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MolSSI-Education · Jul 2, 2024 · 3e152ef · 3e152ef
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diff --git a/_images/88c52027db529de7c3ae7d423a47111ad4d11dc5acab0479ef51e2b280a83398.png b/_images/88c52027db529de7c3ae7d423a47111ad4d11dc5acab0479ef51e2b280a83398.png
diff --git a/_images/a3c950784f486b8b28dce3de97f53fa6c362f0e4dda61f34fff77d7fca88a748.png b/_images/a3c950784f486b8b28dce3de97f53fa6c362f0e4dda61f34fff77d7fca88a748.png
diff --git a/_images/a951e6aad5e398bb17cba2a433ced6358be44b366ddd21b896699eebb23e7172.png b/_images/a951e6aad5e398bb17cba2a433ced6358be44b366ddd21b896699eebb23e7172.png
diff --git a/_images/bd02bcab94c68d2fa2388a53115c0c313bb65e946e426bbbeb940cbe6f70f91d.png b/_images/bd02bcab94c68d2fa2388a53115c0c313bb65e946e426bbbeb940cbe6f70f91d.png
diff --git a/chapters/Creating_Plots_in_Jupyter_Notebooks.html b/chapters/Creating_Plots_in_Jupyter_Notebooks.html
@@ -465,7 +465,7 @@ <h2>Using Matplotlib.pyplot<a class="headerlink" href="#using-matplotlib-pyplot"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;matplotlib.collections.PathCollection at 0x7fae3b0f3ed0&gt;
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;matplotlib.collections.PathCollection at 0x7f7ce4593f90&gt;
 </pre></div>
 </div>
 <img alt="../_images/ceaaf9ece89b08454dd7707908e35945d376737045e460c49eebbcadd1df23cf.png" src="../_images/ceaaf9ece89b08454dd7707908e35945d376737045e460c49eebbcadd1df23cf.png" />
@@ -481,7 +481,7 @@ <h2>Using Matplotlib.pyplot<a class="headerlink" href="#using-matplotlib-pyplot"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7fae3b190f10&gt;]
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7f7ce45a2bd0&gt;]
 </pre></div>
 </div>
 <img alt="../_images/720b0e757eaaa9fb1a4f291e9abd2db1cede159aac7a370b4b02faa4ef0066e2.png" src="../_images/720b0e757eaaa9fb1a4f291e9abd2db1cede159aac7a370b4b02faa4ef0066e2.png" />
@@ -579,7 +579,7 @@ <h2>Scatter Plots with Seaborn<a class="headerlink" href="#scatter-plots-with-se
 <div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;Axes: xlabel=&#39;Protein Concentration (mg/mL)&#39;, ylabel=&#39;A595&#39;&gt;
 </pre></div>
 </div>
-<img alt="../_images/a3c950784f486b8b28dce3de97f53fa6c362f0e4dda61f34fff77d7fca88a748.png" src="../_images/a3c950784f486b8b28dce3de97f53fa6c362f0e4dda61f34fff77d7fca88a748.png" />
+<img alt="../_images/88c52027db529de7c3ae7d423a47111ad4d11dc5acab0479ef51e2b280a83398.png" src="../_images/88c52027db529de7c3ae7d423a47111ad4d11dc5acab0479ef51e2b280a83398.png" />
 </div>
 </div>
 <div class="exercise admonition">
@@ -628,7 +628,7 @@ <h2>Scatter Plots with Seaborn<a class="headerlink" href="#scatter-plots-with-se
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/bd02bcab94c68d2fa2388a53115c0c313bb65e946e426bbbeb940cbe6f70f91d.png" src="../_images/bd02bcab94c68d2fa2388a53115c0c313bb65e946e426bbbeb940cbe6f70f91d.png" />
+<img alt="../_images/a951e6aad5e398bb17cba2a433ced6358be44b366ddd21b896699eebb23e7172.png" src="../_images/a951e6aad5e398bb17cba2a433ced6358be44b366ddd21b896699eebb23e7172.png" />
 </div>
 </div>
 <div class="key admonition">

diff --git a/chapters/MolVis_with_iCN3D.html b/chapters/MolVis_with_iCN3D.html
diff --git a/chapters/binding_site_investigation.html b/chapters/binding_site_investigation.html
@@ -470,7 +470,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"model_id": "b99491671e01419ea6e9dd4d41e4527f", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "1c0a1db552e24401b76ab762e90bcce1"}</script></div>
 </div>
 <p>Text here about NGLView</p>
 <div class="cell docutils container">
@@ -481,7 +481,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"model_id": "2401aa6c72574b7daf42ea1fa5b8be4b", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "f4bf0df4e8374061a847a80ef8387aeb"}</script></div>
 </div>
 <p>This view looks a bit messy. MDAnalysis has a human readable <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/selections.html">selection syntax</a>
 that allows us to isolate parts of our structure. We will take our MDAnalysis Universe (the variable <code class="docutils literal notranslate"><span class="pre">u</span></code>) and use the <code class="docutils literal notranslate"><span class="pre">select_atoms</span></code> function.
