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QualityEvaluation.html
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<title>QualityEvaluation module — NMRlipids databank 4.9.2023 documentation</title>
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<section id="module-QualityEvaluation">
<span id="qualityevaluation-module"></span><h1>QualityEvaluation module<a class="headerlink" href="#module-QualityEvaluation" title="Link to this heading"></a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="QualityEvaluation.Simulation">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">Simulation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">readme</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">OPdata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">FFdata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indexingPath</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#Simulation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.Simulation" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<dl class="py method">
<dt class="sig sig-object py" id="QualityEvaluation.Simulation.getLipids">
<span class="sig-name descname"><span class="pre">getLipids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecules</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">dict_keys(['POPC',</span> <span class="pre">'POPG',</span> <span class="pre">'POPS',</span> <span class="pre">'POPE',</span> <span class="pre">'PYPC',</span> <span class="pre">'PAzePCprot',</span> <span class="pre">'PAzePCdeprot',</span> <span class="pre">'DMPC',</span> <span class="pre">'DPPC',</span> <span class="pre">'DPPE',</span> <span class="pre">'DPPG',</span> <span class="pre">'DEPC',</span> <span class="pre">'DRPC',</span> <span class="pre">'DYPC',</span> <span class="pre">'DLPC',</span> <span class="pre">'DLIPC',</span> <span class="pre">'DOG',</span> <span class="pre">'DOPC',</span> <span class="pre">'DOPE',</span> <span class="pre">'DDOPC',</span> <span class="pre">'DOPS',</span> <span class="pre">'DSPC',</span> <span class="pre">'DAPC',</span> <span class="pre">'DMTAP',</span> <span class="pre">'SDG',</span> <span class="pre">'SDPE',</span> <span class="pre">'SOPC',</span> <span class="pre">'POPI',</span> <span class="pre">'SAPI',</span> <span class="pre">'SAPI24',</span> <span class="pre">'SAPI25',</span> <span class="pre">'SLPI',</span> <span class="pre">'CER',</span> <span class="pre">'CER180',</span> <span class="pre">'CHOL',</span> <span class="pre">'DCHOL',</span> <span class="pre">'DHMDMAB',</span> <span class="pre">'SLiPC',</span> <span class="pre">'SM16',</span> <span class="pre">'SM18',</span> <span class="pre">'TOCL',</span> <span class="pre">'TLCL_0H',</span> <span class="pre">'GM1',</span> <span class="pre">'DPPGK',</span> <span class="pre">'GB3'])</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#Simulation.getLipids"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.Simulation.getLipids" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="QualityEvaluation.Simulation.molarFraction">
<span class="sig-name descname"><span class="pre">molarFraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">molecules</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">dict_keys(['POPC',</span> <span class="pre">'POPG',</span> <span class="pre">'POPS',</span> <span class="pre">'POPE',</span> <span class="pre">'PYPC',</span> <span class="pre">'PAzePCprot',</span> <span class="pre">'PAzePCdeprot',</span> <span class="pre">'DMPC',</span> <span class="pre">'DPPC',</span> <span class="pre">'DPPE',</span> <span class="pre">'DPPG',</span> <span class="pre">'DEPC',</span> <span class="pre">'DRPC',</span> <span class="pre">'DYPC',</span> <span class="pre">'DLPC',</span> <span class="pre">'DLIPC',</span> <span class="pre">'DOG',</span> <span class="pre">'DOPC',</span> <span class="pre">'DOPE',</span> <span class="pre">'DDOPC',</span> <span class="pre">'DOPS',</span> <span class="pre">'DSPC',</span> <span class="pre">'DAPC',</span> <span class="pre">'DMTAP',</span> <span class="pre">'SDG',</span> <span class="pre">'SDPE',</span> <span class="pre">'SOPC',</span> <span class="pre">'POPI',</span> <span class="pre">'SAPI',</span> <span class="pre">'SAPI24',</span> <span class="pre">'SAPI25',</span> <span class="pre">'SLPI',</span> <span class="pre">'CER',</span> <span class="pre">'CER180',</span> <span class="pre">'CHOL',</span> <span class="pre">'DCHOL',</span> <span class="pre">'DHMDMAB',</span> <span class="pre">'SLiPC',</span> <span class="pre">'SM16',</span> <span class="pre">'SM18',</span> <span class="pre">'TOCL',</span> <span class="pre">'TLCL_0H',</span> <span class="pre">'GM1',</span> <span class="pre">'DPPGK',</span> <span class="pre">'GB3'])</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#Simulation.molarFraction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.Simulation.molarFraction" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="QualityEvaluation.Experiment">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">Experiment</span></span><a class="reference internal" href="_modules/QualityEvaluation.html#Experiment"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.Experiment" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.loadMappingFile">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">loadMappingFile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path_to_mapping_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#loadMappingFile"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.loadMappingFile" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.prob_S_in_g">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">prob_S_in_g</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">OP_exp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_error</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">OP_sim</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">op_sim_sd</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#prob_S_in_g"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.prob_S_in_g" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.getFragments">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">getFragments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mapping_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#getFragments"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.getFragments" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.filterCH">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">filterCH</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fragment_key</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fragments</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#filterCH"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.filterCH" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.checkForCH">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">checkForCH</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fragment_key</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fragments</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#checkForCH"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.checkForCH" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.evaluated_percentage">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">evaluated_percentage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fragments</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_op_data</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#evaluated_percentage"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.evaluated_percentage" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.fragmentQuality">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">fragmentQuality</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fragments</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_op_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sim_op_data</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#fragmentQuality"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.fragmentQuality" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.fragmentQualityAvg">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">fragmentQualityAvg</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lipid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fragment_qual_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fragments</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#fragmentQualityAvg"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.fragmentQualityAvg" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.systemQuality">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">systemQuality</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">system_fragment_qualities</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#systemQuality"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.systemQuality" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.calc_k_e">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">calc_k_e</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">SimExpData</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#calc_k_e"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.calc_k_e" title="Link to this definition"></a></dt>
<dd><p>Scaling factor as defined by Kučerka et al. 2008b, doi:10.1529/biophysj.107.122465</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.FormFactorMinFromData">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">FormFactorMinFromData</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">FormFactor</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#FormFactorMinFromData"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.FormFactorMinFromData" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.formfactorQuality">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">formfactorQuality</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">simFFdata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expFFdata</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#formfactorQuality"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.formfactorQuality" title="Link to this definition"></a></dt>
<dd><p>Calculate form factor quality for a simulation as defined by Kučerka et al. 2010, doi:10.1007/s00232-010-9254-5</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.formfactorQualitySIMtoEXP">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">formfactorQualitySIMtoEXP</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">simFFdata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expFFdata</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#formfactorQualitySIMtoEXP"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.formfactorQualitySIMtoEXP" title="Link to this definition"></a></dt>
<dd><p>Calculate form factor quality for a simulation as defined by Kučerka et al. 2010, doi:10.1007/s00232-010-9254-5</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="QualityEvaluation.loadSimulations">
<span class="sig-prename descclassname"><span class="pre">QualityEvaluation.</span></span><span class="sig-name descname"><span class="pre">loadSimulations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/QualityEvaluation.html#loadSimulations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#QualityEvaluation.loadSimulations" title="Link to this definition"></a></dt>
<dd></dd></dl>
</section>
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