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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqUtils-module.html">Package SeqUtils</a> ::
Module IsoelectricPoint
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<h1 class="epydoc">Source Code for <a href="Bio.SeqUtils.IsoelectricPoint-module.html">Module Bio.SeqUtils.IsoelectricPoint</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-docstring">"""Calculate isoelectric points of polypeptides using methods of Bjellqvist.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">pK values and the methos are taken from:</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">J.-Ch., Frutiger, S. & Hochstrasser, D.F.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">The focusing positions of polypeptides in immobilized pH gradients can be predicted</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031. </tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">* Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">Reference points for comparisons of two-dimensional maps of proteins from</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">different human cell types defined in a pH scale where isoelectric points correlate</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">with polypeptide compositions. Electrophoresis 1994, 15, 529-539.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">I designed the algorithm according to a note by David L. Tabb, available at:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf</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">"""</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.SeqUtils.IsoelectricPoint.positive_pKs=Bio.SeqUtils.IsoelectricPoint-module.html#positive_pKs"><a title="Bio.SeqUtils.IsoelectricPoint.positive_pKs" class="py-name" href="#" onclick="return doclink('link-0', 'positive_pKs', 'link-0');">positive_pKs</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-string">'Nterm'</tt><tt class="py-op">:</tt> <tt class="py-number">7.5</tt><tt class="py-op">,</tt> <tt class="py-string">'K'</tt><tt class="py-op">:</tt> <tt class="py-number">10.0</tt><tt class="py-op">,</tt> <tt class="py-string">'R'</tt><tt class="py-op">:</tt> <tt class="py-number">12.0</tt><tt class="py-op">,</tt> <tt class="py-string">'H'</tt><tt class="py-op">:</tt><tt class="py-number">5.98</tt> <tt class="py-op">}</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable Bio.SeqUtils.IsoelectricPoint.negative_pKs=Bio.SeqUtils.IsoelectricPoint-module.html#negative_pKs"><a title="Bio.SeqUtils.IsoelectricPoint.negative_pKs" class="py-name" href="#" onclick="return doclink('link-1', 'negative_pKs', 'link-1');">negative_pKs</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-string">'Cterm'</tt><tt class="py-op">:</tt> <tt class="py-number">3.55</tt><tt class="py-op">,</tt> <tt class="py-string">'D'</tt><tt class="py-op">:</tt> <tt class="py-number">4.05</tt><tt class="py-op">,</tt> <tt class="py-string">'E'</tt><tt class="py-op">:</tt> <tt class="py-number">4.45</tt><tt class="py-op">,</tt> <tt class="py-string">'C'</tt><tt class="py-op">:</tt><tt class="py-number">9.0</tt><tt class="py-op">,</tt> <tt class="py-string">'Y'</tt><tt class="py-op">:</tt><tt class="py-number">10.0</tt> <tt class="py-op">}</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Bio.SeqUtils.IsoelectricPoint.pKcterminal=Bio.SeqUtils.IsoelectricPoint-module.html#pKcterminal"><a title="Bio.SeqUtils.IsoelectricPoint.pKcterminal" class="py-name" href="#" onclick="return doclink('link-2', 'pKcterminal', 'link-2');">pKcterminal</a></tt><tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'D'</tt><tt class="py-op">:</tt><tt class="py-number">4.55</tt><tt class="py-op">,</tt> <tt class="py-string">'E'</tt><tt class="py-op">:</tt><tt class="py-number">4.75</tt><tt class="py-op">}</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.SeqUtils.IsoelectricPoint.pKnterminal=Bio.SeqUtils.IsoelectricPoint-module.html#pKnterminal"><a title="Bio.SeqUtils.IsoelectricPoint.pKnterminal" class="py-name" href="#" onclick="return doclink('link-3', 'pKnterminal', 'link-3');">pKnterminal</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'A'</tt><tt class="py-op">:</tt><tt class="py-number">7.59</tt><tt class="py-op">,</tt> <tt class="py-string">'M'</tt><tt class="py-op">:</tt><tt class="py-number">7.0</tt><tt class="py-op">,</tt> <tt class="py-string">'S'</tt><tt class="py-op">:</tt><tt class="py-number">6.93</tt><tt class="py-op">,</tt> <tt class="py-string">'P'</tt><tt class="py-op">:</tt><tt class="py-number">8.36</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">:</tt><tt class="py-number">6.82</tt><tt class="py-op">,</tt> <tt class="py-string">'V'</tt><tt class="py-op">:</tt><tt class="py-number">7.44</tt><tt class="py-op">,</tt> <tt class="py-string">'E'</tt><tt class="py-op">:</tt><tt class="py-number">7.7</tt><tt class="py-op">}</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable Bio.SeqUtils.IsoelectricPoint.charged_aas=Bio.SeqUtils.IsoelectricPoint-module.html#charged_aas"><a title="Bio.SeqUtils.IsoelectricPoint.charged_aas" class="py-name" href="#" onclick="return doclink('link-4', 'charged_aas', 'link-4');">charged_aas</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'Y'</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"># access this module through ProtParam.ProteinAnalysis class.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># first make a ProteinAnalysis object and then call its isoelectric_point method.</tt> </tt>
<a name="IsoelectricPoint"></a><div id="IsoelectricPoint-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="IsoelectricPoint-toggle" onclick="return toggle('IsoelectricPoint');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html">IsoelectricPoint</a><tt class="py-op">:</tt> </tt>
