Fixed outputs tutorial

biobb_wf_amber/docs/source/abc_setup_tutorial.md

@@ -118,6 +118,7 @@ if 'google.colab' in sys.modules:
 import nglview
 import ipywidgets
 import plotly
+import sys
 import plotly.graph_objs as go
 ```
 
@@ -1773,10 +1774,10 @@ sander_mdrun(input_top_path=dna_leap_top_4fs_path,
 ## Output files
 
 Important **Output files** generated:
- - sander.md.nc: **Final trajectory** of the MD setup protocol (netcdf).
- - structure.ions.parmtop: **Final topology** of the MD system.
- - structure.leap.4fs.top: **Final topology** of the MD system with **hydrogen mass repartition** (allowing 4fs timestep).
- - sander.md.ncrst: **Final restart file** of the MD setup protocol (ncrst).
+ - **output_md_traj_path** (sander.md.nc): **Final trajectory** of the MD setup protocol (netcdf).
+ - **output_ions_top_path** (structure.ions.parmtop): **Final topology** of the MD system.
+ - **dna_leap_top_4fs_path** (structure.leap.4fs.top): **Final topology** of the MD system with **hydrogen mass repartition** (allowing 4fs timestep).
+ - **output_md_rst_path** (sander.md.ncrst): **Final restart file** of the MD setup protocol (ncrst).
 
 
 ```python

biobb_wf_amber/docs/source/md_setup_lig_tutorial.md

@@ -116,6 +116,7 @@ if 'google.colab' in sys.modules:
 import nglview
 import ipywidgets
 import plotly
+import sys
 from plotly import subplots
 import plotly.graph_objs as go
 
@@ -1501,16 +1502,15 @@ view
 ## Output files
 
 Important **Output files** generated:
- - structure.ions.pdb: **System structure** of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  
- - sander.free.netcdf: **Final trajectory** of the MD setup protocol.
- - sander.free.rst: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.
- - structure.ions.parmtop: **Final topology** of the MD system in AMBER Parm7 format.
+ - **output_ions_pdb_path** (structure.ions.pdb): **System structure** of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  
+ - **output_free_traj_path** (sander.free.netcdf): **Final trajectory** of the MD setup protocol.
+ - **output_free_rst_path** (sander.free.rst): **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.
+ - **output_ions_top_path** (structure.ions.parmtop): **Final topology** of the MD system in AMBER Parm7 format.
 
 **Analysis** (MD setup check) output files generated:
- - 3htb_rms_first.dat: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.
- - 3htb_rms_exp.dat: **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.
- - 3htb_rgyr.dat: **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.
-
+ - **output_rms_first** (3htb_rms_first.dat): **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.
+ - **output_rms_exp** (3htb_rms_exp.dat): **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.
+ - **output_rgyr** (3htb_rgyr.dat): **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.
 
 ***
 <a id="questions"></a>

biobb_wf_amber/docs/source/md_setup_ph_tutorial.md

@@ -111,6 +111,7 @@ if 'google.colab' in sys.modules:
 import nglview
 import ipywidgets
 import plotly
+import sys
 from plotly import subplots
 import plotly.graph_objs as go
 
@@ -989,8 +990,8 @@ An additional recommended and useful study is to repeat the **constant pH** simu
 ## Output files
 
 Important **Output files** generated:
- - cphstats.pH.dat: **Predicted pKa values** extracted from the constant pH MD simulation.   
- - cphstats.pH.pop.dat: **Populations** of every state for every **titratable residue**, fraction of snapshots that the system spent in each state for each residue.
+ - **output_pH_dat_path** (cphstats.pH.dat): **Predicted pKa values** extracted from the constant pH MD simulation.   
+ - **output_pH_pop_path** (cphstats.pH.pop.dat): **Populations** of every state for every **titratable residue**, fraction of snapshots that the system spent in each state for each residue.
 
 ***
 <a id="questions"></a>

biobb_wf_amber/docs/source/md_setup_tutorial.md

@@ -111,6 +111,7 @@ if 'google.colab' in sys.modules:
 import nglview
 import ipywidgets
 import plotly
+import sys
 from plotly import subplots
 import plotly.graph_objs as go
 
@@ -1264,15 +1265,15 @@ view
 ## Output files
 
 Important **Output files** generated:
- - structure.ions.pdb: **System structure** of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  
- - sander.free.netcdf: **Final trajectory** of the MD setup protocol.
- - sander.free.rst: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.
- - structure.ions.parmtop: **Final topology** of the MD system in AMBER Parm7 format.
+ - **output_ions_pdb_path** (structure.ions.pdb): **System structure** of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  
+ - **output_free_traj_path** (sander.free.netcdf): **Final trajectory** of the MD setup protocol.
+ - **output_free_rst_path** (sander.free.rst): **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.
+ - **output_ions_top_path** (structure.ions.parmtop): **Final topology** of the MD system in AMBER Parm7 format.
 
