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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.NMR-module.html">Package NMR</a> ::
Module NOEtools
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<h1 class="epydoc">Source Code for <a href="Bio.NMR.NOEtools-module.html">Module Bio.NMR.NOEtools</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># NOEtools.py: A python module for predicting NOE coordinates from</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"># assignment data. </tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The input and output are modelled on nmrview peaklists.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This modules is suitable for directly generating an nmrview</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># peaklist with predicted crosspeaks directly from the</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># input assignment peaklist. </tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">,</tt><tt class="py-string">"/usr/people/robert/development/xpktools/"</tt><tt class="py-op">]</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.NMR.xpktools=Bio.NMR.xpktools-module.html"><a title="Bio.NMR.xpktools" class="py-name" href="#" onclick="return doclink('link-0', 'xpktools', 'link-0');">xpktools</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="predictNOE"></a><div id="predictNOE-def"><a name="L14"></a><tt class="py-lineno">14</tt> <a class="py-toggle" href="#" id="predictNOE-toggle" onclick="return toggle('predictNOE');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NMR.NOEtools-module.html#predictNOE">predictNOE</a><tt class="py-op">(</tt><tt class="py-param">peaklist</tt><tt class="py-op">,</tt><tt class="py-param">originNuc</tt><tt class="py-op">,</tt><tt class="py-param">detectedNuc</tt><tt class="py-op">,</tt><tt class="py-param">originResNum</tt><tt class="py-op">,</tt><tt class="py-param">toResNum</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="predictNOE-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="predictNOE-expanded"><a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-comment"># Predict the i->j NOE position based on self peak (diagonal) assignments</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># example predictNOE(peaklist,"N15","H1",10,12)</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># where peaklist is of the type xpktools.peaklist</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># would generate a .xpk file entry for a crosspeak</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># that originated on N15 of residue 10 and ended up</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as magnetization detected on the H1 nucleus of</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># residue 12.</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># CAVEAT: The initial peaklist is assumed to be diagonal (self peaks only)</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and currently there is not checking done to insure that this</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># assumption holds true. Check your peaklist for errors and</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># off diagonal peaks before attempting to use predictNOE.</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">returnLine</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> <tt class="py-comment"># The modified line to be returned to the caller</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">datamap</tt><tt class="py-op">=</tt><tt id="link-1" class="py-name" targets="Function Bio.NMR.NOEtools._data_map()=Bio.NMR.NOEtools-module.html#_data_map"><a title="Bio.NMR.NOEtools._data_map" class="py-name" href="#" onclick="return doclink('link-1', '_data_map', 'link-1');">_data_map</a></tt><tt class="py-op">(</tt><tt class="py-name">peaklist</tt><tt class="py-op">.</tt><tt class="py-name">datalabels</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-comment"># Construct labels for keying into dictionary</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">originAssCol</tt> <tt class="py-op">=</tt> <tt class="py-name">datamap</tt><tt class="py-op">[</tt><tt class="py-name">originNuc</tt><tt class="py-op">+</tt><tt class="py-string">".L"</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">originPPMCol</tt> <tt class="py-op">=</tt> <tt class="py-name">datamap</tt><tt class="py-op">[</tt><tt class="py-name">originNuc</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-number">1</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">detectedPPMCol</tt> <tt class="py-op">=</tt> <tt class="py-name">datamap</tt><tt class="py-op">[</tt><tt class="py-name">detectedNuc</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-number">1</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-comment"># Make a list of the data lines involving the detected</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">peaklist</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.NMR.xpktools.Peaklist.residue_dict()=Bio.NMR.xpktools.Peaklist-class.html#residue_dict"><a title="Bio.NMR.xpktools.Peaklist.residue_dict" class="py-name" href="#" onclick="return doclink('link-2', 'residue_dict', 'link-2');">residue_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">detectedNuc</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-3', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">toResNum</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">peaklist</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.NMR.xpktools.Peaklist.residue_dict" class="py-name" href="#" onclick="return doclink('link-4', 'residue_dict', 'link-2');">residue_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">detectedNuc</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-5', 'has_key', 'link-3');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">originResNum</tt><tt class="py-op">)</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-name">detectedList</tt><tt class="py-op">=</tt><tt class="py-name">peaklist</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.NMR.xpktools.Peaklist.residue_dict" class="py-name" href="#" onclick="return doclink('link-6', 'residue_dict', 'link-2');">residue_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">detectedNuc</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">toResNum</tt><tt class="py-op">)</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">originList</tt><tt class="py-op">=</tt><tt class="py-name">peaklist</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.NMR.xpktools.Peaklist.residue_dict" class="py-name" href="#" onclick="return doclink('link-7', 'residue_dict', 'link-2');">residue_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">detectedNuc</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">originResNum</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">returnLine</tt><tt class="py-op">=</tt><tt class="py-name">detectedList</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">detectedList</tt><tt class="py-op">:</tt> </tt>
