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<h1 class="epydoc">Source Code for <a href="Bio.SeqUtils.ProtParam-module.html">Module Bio.SeqUtils.ProtParam</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright Yair Benita Y.Benita@pharm.uu.nl</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Biopython (http://biopython.org) license applies</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.SeqUtils.ProtParamData=Bio.SeqUtils.ProtParamData-module.html"><a title="Bio.SeqUtils.ProtParamData" class="py-name" href="#" onclick="return doclink('link-0', 'ProtParamData', 'link-0');">ProtParamData</a></tt><tt class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Module Bio.SeqUtils.IsoelectricPoint=Bio.SeqUtils.IsoelectricPoint-module.html,Class Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html"><a title="Bio.SeqUtils.IsoelectricPoint
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint" class="py-name" href="#" onclick="return doclink('link-1', 'IsoelectricPoint', 'link-1');">IsoelectricPoint</a></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio.SeqUtils.ProtParamData" class="py-name" href="#" onclick="return doclink('link-2', 'ProtParamData', 'link-0');">ProtParamData</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Variable Bio.SeqUtils.ProtParamData.kd=Bio.SeqUtils.ProtParamData-module.html#kd"><a title="Bio.SeqUtils.ProtParamData.kd" class="py-name" href="#" onclick="return doclink('link-3', 'kd', 'link-3');">kd</a></tt> <tt class="py-comment"># Added by Iddo to enable the gravy method</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-4');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-5', 'Seq', 'link-5');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-6', 'Seq', 'link-5');">Seq</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-4');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-8" 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-8', 'Alphabet', 'link-8');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-9', 'IUPAC', 'link-9');">IUPAC</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-4');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Package Bio.Data=Bio.Data-module.html"><a title="Bio.Data" class="py-name" href="#" onclick="return doclink('link-11', 'Data', 'link-11');">Data</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Module Bio.Data.IUPACData=Bio.Data.IUPACData-module.html"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-12', 'IUPACData', 'link-12');">IUPACData</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment">#from BioModule import </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="ProteinAnalysis"></a><div id="ProteinAnalysis-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="ProteinAnalysis-toggle" onclick="return toggle('ProteinAnalysis');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html">ProteinAnalysis</a><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ProteinAnalysis-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> This class contains methods for protein analysis. The class init method takes</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> only one argument, the protein sequence as a string and build a sequence</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> object using the Bio.Seq module. This is done just to make sure the sequence</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> is a protein sequence and not anything else.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> methods:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> count_amino_acids:</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> Simply counts the number times an amino acid is repeated in the protein</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> sequence. Returns a dictionary {AminoAcid:Number} and also stores the</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> dictionary in self.amino_acids_content.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> get_amino_acids_percent:</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> The same as count_amino_acids only returns the Number in percentage of entire</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> sequence. Returns a dictionary and stores the dictionary in</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> self.amino_acids_content_percent.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> molecular_weight:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the molecular weight of a protein.</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> aromaticity:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the aromaticity value of a protein according to Lobry, 1994. It is</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> simply the relative frequency of Phe+Trp+Tyr.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> instability_index:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> Implementation of the method of Guruprasad et al. (Protein Engineering</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> 4:155-161,1990). This method tests a protein for stability. Any value above 40</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> means the protein is unstable (=has a short half life). </tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> flexibility:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> Implementation of the flexibility method of Vihinen et al. (Proteins. 1994 Jun;19(2):141-9).</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> isoelectric_point:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> This method uses the module IsoelectricPoint to calculate the pI of a protein.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> secondary_structure_fraction:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> This methods returns a list of the fraction of amino acids which tend to be in Helix, Turn or Sheet.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> Amino acids in helix: V, I, Y, F, W, L.</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> Amino acids in Turn: N, P, G, S.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> Amino acids in sheet: E, M, A, L.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> The list contains 3 values: [Helix, Turn, Sheet].