@@ -505,7 +505,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"model_id": "e76e61ee77e54089b97cc13e88d4ba18", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "57cc534d74ca4c49bd4b86168af63d12"}</script></div>
 </div>
 <p>Upon viewing this structure, you will notice that our ligand seems to appear twice.
 If you open the PDB file to investigate, you will see the following in the ligand section:</p>
@@ -543,7 +543,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"model_id": "39f72e25876f4a59a5451baa0beb88fd", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "380e3bce47be44c28bb972fd2df092b2"}</script></div>
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@@ -552,7 +552,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"model_id": "86508b08ae76439f89976b8e570328a8", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "a171ea6d7db146da9e45b1b966d34e29"}</script></div>
 </div>
 <p>When we inspect the ligand in the binding site, we notice a few things.
 First, the binding site has a large hydrophobic area on the surface.
@@ -577,7 +577,7 @@ <h2>Making a Map of Ligand Contacts<a class="headerlink" href="#making-a-map-of-
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/janash/miniconda3/envs/iqb-2024/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: &#39;formalcharges&#39; Using default value of &#39;0&#39;
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: &#39;formalcharges&#39; Using default value of &#39;0&#39;
   warnings.warn(&quot;Found no information for attr: &#39;{}&#39;&quot;
 </pre></div>
 </div>
@@ -603,7 +603,9 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 INFO:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
 INFO:Checking and transforming input arguments.
 INFO:Loading topology files.
-INFO:Loading molecule: pdb/protein_2zq2.pdb
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Loading molecule: pdb/protein_2zq2.pdb
 ERROR:Error parsing line: invalid literal for int() with base 10: &#39;&#39;
 ERROR:&lt;REMARK     2&gt;
 ERROR:Truncating remaining errors for record type:REMARK
@@ -666,7 +668,9 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 WARNING:Multiple occupancies found in GLN A 240. At least one of the instances is being ignored.
 INFO:Setting termini states for biomolecule chains.
 INFO:Loading forcefield.
-INFO:Loading hydrogen topology definitions.
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Loading hydrogen topology definitions.
 WARNING:Missing atom CG in residue LYS A 222
 WARNING:Missing atom CD in residue LYS A 222
 WARNING:Missing atom CE in residue LYS A 222
@@ -687,9 +691,15 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 INFO:Updating disulfide bridges.
 INFO:Debumping biomolecule.
 INFO:Adding hydrogens to biomolecule.
-INFO:Debumping biomolecule (again).
-INFO:Optimizing hydrogen bonds
-INFO:Applying force field to biomolecule states.
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Debumping biomolecule (again).
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Optimizing hydrogen bonds
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Applying force field to biomolecule states.
 INFO:Regenerating headers.
 INFO:Regenerating PDB lines.
 WARNING:Ignoring 390 header lines in output.
