Murphy tables are from here:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Murphy L.R., Wallqvist A, Levy RM. (2000) Simplified amino acid alphabets for protein</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># fold recognition and implications for folding. Protein Eng. 13(3):149-152</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_15_tab=Bio.Alphabet.Reduced-module.html#murphy_15_tab"><a title="Bio.Alphabet.Reduced.murphy_15_tab" class="py-name" href="#" onclick="return doclink('link-2', 'murphy_15_tab', 'link-2');">murphy_15_tab</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"L"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-string">"V"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-string">"I"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-string">"M"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-string">"C"</tt><tt class="py-op">:</tt> <tt class="py-string">"C"</tt><tt class="py-op">,</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-string">"A"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-string">"G"</tt><tt class="py-op">:</tt> <tt class="py-string">"G"</tt><tt class="py-op">,</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-string">"S"</tt><tt class="py-op">:</tt> <tt class="py-string">"S"</tt><tt class="py-op">,</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-string">"T"</tt><tt class="py-op">:</tt> <tt class="py-string">"T"</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-string">"P"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-string">"F"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-string">"W"</tt><tt class="py-op">:</tt> <tt class="py-string">"W"</tt><tt class="py-op">,</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-string">"E"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-string">"D"</tt><tt class="py-op">:</tt> <tt class="py-string">"D"</tt><tt class="py-op">,</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-string">"N"</tt><tt class="py-op">:</tt> <tt class="py-string">"N"</tt><tt class="py-op">,</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-string">"Q"</tt><tt class="py-op">:</tt> <tt class="py-string">"Q"</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-string">"K"</tt><tt class="py-op">:</tt> <tt class="py-string">"K"</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-string">"R"</tt><tt class="py-op">:</tt> <tt class="py-string">"K"</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-string">"H"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">}</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
<a name="Murphy15"></a><div id="Murphy15-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="Murphy15-toggle" onclick="return toggle('Murphy15');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.Reduced.Murphy15-class.html">Murphy15</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Murphy15-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Murphy15-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt id="link-3" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-3', 'letters', 'link-3');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"LCAGSTPFWEDNQKH"</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-4', 'size', 'link-4');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-number">15</tt> </tt>
</div><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_15=Bio.Alphabet.Reduced-module.html#murphy_15"><a title="Bio.Alphabet.Reduced.murphy_15" class="py-name" href="#" onclick="return doclink('link-5', 'murphy_15', 'link-5');">murphy_15</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name" targets="Class Bio.Alphabet.Reduced.Murphy15=Bio.Alphabet.Reduced.Murphy15-class.html"><a title="Bio.Alphabet.Reduced.Murphy15" class="py-name" href="#" onclick="return doclink('link-6', 'Murphy15', 'link-6');">Murphy15</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_10_tab=Bio.Alphabet.Reduced-module.html#murphy_10_tab"><a title="Bio.Alphabet.Reduced.murphy_10_tab" class="py-name" href="#" onclick="return doclink('link-7', 'murphy_10_tab', 'link-7');">murphy_10_tab</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"L"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-string">"V"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-string">"I"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-string">"M"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-string">"C"</tt><tt class="py-op">:</tt> <tt class="py-string">"C"</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-string">"A"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-string">"G"</tt><tt class="py-op">:</tt> <tt class="py-string">"G"</tt><tt class="py-op">,</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-string">"S"</tt><tt class="py-op">:</tt> <tt class="py-string">"S"</tt><tt class="py-op">,</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-string">"T"</tt><tt class="py-op">:</tt> <tt class="py-string">"S"</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-string">"P"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-string">"F"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-string">"W"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-string">"E"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-string">"D"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-string">"N"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-string">"Q"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-string">"K"</tt><tt class="py-op">:</tt> <tt class="py-string">"K"</tt><tt class="py-op">,</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-string">"R"</tt><tt class="py-op">:</tt> <tt class="py-string">"K"</tt><tt class="py-op">,</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-string">"H"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">}</tt> </tt>
<a name="Murphy10"></a><div id="Murphy10-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="Murphy10-toggle" onclick="return toggle('Murphy10');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.Reduced.Murphy10-class.html">Murphy10</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Murphy10-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Murphy10-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-8', 'letters', 'link-3');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"LCAGSPFEKH"</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-9', 'size', 'link-4');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-number">10</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt id="link-10" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_10=Bio.Alphabet.Reduced-module.html#murphy_10"><a title="Bio.Alphabet.Reduced.murphy_10" class="py-name" href="#" onclick="return doclink('link-10', 'murphy_10', 'link-10');">murphy_10</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Class Bio.Alphabet.Reduced.Murphy10=Bio.Alphabet.Reduced.Murphy10-class.html"><a title="Bio.Alphabet.Reduced.Murphy10" class="py-name" href="#" onclick="return doclink('link-11', 'Murphy10', 'link-11');">Murphy10</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt id="link-12" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_8_tab=Bio.Alphabet.Reduced-module.html#murphy_8_tab"><a title="Bio.Alphabet.Reduced.murphy_8_tab" class="py-name" href="#" onclick="return doclink('link-12', 'murphy_8_tab', 'link-12');">murphy_8_tab</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"L"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-string">"V"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-string">"I"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-string">"M"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-string">"C"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-string">"A"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-string">"G"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-string">"S"</tt><tt class="py-op">:</tt> <tt class="py-string">"S"</tt><tt class="py-op">,</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-string">"T"</tt><tt class="py-op">:</tt> <tt class="py-string">"S"</tt><tt class="py-op">,</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-string">"P"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-string">"F"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-string">"W"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-string">"E"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-string">"D"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-string">"N"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-string">"Q"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-string">"K"</tt><tt class="py-op">:</tt> <tt class="py-string">"K"</tt><tt class="py-op">,</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-string">"R"</tt><tt class="py-op">:</tt> <tt class="py-string">"K"</tt><tt class="py-op">,</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-string">"H"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">}</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="Murphy8"></a><div id="Murphy8-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="Murphy8-toggle" onclick="return toggle('Murphy8');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.Reduced.Murphy8-class.html">Murphy8</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Murphy8-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Murphy8-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-13', 'letters', 'link-3');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"LASPFEKH"</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-14', 'size', 'link-4');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-number">8</tt> </tt>
</div><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt id="link-15" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_8=Bio.Alphabet.Reduced-module.html#murphy_8"><a title="Bio.Alphabet.Reduced.murphy_8" class="py-name" href="#" onclick="return doclink('link-15', 'murphy_8', 'link-15');">murphy_8</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Class Bio.Alphabet.Reduced.Murphy8=Bio.Alphabet.Reduced.Murphy8-class.html"><a title="Bio.Alphabet.Reduced.Murphy8" class="py-name" href="#" onclick="return doclink('link-16', 'Murphy8', 'link-16');">Murphy8</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt id="link-17" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_4_tab=Bio.Alphabet.Reduced-module.html#murphy_4_tab"><a title="Bio.Alphabet.Reduced.murphy_4_tab" class="py-name" href="#" onclick="return doclink('link-17', 'murphy_4_tab', 'link-17');">murphy_4_tab</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"L"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-string">"V"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-string">"I"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-string">"M"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-string">"C"</tt><tt class="py-op">:</tt> <tt class="py-string">"L"</tt><tt class="py-op">,</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-string">"A"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-string">"G"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-string">"S"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-string">"T"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-string">"P"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-string">"F"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-string">"W"</tt><tt class="py-op">:</tt> <tt class="py-string">"F"</tt><tt class="py-op">,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-string">"E"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-string">"D"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-string">"N"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-string">"Q"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-string">"K"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-string">"R"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">,</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-string">"H"</tt><tt class="py-op">:</tt> <tt class="py-string">"E"</tt><tt class="py-op">}</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="Murphy4"></a><div id="Murphy4-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="Murphy4-toggle" onclick="return toggle('Murphy4');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.Reduced.Murphy4-class.html">Murphy4</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Murphy4-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Murphy4-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt id="link-18" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-18', 'letters', 'link-3');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"LAFE"</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-19', 'size', 'link-4');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-number">4</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt id="link-20" class="py-name" targets="Variable Bio.Alphabet.Reduced.murphy_4=Bio.Alphabet.Reduced-module.html#murphy_4"><a title="Bio.Alphabet.Reduced.murphy_4" class="py-name" href="#" onclick="return doclink('link-20', 'murphy_4', 'link-20');">murphy_4</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name" targets="Class Bio.Alphabet.Reduced.Murphy4=Bio.Alphabet.Reduced.Murphy4-class.html"><a title="Bio.Alphabet.Reduced.Murphy4" class="py-name" href="#" onclick="return doclink('link-21', 'Murphy4', 'link-21');">Murphy4</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt id="link-22" class="py-name" targets="Variable Bio.Alphabet.Reduced.hp_model_tab=Bio.Alphabet.Reduced-module.html#hp_model_tab"><a title="Bio.Alphabet.Reduced.hp_model_tab" class="py-name" href="#" onclick="return doclink('link-22', 'hp_model_tab', 'link-22');">hp_model_tab</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"A"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Hydrophilic</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-string">"G"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-string">"T"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-string">"S"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-string">"N"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-string">"Q"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-string">"D"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-string">"E"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-string">"H"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-string">"R"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-string">"K"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-string">"P"</tt><tt