</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> protein_scale(Scale, WindwonSize, Edge):</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> An amino acid scale is defined by a numerical value assigned to each type of</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> amino acid. The most frequently used scales are the hydrophobicity or</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> hydrophilicity scales and the secondary structure conformational parameters</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> scales, but many other scales exist which are based on different chemical and</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> physical properties of the amino acids. You can set several parameters that</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> control the computation of a scale profile, such as the window size and the</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> window edge relative weight value. WindowSize: The window size is the length</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> of the interval to use for the profile computation. For a window size n, we</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> use the i- ( n-1)/2 neighboring residues on each side of residue it compute</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> the score for residue i. The score for residue is the sum of the scale values</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> for these amino acids, optionally weighted according to their position in the</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> window. Edge: The central amino acid of the window always has a weight of 1.</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> By default, the amino acids at the remaining window positions have the same</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> weight, but you can make the residue at the center of the window have a</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> larger weight than the others by setting the edge value for the residues at</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> the beginning and end of the interval to a value between 0 and 1. For</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> instance, for Edge=0.4 and a window size of 5 the weights will be: 0.4, 0.7,</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> 1.0, 0.7, 0.4. The method returns a list of values which can be plotted to</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> view the change along a protein sequence. Many scales exist. Just add your</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> favorites to the ProtParamData modules.</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ProteinAnalysis.__init__"></a><div id="ProteinAnalysis.__init__-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.__init__-toggle" onclick="return toggle('ProteinAnalysis.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ProtSequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.__init__-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ProtSequence</tt><tt class="py-op">.</tt><tt class="py-name">islower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-13', 'sequence', 'link-13');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-14', 'Seq', 'link-5');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">ProtSequence</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-15', 'IUPAC', 'link-9');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Variable Bio.Alphabet.IUPAC.protein=Bio.Alphabet.IUPAC-module.html#protein"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-16', 'protein', 'link-16');">protein</a></tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-17', 'sequence', 'link-13');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-18', 'Seq', 'link-5');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">ProtSequence</tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-19', 'IUPAC', 'link-9');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-20', 'protein', 'link-16');">protein</a></tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-21', 'length', 'link-21');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-22', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
<a name="ProteinAnalysis.count_amino_acids"></a><div id="ProteinAnalysis.count_amino_acids-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.count_amino_acids-toggle" onclick="return toggle('ProteinAnalysis.count_amino_acids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#count_amino_acids">count_amino_acids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.count_amino_acids-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.count_amino_acids-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">ProtDic</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">[</tt> <tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt id="link-23" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-23', 'IUPACData', 'link-12');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Variable Bio.Data.IUPACData.protein_letters=Bio.Data.IUPACData-module.html#protein_letters"><a title="Bio.Data.IUPACData.protein_letters" class="py-name" href="#" onclick="return doclink('link-24', 'protein_letters', 'link-24');">protein_letters</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-25" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-25', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">ProtDic</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-26', 'keys', 'link-26');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">ProtDic</tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-28', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-29', 'count', 'link-29');">count</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-30', 'i', 'link-25');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt> <tt class="py-op">=</tt> <tt class="py-name">ProtDic</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ProtDic</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-string">"""Calculate the amino acid content in percents.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-string"> input is the dictionary from CountAA.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-string"> output is a dictionary with AA as keys."""</tt> </tt>
<a name="ProteinAnalysis.get_amino_acids_percent"></a><div id="ProteinAnalysis.get_amino_acids_percent-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.get_amino_acids_percent-toggle" onclick="return toggle('ProteinAnalysis.get_amino_acids_percent');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#get_amino_acids_percent">get_amino_acids_percent</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.get_amino_acids_percent-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.get_amino_acids_percent-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.SeqUtils.ProtParam.ProteinAnalysis.count_amino_acids()=Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#count_amino_acids"><a title="Bio.SeqUtils.ProtParam.ProteinAnalysis.count_amino_acids" class="py-name" href="#" onclick="return doclink('link-31', 'count_amino_acids', 'link-31');">count_amino_acids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">PercentAA</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-32" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-32', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-33', 'keys', 'link-26');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt><tt class="py-op">[</tt><tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">PercentAA</tt><tt class="py-op">[</tt><tt id="link-35" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-35', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt><tt class="py-op">[</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-36', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-37', 'length', 'link-21');">length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">PercentAA</tt><tt class="py-op">[</tt><tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt> <tt class="py-op">=</tt> <tt class="py-name">PercentAA</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">PercentAA</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-comment"># Calculate MW from Protein sequence</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Calculate MW from Protein sequence</tt> </tt>