<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-name">aveDetectedPPM</tt> <tt class="py-op">=</tt><tt id="link-8" class="py-name" targets="Function Bio.NMR.NOEtools._col_ave()=Bio.NMR.NOEtools-module.html#_col_ave"><a title="Bio.NMR.NOEtools._col_ave" class="py-name" href="#" onclick="return doclink('link-8', '_col_ave', 'link-8');">_col_ave</a></tt><tt class="py-op">(</tt><tt class="py-name">detectedList</tt><tt class="py-op">,</tt><tt class="py-name">detectedPPMCol</tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">aveOriginPPM</tt> <tt class="py-op">=</tt><tt id="link-9" class="py-name"><a title="Bio.NMR.NOEtools._col_ave" class="py-name" href="#" onclick="return doclink('link-9', '_col_ave', 'link-8');">_col_ave</a></tt><tt class="py-op">(</tt><tt class="py-name">originList</tt><tt class="py-op">,</tt><tt class="py-name">originPPMCol</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-name">originAss</tt> <tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">splitfields</tt><tt class="py-op">(</tt><tt class="py-name">originList</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">originAssCol</tt><tt class="py-op">]</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-name">returnLine</tt><tt class="py-op">=</tt><tt id="link-10" class="py-name"><a title="Bio.NMR.xpktools" class="py-name" href="#" onclick="return doclink('link-10', 'xpktools', 'link-0');">xpktools</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Function Bio.NMR.xpktools.replace_entry()=Bio.NMR.xpktools-module.html#replace_entry"><a title="Bio.NMR.xpktools.replace_entry" class="py-name" href="#" onclick="return doclink('link-11', 'replace_entry', 'link-11');">replace_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">returnLine</tt><tt class="py-op">,</tt><tt class="py-name">originAssCol</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">originAss</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">returnLine</tt><tt class="py-op">=</tt><tt id="link-12" class="py-name"><a title="Bio.NMR.xpktools" class="py-name" href="#" onclick="return doclink('link-12', 'xpktools', 'link-0');">xpktools</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.NMR.xpktools.replace_entry" class="py-name" href="#" onclick="return doclink('link-13', 'replace_entry', 'link-11');">replace_entry</a></tt><tt class="py-op">(</tt><tt class="py-name">returnLine</tt><tt class="py-op">,</tt><tt class="py-name">originPPMCol</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">aveOriginPPM</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">returnLine</tt> </tt>
</div><a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> </tt>
<a name="_data_map"></a><div id="_data_map-def"><a name="L56"></a><tt class="py-lineno">56</tt> <a class="py-toggle" href="#" id="_data_map-toggle" onclick="return toggle('_data_map');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NMR.NOEtools-module.html#_data_map">_data_map</a><tt class="py-op">(</tt><tt class="py-param">labelline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_data_map-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="_data_map-expanded"><a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt class="py-comment"># Generate a map between datalabels and column number</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># based on a labelline</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-14" 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-14', 'i', 'link-14');">i</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment"># A counter</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-name">datamap</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># The data map dictionary</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-name">labelList</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">splitfields</tt><tt class="py-op">(</tt><tt class="py-name">labelline</tt><tt class="py-op">)</tt> <tt class="py-comment"># Get the label line</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-comment"># Get the column number for each label</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-15" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-15', 'i', 'link-14');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">labelList</tt><tt class="py-op">)</tt><tt class="py-op">)</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">datamap</tt><tt class="py-op">[</tt><tt class="py-name">labelList</tt><tt class="py-op">[</tt><tt id="link-16" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-16', 'i', 'link-14');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-17" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-17', 'i', 'link-14');">i</a></tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">datamap</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> </tt>
<a name="_col_ave"></a><div id="_col_ave-def"><a name="L69"></a><tt class="py-lineno">69</tt> <a class="py-toggle" href="#" id="_col_ave-toggle" onclick="return toggle('_col_ave');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NMR.NOEtools-module.html#_col_ave">_col_ave</a><tt class="py-op">(</tt><tt class="py-param">list</tt><tt class="py-op">,</tt><tt class="py-param">col</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_col_ave-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="_col_ave-expanded"><a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"><tt class="py-comment"># Compute average values from a particular column in a string list</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-18" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Function Bio.utils.sum()=Bio.utils-module.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-18', 'sum', 'link-18');">sum</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">;</tt> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-19" class="py-name" targets="Method Martel.LAX.LAX.element()=Martel.LAX.LAX-class.html#element,Method Martel.LAX.LAXAttrs.element()=Martel.LAX.LAXAttrs-class.html#element,Method Martel.LAX.LAXPositions.element()=Martel.LAX.LAXPositions-class.html#element"><a title="Martel.LAX.LAX.element
Martel.LAX.LAXAttrs.element
Martel.LAX.LAXPositions.element" class="py-name" href="#" onclick="return doclink('link-19', 'element', 'link-19');">element</a></tt> <tt class="py-keyword">in</tt> <tt id="link-20" 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-20', 'list', 'link-20');">list</a></tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt id="link-21" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-21', 'sum', 'link-18');">sum</a></tt><tt class="py-op">=</tt><tt id="link-22" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-22', 'sum', 'link-18');">sum</a></tt><tt class="py-op">+</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-23', 'split', 'link-23');">split</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Martel.LAX.LAX.element
Martel.LAX.LAXAttrs.element
Martel.LAX.LAXPositions.element" class="py-name" href="#" onclick="return doclink('link-24', 'element', 'link-19');">element</a></tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-25" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-25', 'sum', 'link-18');">sum</a></tt><tt class="py-op">/</tt><tt class="py-name">n</tt> </tt>
</div><a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> </tt><script type="text/javascript">
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