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Fix typos
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@jvsguerra
jvsguerra committed Oct 1, 2024
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4 changes: 2 additions & 2 deletions docs/_sources/plugins/pymol/tutorial/cage-cavity-detection.rst.txt
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Expand Up @@ -28,7 +28,7 @@ In PyMOL, open `PyMOL pyKVFinder Tools` under `Plugin` tab. The plugin will open

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**3. Select the object C1 to be analyzed with pyKVFinder.**
**3. Select the object C1 to be analyzed with pyKVFinder**

From the **Input PDB** drop-down menu, select the object `C1`. If it does not appear, press the **Refresh** button.

Expand All @@ -38,7 +38,7 @@ From the **Input PDB** drop-down menu, select the object `C1`. If it does not ap

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**4. Set the parameters for the cavity detection.**
**4. Set the parameters for the cavity detection**

Adjust the detection parameters to suit the supramolecular cage.

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4 changes: 2 additions & 2 deletions docs/plugins/pymol/tutorial/cage-cavity-detection.html
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Expand Up @@ -126,13 +126,13 @@ <h1>Supramolecular cage cavity detection<a class="headerlink" href="#supramolecu
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<p><strong>3. Select the object C1 to be analyzed with pyKVFinder.</strong></p>
<p><strong>3. Select the object C1 to be analyzed with pyKVFinder</strong></p>
<p>From the <strong>Input PDB</strong> drop-down menu, select the object <cite>C1</cite>. If it does not appear, press the <strong>Refresh</strong> button.</p>
<a class="reference internal image-reference" href="../../../_images/main_tab_4.png"><img alt="../../../_images/main_tab_4.png" class="align-center" src="../../../_images/main_tab_4.png" style="width: 800px;" /></a>
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<p><strong>4. Set the parameters for the cavity detection.</strong></p>
<p><strong>4. Set the parameters for the cavity detection</strong></p>
<p>Adjust the detection parameters to suit the supramolecular cage.</p>
<p>The detection parameters (i.e., Step Size, Probe In, Probe Out, Removal Distance, Volume Cutoff, and Surface Representation) will strongly influence the results. These parameters are cage dependent and may need to be adjusted to get an optimal detection for your supramolecular cage. Therefore, the best way to proceed is to iterate between changing the parameters and analyzing (visually) the modelled cavity.</p>
<p>For a detailed explanation of these parameters, refer to the paper <a class="reference external" href="https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c00328">J. Chem. Inf. Model. 2023, 63, 3772</a> and additional guidance <a class="reference external" href="https://kvfinder-web.cnpem.br">here</a>.</p>
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4 changes: 2 additions & 2 deletions docs/source/plugins/pymol/tutorial/cage-cavity-detection.rst
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Expand Up @@ -28,7 +28,7 @@ In PyMOL, open `PyMOL pyKVFinder Tools` under `Plugin` tab. The plugin will open

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**3. Select the object C1 to be analyzed with pyKVFinder.**
**3. Select the object C1 to be analyzed with pyKVFinder**

From the **Input PDB** drop-down menu, select the object `C1`. If it does not appear, press the **Refresh** button.

Expand All @@ -38,7 +38,7 @@ From the **Input PDB** drop-down menu, select the object `C1`. If it does not ap

|
**4. Set the parameters for the cavity detection.**
**4. Set the parameters for the cavity detection**

Adjust the detection parameters to suit the supramolecular cage.

Expand Down

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Coverage

Coverage Report
FileStmtsMissCoverMissing
pyKVFinder
   grid.py72911285%918, 922, 2243–2263, 2400–2477, 2749–2766, 2867–2936
   main.py3616981%93, 97, 105, 114, 142–148, 495, 660, 1061, 1068, 1078, 1089, 1108, 1113–1114, 1340, 1345, 1351, 1358, 1361–1364, 1368–1373, 1385, 1395, 1424–1425, 1430–1431, 1436–1437, 1497–1502, 1508, 1513–1518, 1578, 1580, 1593, 1704, 1706, 1712, 1714, 1720, 1725, 1729, 1782–1792, 1818
   utils.py312698%571, 603, 606–608, 630
TOTAL140218787% 

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