<a name="ProteinAnalysis.molecular_weight"></a><div id="ProteinAnalysis.molecular_weight-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.molecular_weight-toggle" onclick="return toggle('ProteinAnalysis.molecular_weight');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#molecular_weight">molecular_weight</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.molecular_weight-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.molecular_weight-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-comment"># make local dictionary for speed</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">MwDict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-comment"># remove a molecule of water from the amino acid weight.</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-40" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-40', 'IUPACData', 'link-12');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Variable Bio.Data.IUPACData.protein_weights=Bio.Data.IUPACData-module.html#protein_weights"><a title="Bio.Data.IUPACData.protein_weights" class="py-name" href="#" onclick="return doclink('link-41', 'protein_weights', 'link-41');">protein_weights</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-42', 'keys', 'link-26');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">MwDict</tt><tt class="py-op">[</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-44', 'IUPACData', 'link-12');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Data.IUPACData.protein_weights" class="py-name" href="#" onclick="return doclink('link-45', 'protein_weights', 'link-41');">protein_weights</a></tt><tt class="py-op">[</tt><tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-46', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-number">18.02</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">MW</tt> <tt class="py-op">=</tt> <tt class="py-number">18.02</tt> <tt class="py-comment"># add just one water molecule for the whole sequence.</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-48', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">MW</tt> <tt class="py-op">+=</tt> <tt class="py-name">MwDict</tt><tt class="py-op">[</tt><tt id="link-49" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-49', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">MW</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-comment"># calculate the aromaticity according to Lobry, 1994.</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Arom=sum of relative frequency of Phe+Trp+Tyr </tt> </tt>
<a name="ProteinAnalysis.aromaticity"></a><div id="ProteinAnalysis.aromaticity-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.aromaticity-toggle" onclick="return toggle('ProteinAnalysis.aromaticity');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#aromaticity">aromaticity</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.aromaticity-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.aromaticity-expanded"><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent()=Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#get_amino_acids_percent"><a title="Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent" class="py-name" href="#" onclick="return doclink('link-50', 'get_amino_acids_percent', 'link-50');">get_amino_acids_percent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">Arom</tt><tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'Y'</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'W'</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'F'</tt><tt class="py-op">]</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">Arom</tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-comment"># a function to calculate the instability index according to:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).</tt> </tt>
<a name="ProteinAnalysis.instability_index"></a><div id="ProteinAnalysis.instability_index-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.instability_index-toggle" onclick="return toggle('ProteinAnalysis.instability_index');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#instability_index">instability_index</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.instability_index-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.instability_index-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment">#make the dictionary local for speed.</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-51" class="py-name" targets="Variable Bio.SeqUtils.ProtParamData.DIWV=Bio.SeqUtils.ProtParamData-module.html#DIWV"><a title="Bio.SeqUtils.ProtParamData.DIWV" class="py-name" href="#" onclick="return doclink('link-51', 'DIWV', 'link-51');">DIWV</a></tt><tt class="py-op">=</tt><tt id="link-52" class="py-name"><a title="Bio.SeqUtils.ProtParamData" class="py-name" href="#" onclick="return doclink('link-52', 'ProtParamData', 'link-0');">ProtParamData</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.SeqUtils.ProtParamData.DIWV" class="py-name" href="#" onclick="return doclink('link-53', 'DIWV', 'link-51');">DIWV</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-54', 'copy', 'link-54');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt id="link-55" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-55', 'score', 'link-55');">score</a></tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-56" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-56', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-57', 'length', 'link-21');">length</a></tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">DiPeptide</tt><tt class="py-op">=</tt><tt id="link-58" class="py-name"><a title="Bio.SeqUtils.ProtParamData.DIWV" class="py-name" href="#" onclick="return doclink('link-58', 'DIWV', 'link-51');">DIWV</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-59', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-60', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-61', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-62', 'i', 'link-25');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</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 id="link-63" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-63', 'score', 'link-55');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">DiPeptide</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-number">10.0</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-64', 'length', 'link-21');">length</a></tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt id="link-65" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-65', 'score', 'link-55');">score</a></tt> </tt>