 **Analysis** (MD setup check) output files generated:
- - 1aki_rms_first.dat: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.
- - 1aki_rms_exp.dat: **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.
- - 1aki_rgyr.dat: **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.
+ - **output_rms_first** (1aki_rms_first.dat): **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.
+ - **output_rms_exp** (1aki_rms_exp.dat): **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.
+ - **output_rgyr** (1aki_rgyr.dat): **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.
 
 
 ***

biobb_wf_amber/html/abc_setup/biobb_wf_amber_abc_setup.web.html

@@ -7664,6 +7664,7 @@ <h2 id="Auxiliary-libraries">Auxiliary libraries<a class="anchor-link" href="#Au
 <div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">nglview</span>
 <span class="kn">import</span> <span class="nn">ipywidgets</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>
 </pre></div>
 </div>
@@ -10127,10 +10128,10 @@ <h2 id="Free-Molecular-Dynamics-Simulation">Free Molecular Dynamics Simulation<a
 <p><a id="output"></a></p>
 <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
 <ul>
-<li>sander.md.nc: <strong>Final trajectory</strong> of the MD setup protocol (netcdf).</li>
-<li>structure.ions.parmtop: <strong>Final topology</strong> of the MD system.</li>
-<li>structure.leap.4fs.top: <strong>Final topology</strong> of the MD system with <strong>hydrogen mass repartition</strong> (allowing 4fs timestep).</li>
-<li>sander.md.ncrst: <strong>Final restart file</strong> of the MD setup protocol (ncrst).</li>
+<li><strong>output_md_traj_path</strong> (sander.md.nc): <strong>Final trajectory</strong> of the MD setup protocol (netcdf).</li>
+<li><strong>output_ions_top_path</strong> (structure.ions.parmtop): <strong>Final topology</strong> of the MD system.</li>
+<li><strong>dna_leap_top_4fs_path</strong> (structure.leap.4fs.top): <strong>Final topology</strong> of the MD system with <strong>hydrogen mass repartition</strong> (allowing 4fs timestep).</li>
+<li><strong>output_md_rst_path</strong> (sander.md.ncrst): <strong>Final restart file</strong> of the MD setup protocol (ncrst).</li>
 </ul>
 </div>
 </div>

biobb_wf_amber/html/md_setup/biobb_wf_amber_md_setup.web.html

@@ -7659,6 +7659,7 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
 <div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">nglview</span>
 <span class="kn">import</span> <span class="nn">ipywidgets</span>
 <span class="kn">import</span> <span class="nn">plotly</span>
+<span class="kn">import</span> <span class="nn">sys</span>
 <span class="kn">from</span> <span class="nn">plotly</span> <span class="kn">import</span> <span class="n">subplots</span>
 <span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
 
@@ -9529,16 +9530,16 @@ <h3 id="Step-2:-Visualizing-the-generated-dehydrated-trajectory.">Step 2: Visual
 <p><a id="output"></a></p>
 <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
 <ul>
-<li>structure.ions.pdb: <strong>System structure</strong> of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  </li>
-<li>sander.free.netcdf: <strong>Final trajectory</strong> of the MD setup protocol.</li>
-<li>sander.free.rst: <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
-<li>structure.ions.parmtop: <strong>Final topology</strong> of the MD system in AMBER Parm7 format.</li>
+<li><strong>output_ions_pdb_path</strong> (structure.ions.pdb): <strong>System structure</strong> of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  </li>
+<li><strong>output_free_traj_path</strong> (sander.free.netcdf): <strong>Final trajectory</strong> of the MD setup protocol.</li>
+<li><strong>output_free_rst_path</strong> (sander.free.rst): <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
+<li><strong>output_ions_top_path</strong> (structure.ions.parmtop): <strong>Final topology</strong> of the MD system in AMBER Parm7 format.</li>
 </ul>
 <p><strong>Analysis</strong> (MD setup check) output files generated:</p>
 <ul>
-<li>1aki_rms_first.dat: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>1aki_rms_exp.dat: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>1aki_rgyr.dat: <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
+<li><strong>output_rms_first</strong> (1aki_rms_first.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
+<li><strong>output_rms_exp</strong> (1aki_rms_exp.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
+<li><strong>output_rgyr</strong> (1aki_rgyr.dat): <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
 </ul>
 </div>
 </div>

biobb_wf_amber/html/md_setup_lig/biobb_wf_amber_md_setup_lig.web.html

@@ -7664,6 +7664,7 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
 <div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">nglview</span>
 <span class="kn">import</span> <span class="nn">ipywidgets</span>
 <span class="kn">import</span> <span class="nn">plotly</span>
+<span class="kn">import</span> <span class="nn">sys</span>
 <span class="kn">from</span> <span class="nn">plotly</span> <span class="kn">import</span> <span class="n">subplots</span>
 <span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
 