</div><div id="IsoelectricPoint-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IsoelectricPoint-expanded"><a name="IsoelectricPoint.__init__"></a><div id="IsoelectricPoint.__init__-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="IsoelectricPoint.__init__-toggle" onclick="return toggle('IsoelectricPoint.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-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">ProteinSequence</tt><tt class="py-op">,</tt> <tt class="py-param">AminoAcidsContent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IsoelectricPoint.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IsoelectricPoint.__init__-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'sequence', 'link-5');">sequence</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ProteinSequence</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">charged_aas_content</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint._select_charged()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#_select_charged"><a title="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint._select_charged" class="py-name" href="#" onclick="return doclink('link-6', '_select_charged', 'link-6');">_select_charged</a></tt><tt class="py-op">(</tt><tt class="py-name">AminoAcidsContent</tt><tt class="py-op">)</tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-comment"># This function creates a dictionary with the contents of each charged aa, </tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># plus Cterm and Nterm.</tt> </tt>
<a name="IsoelectricPoint._select_charged"></a><div id="IsoelectricPoint._select_charged-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="IsoelectricPoint._select_charged-toggle" onclick="return toggle('IsoelectricPoint._select_charged');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#_select_charged">_select_charged</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">AminoAcidsContent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IsoelectricPoint._select_charged-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IsoelectricPoint._select_charged-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">charged</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">aa</tt> <tt class="py-keyword">in</tt> <tt id="link-7" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.charged_aas" class="py-name" href="#" onclick="return doclink('link-7', 'charged_aas', 'link-4');">charged_aas</a></tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">charged</tt><tt class="py-op">[</tt><tt class="py-name">aa</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">AminoAcidsContent</tt><tt class="py-op">[</tt><tt class="py-name">aa</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">charged</tt><tt class="py-op">[</tt><tt class="py-string">'Nterm'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1.0</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">charged</tt><tt class="py-op">[</tt><tt class="py-string">'Cterm'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1.0</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">charged</tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-comment">#This function calculates the total charge of the protein at a given pH. </tt> </tt>
<a name="IsoelectricPoint._chargeR"></a><div id="IsoelectricPoint._chargeR-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="IsoelectricPoint._chargeR-toggle" onclick="return toggle('IsoelectricPoint._chargeR');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#_chargeR">_chargeR</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">pH</tt><tt class="py-op">,</tt> <tt class="py-param">pos_pKs</tt><tt class="py-op">,</tt> <tt class="py-param">neg_pKs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IsoelectricPoint._chargeR-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="IsoelectricPoint._chargeR-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">PositiveCharge</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">aa</tt><tt class="py-op">,</tt> <tt class="py-name">pK</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pos_pKs</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">CR</tt> <tt class="py-op">=</tt> <tt class="py-number">10</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">pK</tt><tt class="py-op">-</tt><tt class="py-name">pH</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">partial_charge</tt> <tt class="py-op">=</tt> <tt class="py-name">CR</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">CR</tt><tt class="py-op">+</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">PositiveCharge</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">charged_aas_content</tt><tt class="py-op">[</tt><tt class="py-name">aa</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">partial_charge</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">NegativeCharge</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">aa</tt><tt class="py-op">,</tt> <tt class="py-name">pK</tt> <tt class="py-keyword">in</tt> <tt class="py-name">neg_pKs</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">CR</tt> <tt class="py-op">=</tt> <tt class="py-number">10</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">pH</tt><tt class="py-op">-</tt><tt class="py-name">pK</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">partial_charge</tt> <tt class="py-op">=</tt> <tt class="py-name">CR</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">CR</tt><tt class="py-op">+</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">NegativeCharge</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">charged_aas_content</tt><tt class="py-op">[</tt><tt class="py-name">aa</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">partial_charge</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">PositiveCharge</tt> <tt class="py-op">-</tt> <tt class="py-name">NegativeCharge</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-comment"># This is the action function, it tries different pH until the charge of the protein is 0 (or close).</tt> </tt>