</div><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-comment"># Calculate the flexibility according to Vihinen, 1994.</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># No argument to change window size because parameters are specific for a window=9. </tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the parameters used are optimized for determining the flexibility.</tt> </tt>
<a name="ProteinAnalysis.flexibility"></a><div id="ProteinAnalysis.flexibility-def"><a name="L153"></a><tt class="py-lineno">153</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.flexibility-toggle" onclick="return toggle('ProteinAnalysis.flexibility');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#flexibility">flexibility</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.flexibility-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.flexibility-expanded"><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt id="link-66" class="py-name" targets="Variable Bio.SeqUtils.ProtParamData.Flex=Bio.SeqUtils.ProtParamData-module.html#Flex"><a title="Bio.SeqUtils.ProtParamData.Flex" class="py-name" href="#" onclick="return doclink('link-66', 'Flex', 'link-66');">Flex</a></tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.SeqUtils.ProtParamData" class="py-name" href="#" onclick="return doclink('link-67', 'ProtParamData', 'link-0');">ProtParamData</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.SeqUtils.ProtParamData.Flex" class="py-name" href="#" onclick="return doclink('link-68', 'Flex', 'link-66');">Flex</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-69', 'copy', 'link-54');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">Window</tt><tt class="py-op">=</tt><tt class="py-number">9</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">Weights</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-number">0.25</tt><tt class="py-op">,</tt><tt class="py-number">0.4375</tt><tt class="py-op">,</tt><tt class="py-number">0.625</tt><tt class="py-op">,</tt><tt class="py-number">0.8125</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">List</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-70" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-70', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-71', 'length', 'link-21');">length</a></tt> <tt class="py-op">-</tt> <tt class="py-name">Window</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">SubSeq</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-72', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-73" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-73', 'i', 'link-25');">i</a></tt><tt class="py-op">:</tt><tt id="link-74" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-74', 'i', 'link-25');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">Window</tt><tt class="py-op">]</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-75', 'score', 'link-55');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">Window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-76', 'score', 'link-55');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="Bio.SeqUtils.ProtParamData.Flex" class="py-name" href="#" onclick="return doclink('link-77', 'Flex', 'link-66');">Flex</a></tt><tt class="py-op">[</tt><tt class="py-name">SubSeq</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt id="link-78" class="py-name"><a title="Bio.SeqUtils.ProtParamData.Flex" class="py-name" href="#" onclick="return doclink('link-78', 'Flex', 'link-66');">Flex</a></tt><tt class="py-op">[</tt><tt class="py-name">SubSeq</tt><tt class="py-op">[</tt><tt class="py-name">Window</tt><tt class="py-op">-</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">Weights</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-79', 'score', 'link-55');">score</a></tt> <tt class="py-op">+=</tt> <tt id="link-80" class="py-name"><a title="Bio.SeqUtils.ProtParamData.Flex" class="py-name" href="#" onclick="return doclink('link-80', 'Flex', 'link-66');">Flex</a></tt><tt class="py-op">[</tt><tt class="py-name">SubSeq</tt><tt class="py-op">[</tt><tt class="py-name">Window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">List</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-81', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-82', 'score', 'link-55');">score</a></tt><tt class="py-op">/</tt><tt class="py-number">5.25</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">List</tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-comment"># calculate the gravy according to kyte and doolittle.</tt> </tt>
<a name="ProteinAnalysis.gravy"></a><div id="ProteinAnalysis.gravy-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.gravy-toggle" onclick="return toggle('ProteinAnalysis.gravy');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#gravy">gravy</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.gravy-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.gravy-expanded"><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">ProtGravy</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-83" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-83', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-84', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">:</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">ProtGravy</tt> <tt class="py-op">+=</tt> <tt id="link-85" class="py-name"><a title="Bio.SeqUtils.ProtParamData.kd" class="py-name" href="#" onclick="return doclink('link-85', 'kd', 'link-3');">kd</a></tt><tt class="py-op">[</tt><tt id="link-86" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-86', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ProtGravy</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-87', 'length', 'link-21');">length</a></tt> </tt>
</div><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment"># this method is used to make a list of relative weight of the</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># window edges compared to the window center. The weights are linear.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># it actually generates half a list. For a window of size 9 and edge 0.4</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># you get a list of [0.4, 0.55, 0.7, 0.85]. </tt> </tt>
