Fixed outputs tutorial

bioexcel · Jun 28, 2024 · 5ff61e5 · 5ff61e5
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diff --git a/biobb_wf_flexdyn/docs/source/tutorial.md b/biobb_wf_flexdyn/docs/source/tutorial.md
@@ -188,6 +188,7 @@ import os
 import nglview
 import simpletraj
 import plotly
+import sys
 import plotly.graph_objs as go
 import numpy as np
 import pandas as pd
@@ -406,7 +407,6 @@ References: <br>
 
 
 ```python
-import sys
 from biobb_flexdyn.flexdyn.concoord_dist import concoord_dist
 
 concoord_dist_pdb = pdbCode + "_dist.pdb"
@@ -440,7 +440,6 @@ concoord_dist(  input_structure_path=monomer,
 
 
 ```python
-import sys
 from biobb_flexdyn.flexdyn.concoord_disco import concoord_disco
 
 concoord_disco_pdb = pdbCode + "_disco_traj.pdb"
@@ -2252,9 +2251,3 @@ Questions, issues, suggestions and comments are really welcome!
 
 * BioExcel forum:
     * [https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library](https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library)
-
-
-
-```python
-
-```
diff --git a/biobb_wf_flexdyn/html/biobb_wf_flexdyn.web.html b/biobb_wf_flexdyn/html/biobb_wf_flexdyn.web.html
@@ -7720,6 +7720,7 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
 <span class="kn">import</span> <span class="nn">nglview</span>
 <span class="kn">import</span> <span class="nn">simpletraj</span>
 <span class="kn">import</span> <span class="nn">plotly</span>
+<span class="kn">import</span> <span class="nn">sys</span>
 <span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
@@ -8125,8 +8126,7 @@ <h2 id="CONCOORD">CONCOORD<a class="anchor-link" href="#CONCOORD">¶</a></h2><p>
 <div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span>
-<span class="kn">from</span> <span class="nn">biobb_flexdyn.flexdyn.concoord_dist</span> <span class="kn">import</span> <span class="n">concoord_dist</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">biobb_flexdyn.flexdyn.concoord_dist</span> <span class="kn">import</span> <span class="n">concoord_dist</span>
 
 <span class="n">concoord_dist_pdb</span> <span class="o">=</span> <span class="n">pdbCode</span> <span class="o">+</span> <span class="s2">"_dist.pdb"</span>
 <span class="n">concoord_dist_gro</span> <span class="o">=</span> <span class="n">pdbCode</span> <span class="o">+</span> <span class="s2">"_dist.gro"</span>
@@ -8167,8 +8167,7 @@ <h2 id="CONCOORD">CONCOORD<a class="anchor-link" href="#CONCOORD">¶</a></h2><p>
 <div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span>
-<span class="kn">from</span> <span class="nn">biobb_flexdyn.flexdyn.concoord_disco</span> <span class="kn">import</span> <span class="n">concoord_disco</span>
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">biobb_flexdyn.flexdyn.concoord_disco</span> <span class="kn">import</span> <span class="n">concoord_disco</span>
 
 <span class="n">concoord_disco_pdb</span> <span class="o">=</span> <span class="n">pdbCode</span> <span class="o">+</span> <span class="s2">"_disco_traj.pdb"</span>
 <span class="n">concoord_disco_rmsd</span> <span class="o">=</span> <span class="n">pdbCode</span> <span class="o">+</span> <span class="s2">"_disco_rmsd.dat"</span>
@@ -11282,20 +11281,6 @@ <h2 id="Questions-&amp;-Comments">Questions &amp; Comments<a class="anchor-link"
 </div>
 </div>
 </div>
-</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
-<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
-<div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span> 
-</pre></div>
-</div>
-</div>
-</div>
-</div>
 </div>
 </main>
 </body>

diff --git a/biobb_wf_flexdyn/notebooks/biobb_wf_flexdyn.ipynb b/biobb_wf_flexdyn/notebooks/biobb_wf_flexdyn.ipynb
@@ -219,6 +219,7 @@
     "import nglview\n",
     "import simpletraj\n",
     "import plotly\n",
+    "import sys\n",
     "import plotly.graph_objs as go\n",
     "import numpy as np\n",
     "import pandas as pd\n",
@@ -526,7 +527,6 @@
    },
    "outputs": [],
    "source": [
-    "import sys\n",
     "from biobb_flexdyn.flexdyn.concoord_dist import concoord_dist\n",
     "\n",
     "concoord_dist_pdb = pdbCode + \"_dist.pdb\"\n",
@@ -563,7 +563,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sys\n",
     "from biobb_flexdyn.flexdyn.concoord_disco import concoord_disco\n",
     "\n",
     "concoord_disco_pdb = pdbCode + \"_disco_traj.pdb\"\n",
@@ -2922,13 +2921,6 @@
     "* BioExcel forum:\n",
     "    * [https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library](https://ask.bioexcel.eu/c/BioExcel-Building-Blocks-library)\n"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {