- Updated template notebooks

EnzymeML · Nov 9, 2020 · 1387ca7 · 1387ca7
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diff --git a/templates/ExportTutorial.html b/templates/ExportTutorial.html
@@ -13569,7 +13569,7 @@ <h3 id="Add-replicate-data">Add replicate data<a class="anchor-link" href="#Add-
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[15]:</div>
+<div class="prompt input_prompt">In&nbsp;[14]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">reaction_1</span><span class="o">.</span><span class="n">addReplicate</span><span class="p">(</span><span class="n">replicate_1</span><span class="p">,</span> <span class="n">enzmldoc</span><span class="p">)</span>
@@ -13585,7 +13585,7 @@ <h3 id="Add-replicate-data">Add replicate data<a class="anchor-link" href="#Add-
 
 <div class="output_area">
 
-    <div class="prompt output_prompt">Out[15]:</div>
+    <div class="prompt output_prompt">Out[14]:</div>
 
 
 
@@ -13612,7 +13612,7 @@ <h3 id="Add-reaction-to-EnzymeMLDocument">Add reaction to <em>EnzymeMLDocument</
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[16]:</div>
+<div class="prompt input_prompt">In&nbsp;[15]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">reaction1</span> <span class="o">=</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">addReaction</span><span class="p">(</span><span class="n">reaction_1</span><span class="p">)</span>
@@ -13659,14 +13659,14 @@ <h1 id="Modelling">Modelling<a class="anchor-link" href="#Modelling">&#182;</a><
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[21]:</div>
+<div class="prompt input_prompt">In&nbsp;[17]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">equation</span> <span class="o">=</span> <span class="s2">&quot;s0 * vmax / ( s0 + Km )&quot;</span>
 
 <span class="n">parameters</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
-<span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;Km&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="s2">&quot;mmole / s&quot;</span><span class="p">)</span>
-<span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;vmax&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="mf">10.0</span><span class="p">,</span> <span class="s2">&quot;mmole / l&quot;</span><span class="p">)</span>
+<span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;Km_s0&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="s2">&quot;mmole / s&quot;</span><span class="p">)</span>
+<span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;vmax_s0&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="mf">10.0</span><span class="p">,</span> <span class="s2">&quot;mmole / l&quot;</span><span class="p">)</span>
 
 <span class="n">kinetic_model</span> <span class="o">=</span> <span class="n">KineticModel</span><span class="p">(</span> <span class="n">equation</span><span class="o">=</span><span class="n">equation</span><span class="p">,</span> <span class="n">parameters</span><span class="o">=</span><span class="n">parameters</span> <span class="p">)</span>
 </pre></div>
@@ -13678,7 +13678,7 @@ <h1 id="Modelling">Modelling<a class="anchor-link" href="#Modelling">&#182;</a><
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[22]:</div>
+<div class="prompt input_prompt">In&nbsp;[20]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">enzmldoc</span><span class="o">.</span><span class="n">getReaction</span><span class="p">(</span><span class="n">reaction1</span><span class="p">)</span><span class="o">.</span><span class="n">setModel</span><span class="p">(</span><span class="n">kinetic_model</span><span class="p">)</span>
@@ -13701,7 +13701,7 @@ <h1 id="Ready-to-write">Ready to write<a class="anchor-link" href="#Ready-to-wri
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[23]:</div>
+<div class="prompt input_prompt">In&nbsp;[21]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">enzmldoc</span><span class="o">.</span><span class="n">printUnits</span><span class="p">()</span>
@@ -13745,7 +13745,7 @@ <h1 id="Ready-to-write">Ready to write<a class="anchor-link" href="#Ready-to-wri
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[24]:</div>
+<div class="prompt input_prompt">In&nbsp;[22]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">out_dir</span> <span class="o">=</span> <span class="s2">&quot;YourDirectory/YourFilename&quot;</span>
@@ -13775,19 +13775,6 @@ <h1 id="Ready-to-write">Ready to write<a class="anchor-link" href="#Ready-to-wri
 </div>
 </div>
 
-</div>
-<div class="cell border-box-sizing code_cell rendered">
-<div class="input">
-<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
-<div class="inner_cell">
-    <div class="input_area">
-<div class=" highlight hl-ipython3"><pre><span></span> 
-</pre></div>
-
-    </div>
-</div>
-</div>
-
 </div>
     </div>
   </div>

diff --git a/templates/ImportTutorial.html b/templates/ImportTutorial.html
@@ -13173,7 +13173,7 @@ <h2 id="Read-.omex-file">Read .omex file<a class="anchor-link" href="#Read-.omex
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[3]:</div>
+<div class="prompt input_prompt">In&nbsp;[2]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">path</span> <span class="o">=</span> <span class="s2">&quot;Example.omex&quot;</span>
@@ -13202,7 +13202,7 @@ <h2 id="User-information">User information<a class="anchor-link" href="#User-inf
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[4]:</div>
+<div class="prompt input_prompt">In&nbsp;[3]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">user_info</span> <span class="o">=</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">getCreator</span><span class="p">()</span>
@@ -13240,7 +13240,7 @@ <h2 id="Unit-Definitions">Unit Definitions<a class="anchor-link" href="#Unit-Def
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[5]:</div>
+<div class="prompt input_prompt">In&nbsp;[4]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">enzmldoc</span><span class="o">.</span><span class="n">printUnits</span><span class="p">()</span>
@@ -13275,7 +13275,7 @@ <h2 id="Unit-Definitions">Unit Definitions<a class="anchor-link" href="#Unit-Def
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[6]:</div>
+<div class="prompt input_prompt">In&nbsp;[5]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">id_</span><span class="p">,</span> <span class="n">unitdef</span> <span class="ow">in</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">getUnitDict</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
@@ -13320,7 +13320,7 @@ <h2 id="Proteins">Proteins<a class="anchor-link" href="#Proteins">&#182;</a></h2
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[7]:</div>
+<div class="prompt input_prompt">In&nbsp;[6]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">enzmldoc</span><span class="o">.</span><span class="n">printProteins</span><span class="p">()</span>
@@ -13352,7 +13352,7 @@ <h2 id="Proteins">Proteins<a class="anchor-link" href="#Proteins">&#182;</a></h2
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[8]:</div>
+<div class="prompt input_prompt">In&nbsp;[7]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">id_</span> <span class="ow">in</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">getProteinDict</span><span class="p">():</span>
@@ -13395,7 +13395,7 @@ <h2 id="Reactants">Reactants<a class="anchor-link" href="#Reactants">&#182;</a><
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[9]:</div>
+<div class="prompt input_prompt">In&nbsp;[8]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">enzmldoc</span><span class="o">.</span><span class="n">printReactants</span><span class="p">()</span>
@@ -13427,7 +13427,7 @@ <h2 id="Reactants">Reactants<a class="anchor-link" href="#Reactants">&#182;</a><
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[10]:</div>
+<div class="prompt input_prompt">In&nbsp;[9]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">id_</span> <span class="ow">in</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">getReactantDict</span><span class="p">():</span>
@@ -13487,7 +13487,7 @@ <h2 id="Reactions">Reactions<a class="anchor-link" href="#Reactions">&#182;</a><
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[11]:</div>
+<div class="prompt input_prompt">In&nbsp;[10]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">enzmldoc</span><span class="o">.</span><span class="n">printReactions</span><span class="p">()</span>
@@ -13519,7 +13519,7 @@ <h2 id="Reactions">Reactions<a class="anchor-link" href="#Reactions">&#182;</a><
 </div>
 <div class="cell border-box-sizing code_cell rendered">
 <div class="input">
-<div class="prompt input_prompt">In&nbsp;[17]:</div>
+<div class="prompt input_prompt">In&nbsp;[13]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">id_</span> <span class="ow">in</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">getReactionDict</span><span class="p">():</span>
@@ -13578,7 +13578,7 @@ <h2 id="Reactions">Reactions<a class="anchor-link" href="#Reactions">&#182;</a><
 
     <span class="c1">############## MODIFIERS ##############</span>
 
-    <span class="k">for</span> <span class="n">reactant_id</span><span class="p">,</span> <span class="n">stoich</span> <span class="ow">in</span> <span class="n">reaction_modifiers</span><span class="p">:</span>
+    <span class="k">for</span> <span class="n">reactant_id</span><span class="p">,</span> <span class="n">stoich</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">replicates</span><span class="p">,</span> <span class="n">init_concs</span> <span class="ow">in</span> <span class="n">reaction_modifiers</span><span class="p">:</span>
 
         <span class="k">if</span> <span class="s1">&#39;s&#39;</span> <span class="ow">in</span> <span class="n">reactant_id</span><span class="p">:</span> <span class="n">reactant</span> <span class="o">=</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">getReactant</span><span class="p">(</span><span class="n">reactant_id</span><span class="p">);</span>  <span class="c1"># Return Reactant object</span>
         <span class="k">if</span> <span class="s1">&#39;p&#39;</span> <span class="ow">in</span> <span class="n">reactant_id</span><span class="p">:</span> <span class="n">reactant</span> <span class="o">=</span> <span class="n">enzmldoc</span><span class="o">.</span><span class="n">getProtein</span><span class="p">(</span><span class="n">reactant_id</span><span class="p">);</span>  <span class="c1"># Return Reactant object</span>

diff --git a/templates/TL_ExportTemplate.ipynb b/templates/TL_ExportTemplate.ipynb
@@ -396,7 +396,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -405,7 +405,7 @@
        "1"
       ]
      },
-     "execution_count": 15,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -425,7 +425,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
@@ -459,22 +459,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
     "equation = \"s0 * vmax / ( s0 + Km )\"\n",
     "\n",
     "parameters = dict()\n",
-    "parameters['Km'] = (1.0, \"mmole / s\")\n",
-    "parameters['vmax'] = (10.0, \"mmole / l\")\n",
+    "parameters['Km_s0'] = (1.0, \"mmole / s\")\n",
+    "parameters['vmax_s0'] = (10.0, \"mmole / l\")\n",
     "\n",
     "kinetic_model = KineticModel( equation=equation, parameters=parameters )"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -492,7 +492,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [
     {
@@ -522,7 +522,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
@@ -538,13 +538,6 @@
     "out_dir = \"YourDirectory/YourFilename\"\n",
     "EnzymeMLWriter().toFile( enzmldoc=enzmldoc, path=out_dir )"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/templates/TL_ImportTemplate.ipynb b/templates/TL_ImportTemplate.ipynb
@@ -48,7 +48,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -105,7 +105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -126,7 +126,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -166,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -184,7 +184,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -222,7 +222,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -240,7 +240,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -294,7 +294,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -312,7 +312,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -372,7 +372,7 @@
     "    \n",
     "    ############## MODIFIERS ##############\n",
     "    \n",
-    "    for reactant_id, stoich in reaction_modifiers:\n",
+    "    for reactant_id, stoich, _, replicates, init_concs in reaction_modifiers:\n",
     "        \n",
     "        if 's' in reactant_id: reactant = enzmldoc.getReactant(reactant_id);  # Return Reactant object\n",
     "        if 'p' in reactant_id: reactant = enzmldoc.getProtein(reactant_id);  # Return Reactant object\n",

diff --git a/templates/YourDirectory/YourFilename/Your experiment name/Your_experiment_name.omex b/templates/YourDirectory/YourFilename/Your experiment name/Your_experiment_name.omex