Update docs

AddData.html

@@ -45,7 +45,7 @@
 <li class="toctree-l1"><a class="reference internal" href="listOfFiles.html">List and descriptions of NMRlipids databank files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="READMEcontent.html">User input and content of README.yaml files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="addingData.html">Adding simulations into the NMRlipids databank</a></li>
-<li class="toctree-l1"><a class="reference internal" href="addingExpData.html">Adding experimental data in the NMRlipids databank</a></li>
+<li class="toctree-l1"><a class="reference internal" href="addingExpData.html">Adding experimental data into the NMRlipids databank</a></li>
 <li class="toctree-l1"><a class="reference internal" href="moleculesAndMapping.html">Universal molecule and atom names</a></li>
 <li class="toctree-l1"><a class="reference internal" href="databankLibrary.html">NMRlipids databank API functions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="exampleAndTutorials.html">Examples and tutorials</a></li>

QualityEvaluation.html

@@ -83,12 +83,12 @@
 <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">'SLPI',</span> <span class="pre">'CER',</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></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>
+<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">'SLPI',</span> <span class="pre">'CER',</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">'GM1'])</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">'SLPI',</span> <span class="pre">'CER',</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></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>
+<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">'SLPI',</span> <span class="pre">'CER',</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">'GM1'])</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>

READMEcontent.html

@@ -297,6 +297,7 @@ <h2>COMPOSITION (compulsory)<a class="headerlink" href="#composition-compulsory"
   MAPPING: mappingCLA.txt
 </pre></div>
 </div>
+<p>When running <code class="docutils literal notranslate"><span class="pre">AddData.py</span></code>, the numbers of molecules are added in additional <code class="docutils literal notranslate"><span class="pre">COUNT</span></code> keys into dictionaries of each molecule, see COMPOSITION (ouput) below.</p>
 </section>
 <section id="dir-wrk-compulsory">
 <h2>DIR_WRK (compulsory)<a class="headerlink" href="#dir-wrk-compulsory" title="Link to this heading"></a></h2>
@@ -388,7 +389,7 @@ <h2>EXPERIMENT<a class="headerlink" href="#experiment" title="Link to this headi
 </section>
 <section id="composition-output">
 <h2>COMPOSITION (output)<a class="headerlink" href="#composition-output" title="Link to this heading"></a></h2>
-<p>When adding a simulation into NMRlipids databank by the AddData.py script, numbers of lipid molecules per membrane leaflet are automatically calculated and stored into the key called COUNT in the COMPOSITION dictionary. For example, the result for the simulation with COMPOSITION input exemplified above is:</p>
+<p>When adding a simulation into NMRlipids databank with the <code class="docutils literal notranslate"><span class="pre">AddData.py</span></code>, numbers of molecules are automatically calculated and stored into <code class="docutils literal notranslate"><span class="pre">COUNT</span></code> keys for each molecule in the COMPOSITION dictionary. Number of lipids are calculated separately for both membrane leaflets. For example, the result for the simulation with COMPOSITION input exemplified above is:</p>
 <div class="highlight-none notranslate"><div class="highlight"><pre><span></span>    COMPOSITION:
      CHOL:
       NAME: CHL1

_modules/databankLibrary.html

@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../listOfFiles.html">List and descriptions of NMRlipids databank files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../READMEcontent.html">User input and content of README.yaml files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../addingData.html">Adding simulations into the NMRlipids databank</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../addingExpData.html">Adding experimental data in the NMRlipids databank</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../addingExpData.html">Adding experimental data into the NMRlipids databank</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../moleculesAndMapping.html">Universal molecule and atom names</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../databankLibrary.html">NMRlipids databank API functions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../exampleAndTutorials.html">Examples and tutorials</a></li>
@@ -1444,6 +1444,7 @@ <h1>Source code for databankLibrary</h1><div class="highlight"><pre>
         <span class="n">plotFormFactor</span><span class="p">(</span><span class="n">FFexp</span><span class="p">,</span><span class="n">FFq</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;Experiment&#39;</span><span class="p">,</span><span class="s1">&#39;black&#39;</span><span class="p">)</span>
         <span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
     <span class="k">except</span><span class="p">:</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
         <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Form factor plotting failed&#39;</span><span class="p">)</span>
 
     <span class="n">plotOrderParameters</span><span class="p">(</span><span class="n">OPsim</span><span class="p">,</span> <span class="n">OPexp</span><span class="p">)</span></div>
@@ -1464,13 +1465,13 @@ <h1>Source code for databankLibrary</h1><div class="highlight"><pre>
 <span class="sd">    :return: force field specific atom name</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="n">mapping_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">realpath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span> <span class="o">+</span> <span class="s1">&#39;/mapping_files/&#39;</span> <span class="o">+</span> <span class="n">system</span><span class="p">[</span><span class="s1">&#39;COMPOSITION&#39;</span><span class="p">][</span><span class="n">molecule</span><span class="p">][</span><span class="s1">&#39;MAPPING&#39;</span><span class="p">]</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">mapping_file</span><span class="p">,</span> <span class="s2">&quot;rt&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">mapping_file</span><span class="p">:</span>
+    <span class="n">mapping_file_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">realpath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span> <span class="o">+</span> <span class="s1">&#39;/mapping_files/&#39;</span> <span class="o">+</span> <span class="n">system</span><span class="p">[</span><span class="s1">&#39;COMPOSITION&#39;</span><span class="p">][</span><span class="n">molecule</span><span class="p">][</span><span class="s1">&#39;MAPPING&#39;</span><span class="p">]</span>
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">mapping_file_path</span><span class="p">,</span> <span class="s2">&quot;rt&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">mapping_file</span><span class="p">:</span>
         <span class="n">mapping</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">mapping_file</span><span class="p">,</span> <span class="n">Loader</span><span class="o">=</span><span class="n">yaml</span><span class="o">.</span><span class="n">FullLoader</span><span class="p">)</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">m_atom1</span> <span class="o">=</span> <span class="n">mapping</span><span class="p">[</span><span class="n">atom</span><span class="p">][</span><span class="s2">&quot;ATOMNAME&quot;</span><span class="p">]</span>
         <span class="k">except</span><span class="p">:</span>
-            <span class="nb">print</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="s1">&#39; was not found from &#39;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">mapping_file</span><span class="p">))</span>
+            <span class="nb">print</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="s1">&#39; was not found from &#39;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">mapping_file_path</span><span class="p">))</span>
             <span class="k">return</span>   
     <span class="k">return</span> <span class="n">m_atom1</span></div>
 
@@ -2005,7 +2006,7 @@ <h1>Source code for databankLibrary</h1><div class="highlight"><pre>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Calculates the P-N vector angles with respect to membrane normal from the simulation defined by the MDAnalysis universe. </span>
 
-<span class="sd">    :param molename: residue name of the molecule for which the P-N vector angle will be calculated</span>
+<span class="sd">    :param molname: residue name of the molecule for which the P-N vector angle will be calculated</span>
 <span class="sd">    :param atom1: name of the P atom in the simulation</span>
 <span class="sd">    :param atom2: name of the N atom in the simulation</span>
 <span class="sd">    :param MDAuniverse: MDAnalysis universe of the simulation to be analyzed</span>

_modules/index.html

@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../listOfFiles.html">List and descriptions of NMRlipids databank files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../READMEcontent.html">User input and content of README.yaml files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../addingData.html">Adding simulations into the NMRlipids databank</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../addingExpData.html">Adding experimental data in the NMRlipids databank</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../addingExpData.html">Adding experimental data into the NMRlipids databank</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../moleculesAndMapping.html">Universal molecule and atom names</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../databankLibrary.html">NMRlipids databank API functions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../exampleAndTutorials.html">Examples and tutorials</a></li>

_sources/READMEcontent.md.txt

@@ -86,7 +86,7 @@ For example, the COMPOSITION dictionary input for [a system](https://doi.org/10.
       NAME: CLA
       MAPPING: mappingCLA.txt
 
-
+When running ``AddData.py``, the numbers of molecules are added in additional ``COUNT`` keys into dictionaries of each molecule, see COMPOSITION (ouput) below. 
 
 #### DIR\_WRK (compulsory)
 Give the path of the working directory in your local computer. The trajectory and topology files will be downloaded to this trajectory, and temporary files created during processing will be stored here. 
@@ -156,7 +156,8 @@ Date when added into the databank.
 Potentially connected experimental data.
 
 #### COMPOSITION (output)
-When adding a simulation into NMRlipids databank by the AddData.py script, numbers of lipid molecules per membrane leaflet are automatically calculated and stored into the key called COUNT in the COMPOSITION dictionary. For example, the result for the simulation with COMPOSITION input exemplified above is:
+When adding a simulation into NMRlipids databank with the ``AddData.py``, numbers of molecules are automatically calculated and stored into ``COUNT`` keys for each molecule in the COMPOSITION dictionary. Number of lipids are calculated separately for both membrane leaflets. For example, the result for the simulation with COMPOSITION input exemplified above is:
+
 
         COMPOSITION:
          CHOL: