Update documentation

docs/_sources/package/tutorial/index.rst.txt

@@ -990,6 +990,8 @@ We can preview our modelled molecule in the 3D grid by running:
   :width: 500
   :align: center
 
+|
+
 We can also export our modelled molecule int the 3D grid by running:
 
 .. code-block:: python
@@ -1050,6 +1052,8 @@ We can preview our modelled molecule in the 3D grid by running:
   :width: 500
   :align: center
 
+|
+
 Now, we can estimate the vdW volume by running:
 
 .. code-block:: python
@@ -1104,6 +1108,8 @@ We can preview our modelled molecule in the 3D grid by running:
   :width: 500
   :align: center
 
+|
+
 Now, we can estimate the vdW volume by running:
 
 .. code-block:: python

docs/_sources/plugins/pymol/tutorial/biomolecular-cavity-detection.rst.txt

@@ -12,6 +12,8 @@ First, load the `1FMO.pdb` and `ADN.pdb` file into PyMOL:
     :width: 800
     :align: center
 
+|
+
 Whole biomolecule detection
 ---------------------------
 
@@ -25,23 +27,31 @@ The **Input PDB** selection sets which object will be analyzed by pyKVFinder. Se
     :width: 800
     :align: center
 
+|
+
 To run pyKVFinder with the default parameters, just click **Run pyKVFinder** button.
 
 .. image:: ../images/main_tab_2.png
     :width: 800
     :align: center
 
+|
+
 After execution is complete, cavities PDB is loaded into PyMOL viewer as \<Output Base Name\>.KVFinder.output object and the results file is loaded on the **Results** tab. In addition, the focus automatically shifts to **Results** tab.
 
 .. image:: ../images/results_tab_1.png
     :width: 800
     :align: center
 
+|
+
 We can select cavities in the **Volume** or **Surface Area** lists to highlight them on a new object called **cavities**, identifying each cavity. Additionally, we can select cavity tags in the **Interface Residues** list to highlight residues around the cavities on a new object named **residues**.
 
 .. image:: ../images/results_tab_2.png
     :width: 800
 
+|
+
 .. note::
 
     The interface residues surrounding the cavity KAH are colored in green (sticks), the surface points are colored in red (nb_spheres) and the remaining cavity points are colored in blue (non_bounded).
@@ -51,6 +61,8 @@ We can visualize depth of the cavity points by clicking on **Depth** option on *
 .. image:: ../images/results_tab_3.png
     :width: 800
 
+|
+
 .. note::
 
     The cavity points are colored using a gradient from blue to red to represent the depth of each point. The blue points correspond to the shallowest points on the cavity-bulk boundary, while the red points correspond to the deepest points. The depth scale ranges from 0.0 to the maximum depth of all cavities
@@ -60,6 +72,8 @@ We can visualize hydropathy of the surface points by clicking on **Hydropathy**
 .. image:: ../images/results_tab_4.png
     :width: 800
 
+|
+
 .. note::
 
     The surface points are colored based on the closest amino acid to it. The Eisenberg & Weiss hydrophobicity scale ranges from -1.42 (highly hydrophobic) to 2.6 (highly hydrophilic).
@@ -93,6 +107,8 @@ As mentioned above, adjusting the Probe Out size changes the level of the cavity
 .. image:: ../images/pymol_viewer_2.png
     :width: 800
 
+|
+
 Again, copy the cavity KAF (same region of the previous detection) to a new object (KAF_PO).
 
 .. code-block:: bash
@@ -105,6 +121,8 @@ Again, copy the cavity KAF (same region of the previous detection) to a new obje
 .. image:: ../images/pymol_viewer_3.png
     :width: 800
 
+|
+
 The cavity detected with the 4 Å Probe Out (magenta) has a lower boundary than that detected with the 8 Å probe (white). Therefore, by increasing the size of the Probe Out, the cavity boundary is also raised.
 