<a name="ProteinAnalysis._weight_list"></a><div id="ProteinAnalysis._weight_list-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="ProteinAnalysis._weight_list-toggle" onclick="return toggle('ProteinAnalysis._weight_list');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#_weight_list">_weight_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">window</tt><tt class="py-op">,</tt> <tt class="py-param">edge</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis._weight_list-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis._weight_list-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">unit</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">-</tt><tt class="py-name">edge</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">window</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">2</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt id="link-88" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-88', 'list', 'link-88');">list</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0.0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-89" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-89', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt id="link-90" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-90', 'list', 'link-88');">list</a></tt><tt class="py-op">[</tt><tt id="link-91" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-91', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">edge</tt> <tt class="py-op">+</tt> <tt class="py-name">unit</tt> <tt class="py-op">*</tt> <tt id="link-92" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-92', 'i', 'link-25');">i</a></tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-93" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-93', 'list', 'link-88');">list</a></tt> </tt>
</div><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment"># this method allows you to compute and represent the profile produced</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># by any amino acid scale on a selected protein.</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Similar to expasy's ProtScale: http://www.expasy.org/cgi-bin/protscale.pl</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># The weight list returns only one tail. If the list should be [0.4,0.7,1.0,0.7,0.4]</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># what you actually get from _weights_list is [0.4,0.7]. The correct calculation is done</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in the loop.</tt> </tt>
<a name="ProteinAnalysis.protein_scale"></a><div id="ProteinAnalysis.protein_scale-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.protein_scale-toggle" onclick="return toggle('ProteinAnalysis.protein_scale');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#protein_scale">protein_scale</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ParamDict</tt><tt class="py-op">,</tt> <tt class="py-param">Window</tt><tt class="py-op">,</tt> <tt class="py-param">Edge</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.protein_scale-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.protein_scale-expanded"><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-comment"># generate the weights</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">weight</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method Bio.SeqUtils.ProtParam.ProteinAnalysis._weight_list()=Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#_weight_list"><a title="Bio.SeqUtils.ProtParam.ProteinAnalysis._weight_list" class="py-name" href="#" onclick="return doclink('link-94', '_weight_list', 'link-94');">_weight_list</a></tt><tt class="py-op">(</tt><tt class="py-name">Window</tt><tt class="py-op">,</tt><tt class="py-name">Edge</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-95" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-95', 'list', 'link-88');">list</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-comment"># the score in each Window is divided by the sum of weights</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sum_of_weights</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-96" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-96', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">weight</tt><tt class="py-op">:</tt> <tt class="py-name">sum_of_weights</tt> <tt class="py-op">+=</tt> <tt id="link-97" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-97', 'i', 'link-25');">i</a></tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-comment"># since the weight list is one sided:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sum_of_weights</tt> <tt class="py-op">=</tt> <tt class="py-name">sum_of_weights</tt><tt class="py-op">*</tt><tt class="py-number">2</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-98" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-98', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-99', 'length', 'link-21');">length</a></tt><tt class="py-op">-</tt><tt class="py-name">Window</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">subsequence</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-100', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-101" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-101', 'i', 'link-25');">i</a></tt><tt class="py-op">:</tt><tt id="link-102" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-102', 'i', 'link-25');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">Window</tt><tt class="py-op">]</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt id="link-103" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-103', 'score', 'link-55');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">Window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-comment"># walk from the outside of the Window towards the middle.</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Iddo: try/except clauses added to avoid raising an exception on a non-standad amino acid</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-104', 'score', 'link-55');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">weight</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">ParamDict</tt><tt class="py-op">[</tt><tt class="py-name">subsequence</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">weight</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">ParamDict</tt><tt class="py-op">[</tt><tt class="py-name">subsequence</tt><tt class="py-op">[</tt><tt class="py-name">Window</tt><tt class="py-op">-</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-105', 'write', 'link-105');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'warning: %s or %s is not a standard amino acid.\n'</tt> <tt class="py-op">%</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">subsequence</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">subsequence</tt><tt class="py-op">[</tt><tt class="py-name">Window</tt><tt class="py-op">-</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-comment"># Now add the middle value, which always has a weight of 1.