@@ -722,6 +732,20 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 </pre></div>
 </div>
 </div>
+<div class="cell_output docutils container">
+<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
+<span class="ne">OSError</span><span class="g g-Whitespace">                                   </span>Traceback (most recent call last)
+<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">14</span><span class="p">],</span> <span class="n">line</span> <span class="mi">5</span>
+<span class="g g-Whitespace">      </span><span class="mi">1</span> <span class="kn">from</span> <span class="nn">rdkit</span> <span class="kn">import</span> <span class="n">Chem</span>
+<span class="g g-Whitespace">      </span><span class="mi">3</span> <span class="kn">from</span> <span class="nn">rdkit.Chem.AllChem</span> <span class="kn">import</span> <span class="n">AssignBondOrdersFromTemplate</span>
+<span class="ne">----&gt; </span><span class="mi">5</span> <span class="n">template</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">MolFromMol2File</span><span class="p">(</span><span class="s2">&quot;ligands/13U_ideal.mol2&quot;</span><span class="p">)</span>
+<span class="g g-Whitespace">      </span><span class="mi">6</span> <span class="n">pdb_ligand</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">MolFromPDBFile</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;pdb/ligand_A.pdb&quot;</span><span class="p">)</span>
+<span class="g g-Whitespace">      </span><span class="mi">8</span> <span class="n">template</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">RemoveAllHs</span><span class="p">(</span><span class="n">template</span><span class="p">)</span>
+
+<span class="ne">OSError</span>: Bad input file ligands/13U_ideal.mol2
+</pre></div>
+</div>
+</div>
 </div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">

diff --git a/chapters/nonlinear_regression_part_2.html b/chapters/nonlinear_regression_part_2.html
@@ -557,7 +557,7 @@ <h2>The Michaelis-Menten equation<a class="headerlink" href="#the-michaelis-ment
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7fcddd22e6d0&gt;]
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7efd3ce69790&gt;]
 </pre></div>
 </div>
 <img alt="../_images/ed2e8a80cd568b164f79f3c9cf21556ba7d5baac33497c50cc6db1e0744d85e0.png" src="../_images/ed2e8a80cd568b164f79f3c9cf21556ba7d5baac33497c50cc6db1e0744d85e0.png" />

diff --git a/chapters/rcsb_api.html b/chapters/rcsb_api.html
@@ -680,7 +680,7 @@ <h2>PDB Search API<a class="headerlink" href="#pdb-search-api" title="Link to th
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;bc667b42-9091-4a62-af30-c23666e5e7ba&#39;,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;817f2b57-9670-4609-9431-50845964fd08&#39;,
  &#39;result_type&#39;: &#39;entry&#39;,
  &#39;total_count&#39;: 668,
  &#39;result_set&#39;: [{&#39;identifier&#39;: &#39;2BMM&#39;, &#39;score&#39;: 1.0},
@@ -802,7 +802,7 @@ <h2>PDB Search API<a class="headerlink" href="#pdb-search-api" title="Link to th
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;f987c8a2-8c6f-487d-96af-dd0b32e8a43d&#39;,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;dc4f4404-d744-4a64-9bda-67402b963e68&#39;,
  &#39;result_type&#39;: &#39;entry&#39;,
  &#39;total_count&#39;: 571,
  &#39;result_set&#39;: [{&#39;identifier&#39;: &#39;1MBN&#39;, &#39;score&#39;: 1.0},

diff --git a/reports/chapters/binding_site_investigation.err.log b/reports/chapters/binding_site_investigation.err.log
@@ -0,0 +1,42 @@
+Traceback (most recent call last):
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 1314, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
+    return loop.run_until_complete(inner)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
+    return future.result()
+           ^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 709, in async_execute
+    await self.async_execute_cell(
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 1062, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
+    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
+nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
+------------------
+from rdkit import Chem
+
+from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
+
+template = Chem.MolFromMol2File("ligands/13U_ideal.mol2")
+pdb_ligand = Chem.MolFromPDBFile(f"pdb/ligand_A.pdb")
+
+template = Chem.RemoveAllHs(template)
+------------------
+
+
+[0;31m---------------------------------------------------------------------------[0m
+[0;31mOSError[0m                                   Traceback (most recent call last)
+Cell [0;32mIn[14], line 5[0m
+[1;32m      1[0m [38;5;28;01mfrom[39;00m [38;5;21;01mrdkit[39;00m [38;5;28;01mimport[39;00m Chem
+[1;32m      3[0m [38;5;28;01mfrom[39;00m [38;5;21;01mrdkit[39;00m[38;5;21;01m.[39;00m[38;5;21;01mChem[39;00m[38;5;21;01m.[39;00m[38;5;21;01mAllChem[39;00m [38;5;28;01mimport[39;00m AssignBondOrdersFromTemplate
+[0;32m----> 5[0m template [38;5;241m=[39m [43mChem[49m[38;5;241;43m.[39;49m[43mMolFromMol2File[49m[43m([49m[38;5;124;43m"[39;49m[38;5;124;43mligands/13U_ideal.mol2[39;49m[38;5;124;43m"[39;49m[43m)[49m
+[1;32m      6[0m pdb_ligand [38;5;241m=[39m Chem[38;5;241m.[39mMolFromPDBFile([38;5;124mf[39m[38;5;124m"[39m[38;5;124mpdb/ligand_A.pdb[39m[38;5;124m"[39m)
+[1;32m      8[0m template [38;5;241m=[39m Chem[38;5;241m.[39mRemoveAllHs(template)
+
+[0;31mOSError[0m: Bad input file ligands/13U_ideal.mol2
+
diff --git a/searchindex.js b/searchindex.js