 Adjusting Removal Distance
@@ -115,6 +133,8 @@ Besides adjusting the Probe Out size, we can also adjust the Removal Distance to
 .. image:: ../images/pymol_viewer_4.png
     :width: 800
 
+|
+
 Again, copy the cavity KAG (same region of the previous detections) to a new object (KAG_RD).
 
 .. code-block:: bash
@@ -152,18 +172,24 @@ On the **Search Space** tab, select **Box Adjustment** check box. This will enab
 .. image:: ../images/search_space_tab_1.png
     :width: 800
 
+|
+
 Then, select the adenosine ligand on ADN object. This can be made on the PyMOL viewer by clicking on the ligand structure or using ``select resn ADN`` PyMOL command.
 
 Click on **Draw Box** Button. This will create a custom box that limits the search space. It is fully customizable, but we will not change it for now.
 
 .. image:: ../images/pymol_viewer_6.png
     :width: 800
 
+|
+
 On the **Main** tab, change **Removal Distance** back to 2.4 Å. Run pyKVFinder again.
 
 .. image:: ../images/pymol_viewer_7.png
     :width: 800
 
+|
+
 Now, let's customize the box parameters to segment the binding site of our target protein.
 
 Each axis is associated with one color (red with X, green with Y and blue with Z). The adjustment is made by the arrows or directly setting the value in the entry on the **Search Space** tab in the **Box Adjustment** group. We can also adjust the box angles by the same procedure. After altering the values, just click on **Redraw** button to redraw the box object using the new values.
@@ -173,6 +199,8 @@ Then, on the **Search Space** tab, reduce **Maximum X** to 1.0 Å and click **Re
 .. image:: ../images/pymol_viewer_8.png
     :width: 800
 
+|
+
 Lastly, click on **Delete Box** button to delete the custom box.
 
 Ligand adjustment mode
@@ -187,12 +215,18 @@ Still on the **Search Space** tab, click on the check button **Ligand Adjustment
 .. image:: ../images/search_space_tab_2.png
     :width: 800
 
+|
+
 Click the **Refresh** button to display all objects in the scene in the Ligand PDB combo box. Select the **ADN** on the combo box and reduce Ligand Cutoff to 3.0 Å. Run pyKVFinder again.
 
 .. image:: ../images/pymol_viewer_9.png
     :width: 800
 
+|
+
 On the **Search Space** tab, increase **Ligand Cutoff** back to 5.0 Å. Back on the **Main** tab, increase **Probe Out** to 10.0 Å and reduce **Removal Distance** to 0.0 Å. Run pyKVFinder again.
 
 .. image:: ../images/pymol_viewer_10.png
     :width: 800
+
+|

docs/package/tutorial/index.html

@@ -1100,6 +1100,9 @@ <h3>1. vdW volume<a class="headerlink" href="#vdw-volume" title="Link to this he
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="../../_images/vdw-grid.png"><img alt="../../_images/vdw-grid.png" class="align-center" src="../../_images/vdw-grid.png" style="width: 500px;" /></a>
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
 <p>We can also export our modelled molecule int the 3D grid by running:</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">molecule</span><span class="o">.</span><span class="n">preview</span><span class="p">()</span>
 </pre></div>
@@ -1149,6 +1152,9 @@ <h3>2. SES volume<a class="headerlink" href="#ses-volume" title="Link to this he
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="../../_images/ses-grid.png"><img alt="../../_images/ses-grid.png" class="align-center" src="../../_images/ses-grid.png" style="width: 500px;" /></a>
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
 <p>Now, we can estimate the vdW volume by running:</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">molecule</span><span class="o">.</span><span class="n">volume</span><span class="p">()</span>
 <span class="go">90.8</span>
@@ -1194,6 +1200,9 @@ <h3>3. SAS volume<a class="headerlink" href="#sas-volume" title="Link to this he
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="../../_images/sas-grid.png"><img alt="../../_images/sas-grid.png" class="align-center" src="../../_images/sas-grid.png" style="width: 500px;" /></a>
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
 <p>Now, we can estimate the vdW volume by running:</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">molecule</span><span class="o">.</span><span class="n">volume</span><span class="p">()</span>
 <span class="go">340.28</span>