class="py-op">:</tt> <tt class="py-string">"P"</tt><tt class="py-op">,</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-string">"C"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Hydrophobic</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-string">"M"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">,</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-string">"F"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">,</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-string">"I"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">,</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-string">"L"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">,</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-string">"V"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">,</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-string">"W"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">,</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-string">"H"</tt><tt class="py-op">}</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="HPModel"></a><div id="HPModel-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="HPModel-toggle" onclick="return toggle('HPModel');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.Reduced.HPModel-class.html">HPModel</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="HPModel-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HPModel-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-23', 'letters', 'link-3');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"HP"</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-24', 'size', 'link-4');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt> </tt>
</div><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt id="link-25" class="py-name" targets="Variable Bio.Alphabet.Reduced.hp_model=Bio.Alphabet.Reduced-module.html#hp_model"><a title="Bio.Alphabet.Reduced.hp_model" class="py-name" href="#" onclick="return doclink('link-25', 'hp_model', 'link-25');">hp_model</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name" targets="Class Bio.Alphabet.Reduced.HPModel=Bio.Alphabet.Reduced.HPModel-class.html"><a title="Bio.Alphabet.Reduced.HPModel" class="py-name" href="#" onclick="return doclink('link-26', 'HPModel', 'link-26');">HPModel</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt id="link-27" class="py-name" targets="Variable Bio.Alphabet.Reduced.pc_5_table=Bio.Alphabet.Reduced-module.html#pc_5_table"><a title="Bio.Alphabet.Reduced.pc_5_table" class="py-name" href="#" onclick="return doclink('link-27', 'pc_5_table', 'link-27');">pc_5_table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"I"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Aliphatic</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-string">"V"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-string">"L"</tt><tt class="py-op">:</tt> <tt class="py-string">"A"</tt><tt class="py-op">,</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-string">"F"</tt><tt class="py-op">:</tt> <tt class="py-string">"R"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Aromatic</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-string">"Y"</tt><tt class="py-op">:</tt> <tt class="py-string">"R"</tt><tt class="py-op">,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-string">"W"</tt><tt class="py-op">:</tt> <tt class="py-string">"R"</tt><tt class="py-op">,</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-string">"H"</tt><tt class="py-op">:</tt> <tt class="py-string">"R"</tt><tt class="py-op">,</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-string">"K"</tt><tt class="py-op">:</tt> <tt class="py-string">"C"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Charged</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-string">"R"</tt><tt class="py-op">:</tt> <tt class="py-string">"C"</tt><tt class="py-op">,</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-string">"D"</tt><tt class="py-op">:</tt> <tt class="py-string">"C"</tt><tt class="py-op">,</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-string">"E"</tt><tt class="py-op">:</tt> <tt class="py-string">"C"</tt><tt class="py-op">,</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-string">"G"</tt><tt class="py-op">:</tt> <tt class="py-string">"T"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Tiny</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-string">"A"</tt><tt class="py-op">:</tt> <tt class="py-string">"T"</tt><tt class="py-op">,</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-string">"C"</tt><tt class="py-op">:</tt> <tt class="py-string">"T"</tt><tt class="py-op">,</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-string">"S"</tt><tt class="py-op">:</tt> <tt class="py-string">"T"</tt><tt class="py-op">,</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-string">"T"</tt><tt class="py-op">:</tt> <tt class="py-string">"D"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Diverse</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-string">"M"</tt><tt class="py-op">:</tt> <tt class="py-string">"D"</tt><tt class="py-op">,</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-string">"Q"</tt><tt class="py-op">:</tt> <tt class="py-string">"D"</tt><tt class="py-op">,</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-string">"N"</tt><tt class="py-op">:</tt> <tt class="py-string">"D"</tt><tt class="py-op">,</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-string">"P"</tt><tt class="py-op">:</tt> <tt class="py-string">"D"</tt><tt class="py-op">}</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="PC5"></a><div id="PC5-def"><a name="L169"></a><tt class="py-lineno">169</tt> <a class="py-toggle" href="#" id="PC5-toggle" onclick="return toggle('PC5');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.Reduced.PC5-class.html">PC5</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PC5-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PC5-expanded"><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-28', 'letters', 'link-3');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ARCTD"</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt id="link-29" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-29', 'size', 'link-4');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt id="link-30" class="py-name"><a title="Bio.Alphabet.Reduced.hp_model" class="py-name" href="#" onclick="return doclink('link-30', 'hp_model', 'link-25');">hp_model</a></tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.Alphabet.Reduced.HPModel" class="py-name" href="#" onclick="return doclink('link-31', 'HPModel', 'link-26');">HPModel</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt><script type="text/javascript">
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