</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">subsequence</tt><tt class="py-op">[</tt><tt class="py-name">Window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ParamDict</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt id="link-106" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-106', 'score', 'link-55');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">ParamDict</tt><tt class="py-op">[</tt><tt class="py-name">subsequence</tt><tt class="py-op">[</tt><tt class="py-name">Window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-107', 'write', 'link-105');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'warning: %s is not a standard amino acid.\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">subsequence</tt><tt class="py-op">[</tt><tt class="py-name">Window</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt id="link-108" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-108', 'list', 'link-88');">list</a></tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-109', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt id="link-110" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-110', 'score', 'link-55');">score</a></tt><tt class="py-op">/</tt><tt class="py-name">sum_of_weights</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-111" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-111', 'list', 'link-88');">list</a></tt> </tt>
</div><a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-comment"># calculate the isoelectric point. </tt> </tt>
<a name="ProteinAnalysis.isoelectric_point"></a><div id="ProteinAnalysis.isoelectric_point-def"><a name="L224"></a><tt class="py-lineno">224</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.isoelectric_point-toggle" onclick="return toggle('ProteinAnalysis.isoelectric_point');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#isoelectric_point">isoelectric_point</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.isoelectric_point-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.isoelectric_point-expanded"><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt><tt class="py-op">:</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.SeqUtils.ProtParam.ProteinAnalysis.count_amino_acids" class="py-name" href="#" onclick="return doclink('link-112', 'count_amino_acids', 'link-31');">count_amino_acids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">X</tt> <tt class="py-op">=</tt> <tt id="link-113" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint" class="py-name" href="#" onclick="return doclink('link-113', 'IsoelectricPoint', 'link-1');">IsoelectricPoint</a></tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint" class="py-name" href="#" onclick="return doclink('link-114', 'IsoelectricPoint', 'link-1');">IsoelectricPoint</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-115', 'sequence', 'link-13');">sequence</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_content</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">X</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Variable Bio.Affy.CelFile.pi=Bio.Affy.CelFile-module.html#pi,Variable Bio.LogisticRegression.pi=Bio.LogisticRegression-module.html#pi,Variable Bio.MarkovModel.pi=Bio.MarkovModel-module.html#pi,Variable Bio.MaxEntropy.pi=Bio.MaxEntropy-module.html#pi,Variable Bio.NaiveBayes.pi=Bio.NaiveBayes-module.html#pi,Variable Bio.PDB.Vector'.pi=Bio.PDB.Vector%27-module.html#pi,Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#pi,Variable Bio.Statistics.lowess.pi=Bio.Statistics.lowess-module.html#pi,Variable Bio.distance.pi=Bio.distance-module.html#pi,Variable Bio.kNN.pi=Bio.kNN-module.html#pi"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-116', 'pi', 'link-116');">pi</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-comment"># calculate fraction of helix, turn and sheet</tt> </tt>
<a name="ProteinAnalysis.secondary_structure_fraction"></a><div id="ProteinAnalysis.secondary_structure_fraction-def"><a name="L231"></a><tt class="py-lineno">231</tt> <a class="py-toggle" href="#" id="ProteinAnalysis.secondary_structure_fraction-toggle" onclick="return toggle('ProteinAnalysis.secondary_structure_fraction');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#secondary_structure_fraction">secondary_structure_fraction</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinAnalysis.secondary_structure_fraction-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="ProteinAnalysis.secondary_structure_fraction-expanded"><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.SeqUtils.ProtParam.ProteinAnalysis.get_amino_acids_percent" class="py-name" href="#" onclick="return doclink('link-117', 'get_amino_acids_percent', 'link-50');">get_amino_acids_percent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">Helix</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'V'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'I'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'Y'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'F'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'W'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'L'</tt><tt class="py-op">]</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">Turn</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'N'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'P'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'G'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'S'</tt><tt class="py-op">]</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">Sheet</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'E'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'M'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'A'</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">amino_acids_percent</tt><tt class="py-op">[</tt><tt class="py-string">'L'</tt><tt class="py-op">]</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">Helix</tt><tt class="py-op">,</tt> <tt class="py-name">Turn</tt><tt class="py-op">,</tt> <tt class="py-name">Sheet</tt> </tt>
</div></div><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-comment">#---------------------------------------------------------#</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-string">"""</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-string">X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-string">print X.count_amino_acids()</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-string">print X.get_amino_acids_percent()</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-string">print X.molecular_weight()</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-string">print X.aromaticity()</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-string">print X.instability_index()</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-string">print X.flexibility()</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-string">print X.pi()</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-string">print X.secondary_structure_fraction()</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-string">print X.protein_scale(ProtParamData.kd, 9, 0.4)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt><script type="text/javascript">
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