<a name="IsoelectricPoint.pi"></a><div id="IsoelectricPoint.pi-def"><a name="L63"></a><tt class="py-lineno"> 63</tt> <a class="py-toggle" href="#" id="IsoelectricPoint.pi-toggle" onclick="return toggle('IsoelectricPoint.pi');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#pi">pi</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">pos_pKs</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.positive_pKs" class="py-name" href="#" onclick="return doclink('link-8', 'positive_pKs', 'link-0');">positive_pKs</a></tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">neg_pKs</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.negative_pKs" class="py-name" href="#" onclick="return doclink('link-9', 'negative_pKs', 'link-1');">negative_pKs</a></tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">nterm</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'sequence', 'link-5');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">cterm</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'sequence', 'link-5');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nterm</tt> <tt class="py-keyword">in</tt> <tt id="link-12" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.pKnterminal" class="py-name" href="#" onclick="return doclink('link-12', 'pKnterminal', 'link-3');">pKnterminal</a></tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">pos_pKs</tt><tt class="py-op">[</tt><tt class="py-string">'Nterm'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.pKnterminal" class="py-name" href="#" onclick="return doclink('link-14', 'pKnterminal', 'link-3');">pKnterminal</a></tt><tt class="py-op">[</tt><tt class="py-name">nterm</tt><tt class="py-op">]</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cterm</tt> <tt class="py-keyword">in</tt> <tt id="link-15" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.pKcterminal" class="py-name" href="#" onclick="return doclink('link-15', 'pKcterminal', 'link-2');">pKcterminal</a></tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">neg_pKs</tt><tt class="py-op">[</tt><tt class="py-string">'Cterm'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.pKcterminal" class="py-name" href="#" onclick="return doclink('link-17', 'pKcterminal', 'link-2');">pKcterminal</a></tt><tt class="py-op">[</tt><tt class="py-name">cterm</tt><tt class="py-op">]</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># Bracket between pH1 and pH2</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pH</tt> <tt class="py-op">=</tt> <tt class="py-number">7.0</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">Charge</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint._chargeR()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#_chargeR"><a title="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint._chargeR" class="py-name" href="#" onclick="return doclink('link-18', '_chargeR', 'link-18');">_chargeR</a></tt><tt class="py-op">(</tt><tt class="py-name">pH</tt><tt class="py-op">,</tt> <tt class="py-name">pos_pKs</tt><tt class="py-op">,</tt> <tt class="py-name">neg_pKs</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">Charge</tt> <tt class="py-op">></tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">pH1</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">Charge1</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">Charge1</tt> <tt class="py-op">></tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">pH</tt> <tt class="py-op">=</tt> <tt class="py-name">pH1</tt> <tt class="py-op">+</tt> <tt class="py-number">1.0</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">Charge</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint._chargeR" class="py-name" href="#" onclick="return doclink('link-19', '_chargeR', 'link-18');">_chargeR</a></tt><tt class="py-op">(</tt><tt class="py-name">pH</tt><tt class="py-op">,</tt> <tt class="py-name">pos_pKs</tt><tt class="py-op">,</tt> <tt class="py-name">neg_pKs</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">Charge</tt> <tt class="py-op">></tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">pH1</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">Charge1</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">pH2</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">Charge2</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">else</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">pH2</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">Charge2</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">Charge2</tt> <tt class="py-op"><</tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">pH</tt> <tt class="py-op">=</tt> <tt class="py-name">pH2</tt> <tt class="py-op">-</tt> <tt class="py-number">1.0</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">Charge</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint._chargeR" class="py-name" href="#" onclick="return doclink('link-20', '_chargeR', 'link-18');">_chargeR</a></tt><tt class="py-op">(</tt><tt class="py-name">pH</tt><tt class="py-op">,</tt> <tt class="py-name">pos_pKs</tt><tt class="py-op">,</tt> <tt class="py-name">neg_pKs</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">Charge</tt> <tt class="py-op"><</tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">pH2</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">Charge2</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">pH1</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">Charge1</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-comment"># Bisection</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">pH2</tt> <tt class="py-op">-</tt> <tt class="py-name">pH1</tt> <tt class="py-op">></tt> <tt class="py-number">0.0001</tt> <tt class="py-keyword">and</tt> <tt class="py-name">Charge</tt><tt class="py-op">!=</tt><tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">pH</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">pH1</tt> <tt class="py-op">+</tt> <tt class="py-name">pH2</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-number">2.0</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">Charge</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint._chargeR" class="py-name" href="#" onclick="return doclink('link-21', '_chargeR', 'link-18');">_chargeR</a></tt><tt class="py-op">(</tt><tt class="py-name">pH</tt><tt class="py-op">,</tt> <tt class="py-name">pos_pKs</tt><tt class="py-op">,</tt> <tt class="py-name">neg_pKs</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">Charge</tt> <tt class="py-op">></tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">pH1</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">Charge1</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">else</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">pH2</tt> <tt class="py-op">=</tt> <tt class="py-name">pH</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">Charge2</tt> <tt class="py-op">=</tt> <tt class="py-name">Charge</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">pH</tt> </tt>
</div></div><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> </tt><script type="text/javascript">
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