@@ -9914,16 +9915,16 @@ <h3 id="Step-2:-Visualizing-the-generated-dehydrated-trajectory.">Step 2: Visual
 <p><a id="output"></a></p>
 <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
 <ul>
-<li>structure.ions.pdb: <strong>System structure</strong> of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  </li>
-<li>sander.free.netcdf: <strong>Final trajectory</strong> of the MD setup protocol.</li>
-<li>sander.free.rst: <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
-<li>structure.ions.parmtop: <strong>Final topology</strong> of the MD system in AMBER Parm7 format.</li>
+<li>output_ions_pdb_path (structure.ions.pdb): <strong>System structure</strong> of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  </li>
+<li>output_free_traj_path (sander.free.netcdf): <strong>Final trajectory</strong> of the MD setup protocol.</li>
+<li>output_free_rst_path (sander.free.rst): <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
+<li>output_ions_top_path (structure.ions.parmtop): <strong>Final topology</strong> of the MD system in AMBER Parm7 format.</li>
 </ul>
 <p><strong>Analysis</strong> (MD setup check) output files generated:</p>
 <ul>
-<li>3htb_rms_first.dat: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>3htb_rms_exp.dat: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>3htb_rgyr.dat: <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
+<li>output_rms_first (3htb_rms_first.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
+<li>output_rms_exp (3htb_rms_exp.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
+<li>output_rgyr (3htb_rgyr.dat): <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
 </ul>
 </div>
 </div>

biobb_wf_amber/html/md_setup_ph/biobb_wf_amber_md_setup_ph.web.html

@@ -7662,6 +7662,7 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
 <div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">nglview</span>
 <span class="kn">import</span> <span class="nn">ipywidgets</span>
 <span class="kn">import</span> <span class="nn">plotly</span>
+<span class="kn">import</span> <span class="nn">sys</span>
 <span class="kn">from</span> <span class="nn">plotly</span> <span class="kn">import</span> <span class="n">subplots</span>
 <span class="kn">import</span> <span class="nn">plotly.graph_objs</span> <span class="k">as</span> <span class="nn">go</span>
 
@@ -9087,8 +9088,8 @@ <h3 id="Last-Remarks">Last Remarks<a class="anchor-link" href="#Last-Remarks">¶
 <p><a id="output"></a></p>
 <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
 <ul>
-<li>cphstats.pH.dat: <strong>Predicted pKa values</strong> extracted from the constant pH MD simulation.</li>
-<li>cphstats.pH.pop.dat: <strong>Populations</strong> of every state for every <strong>titratable residue</strong>, fraction of snapshots that the system spent in each state for each residue.</li>
+<li><strong>output_pH_dat_path</strong> (cphstats.pH.dat): <strong>Predicted pKa values</strong> extracted from the constant pH MD simulation.</li>
+<li><strong>output_pH_pop_path</strong> (cphstats.pH.pop.dat): <strong>Populations</strong> of every state for every <strong>titratable residue</strong>, fraction of snapshots that the system spent in each state for each residue.</li>
 </ul>
 </div>
 </div>

biobb_wf_amber/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb

@@ -149,6 +149,7 @@
     "import nglview\n",
     "import ipywidgets\n",
     "import plotly\n",
+    "import sys\n",
     "import plotly.graph_objs as go"
    ]
   },
@@ -2127,10 +2128,10 @@
     "## Output files\n",
     "\n",
     "Important **Output files** generated:\n",
-    " - {{output_md_traj_path}}: **Final trajectory** of the MD setup protocol (netcdf).\n",
-    " - {{output_ions_top_path}}: **Final topology** of the MD system.\n",
-    " - {{dna_leap_top_4fs_path}}: **Final topology** of the MD system with **hydrogen mass repartition** (allowing 4fs timestep).\n",
-    " - {{output_md_rst_path}}: **Final restart file** of the MD setup protocol (ncrst)."
+    " - **output_md_traj_path** (sander.md.nc): **Final trajectory** of the MD setup protocol (netcdf).\n",
+    " - **output_ions_top_path** (structure.ions.parmtop): **Final topology** of the MD system.\n",
+    " - **dna_leap_top_4fs_path** (structure.leap.4fs.top): **Final topology** of the MD system with **hydrogen mass repartition** (allowing 4fs timestep).\n",
+    " - **output_md_rst_path** (sander.md.ncrst): **Final restart file** of the MD setup protocol (ncrst)."
    ]
   },
   {