Publish lessons - additions from UCL chemistry

_config.yml

@@ -3,6 +3,8 @@
 
 title: Python in Chemistry
 author: The Python in Chemistry Community 
+copyright: "2025"
+
 # logo: ./logo/logo.png
 
 # Force re-execution of notebooks on each build.

_toc.yml

@@ -6,36 +6,53 @@ root: intro
 parts:
   - caption: Python Lessons
     chapters:
-    - file: lessons/basics.md
+    - file: lessons/basics/basics.md
       sections:
       - file: lessons/basics/write_run_python.md
-      - file: lessons/basics/notebook.md
-    - file: lessons/manipulating_variables.md
+      - file: lessons/basics/using_jupyter_notebook.md
+      - file: lessons/basics/python_introduction.ipynb
+    - file: lessons/variables/manipulating_variables.md
       sections:
       - file: lessons/variables/Variable_data_types.ipynb
-      - file: lessons/variables/mathematical-operators.ipynb
-      - file: lessons/variables/Conditions.ipynb
-    - file: lessons/organising_code.md
+      - file: lessons/variables/lists_and_indexing.ipynb
+      - file: lessons/variables/mathematical_operators.ipynb
+      - file: lessons/variables/Comparisons.ipynb
+    - file: lessons/loops_functions/organising_code.md
       sections:
-      - file: lessons/loops_functions/For_Loop_Lesson.ipynb
-      - file: lessons/loops_functions/PyinC_while_loops_WIP.ipynb
+      - file: lessons/loops_functions/conditional_statements.ipynb
+      - file: lessons/loops_functions/for_loops.ipynb
+      - file: lessons/loops_functions/while_loops.ipynb
       - file: lessons/loops_functions/functions_and_scope.ipynb
-    - file: lessons/files.md
+      - file: lessons/loops_functions/tut_import_mod.ipynb
+    - file: lessons/files/files.md
       sections:
+      - file: lessons/files/files_file_types.ipynb
       - file: lessons/files/reading_files.ipynb
       - file: lessons/files/writing_files.ipynb
-    - file: lessons/common_libraries.md
+    - file: lessons/solving_problems/solving-problems.md
       sections:
-      - file: lessons/common_libs/python-in-chem_pyplot_basics_SM.ipynb
+      - file: lessons/solving_problems/errors_and_debug.ipynb
+      - file: lessons/solving_problems/writing_a_program.ipynb
+      - file: lessons/solving_problems/version_control.ipynb
+      - file: lessons/solving_problems/command_line.md
+      - file: lessons/solving_problems/flowcharts.ipynb
+      - file: lessons/solving_problems/style-and-comments.ipynb
+    - file: lessons/common_libs/common_libraries.md
+      sections:
+      - file: lessons/common_libs/matplotlib_pyplot_basics.ipynb
       - file: lessons/common_libs/Matplotlib_Documentation.ipynb
       - file: lessons/common_libs/Introduction_to_NumPy.ipynb
       - file: lessons/common_libs/NumPy_axes_operations.ipynb
+      - file: lessons/common_libs/argparse.ipynb
       - file: lessons/common_libs/intro_to_pandas.ipynb
-    - file: lessons/advanced_libraries.md
+    - file: lessons/advanced_libs/advanced_libraries.md
       sections:
       - file: lessons/advanced_libs/Intro_to_ASE.ipynb
       - file: lessons/advanced_libs/PiC_scipy.ipynb
       - file: lessons/advanced_libs/RDKit_drawing.ipynb
+    - file: lessons/further_info/further_info.md
+      sections:
+      - file: lessons/further_info/numerical_errors.ipynb
   - caption: Teaching Python in Chemistry Meeting Blogs
     chapters:
     - file: 2025-meeting

lessons/advanced_libs/Intro_to_ASE.ipynb

@@ -5,7 +5,7 @@
    "id": "1639ee9d-703b-4c01-9a65-45d2a84cf4b0",
    "metadata": {},
    "source": [
-    "## The Atomic Simulation Environment, ASE"
+    "# The Atomic Simulation Environment, ASE"
    ]
   },
   {

lessons/advanced_libs/RDKit_drawing.ipynb

@@ -215,6 +215,90 @@
     "Draw.MolToImage(m)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-success\"><b>Task 5: Using loops</b> \n",
+    "\n",
+    "When chemists want to store molecular structures in a computer they can store in an encoded way called SMILES strings.  You don't need to understand what these mean but just to know that libraries that can handle chemical structure can read them. The code below will import the RDKit package and print the structure of benzoic acid.  The code works by passing the SMILES string for benzoic acid to the function display_molecule that then draws it out.  Check out the functions lesson if you want to understand more about functions, but for this lesson all you just need to follow the syntax below.\n",
+    "\n",
+    "</div>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from rdkit import Chem\n",
+    "\n",
+    "def display_molecule (smiles_string):\n",
+    "    mol = Chem.MolFromSmiles(smiles_string)\n",
+    "    img=Chem.Draw.MolToImage(mol)\n",
+    "    display(img)\n",
+    "\n",
+    "# display the structure of benzoic acid\n",
+    "benzoic_acid_miles = \"C1=CC=C(C=C1)C(=O)O\"\n",
+    "display_molecule(benzoic_acid_miles)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-success\"><b>Task 5 continued</b> \n",
+    "Now you know how to print one molecule lets use your understanding of for loops to print lots of molecules.  Here are a list of the smiles strings of some interesting molecules, Dolutegravir a very important anti-hiv drug, Atovaquone which treats malaria and paclitaxol that is an important \n",
+    "\n",
+    "\n",
+    "<div>\n",
+    "<ul>\n",
+    "<li>C[C@@H]1CCO[C@@H]2N1C(=O)C3=C(C(=O)C(=CN3C2)C(=O)NCC4=C(C=C(C=C4)F)F)O\n",
+    "<li>C1CC(CCC1C2=CC=C(C=C2)Cl)C3=C(C4=CC=CC=C4C(=O)C3=O)O\n",
+    "<li>CC1=C2[C@H](C(=O)[C@@]3([C@H](C[C@@H]4[C@]([C@H]3[C@@H]([C@@](C2(C)C)(C[C@@H]1OC(=O)[C@@H]([C@H](C5=CC=CC=C5)NC(=O)C6=CC=CC=C6)O)O)OC(=O)C7=CC=CC=C7)(CO4)OC(=O)C)O)C)OC(=O)C\n",
+    "</ul>\n",
+    "    \n",
+    "</div>\n",
+    "\n",
+    "Using the concepts above write a for loop that will draw the structrue of all 3 molecules. You need to:\n",
+    "- define a list of the smiles strings\n",
+    "- loop through the list and display each molecule using the display_molecule function\n",
+    "\n",
+    "</div>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molecule_smiles = ['C[C@@H]1CCO[C@@H]2N1C(=O)C3=C(C(=O)C(=CN3C2)C(=O)NCC4=C(C=C(C=C4)F)F)O',\n",
+    "'C1CC(CCC1C2=CC=C(C=C2)Cl)C3=C(C4=CC=CC=C4C(=O)C3=O)O',\n",
+    "'CC1=C2[C@H](C(=O)[C@@]3([C@H](C[C@@H]4[C@]([C@H]3[C@@H]([C@@](C2(C)C)(C[C@@H]1OC(=O)[C@@H]([C@H](C5=CC=CC=C5)NC(=O)C6=CC=CC=C6)O)O)OC(=O)C7=CC=CC=C7)(CO4)OC(=O)C)O)C)OC(=O)C']\n",
+    "\n",
+    "for smiles in molecule_smiles:\n",
+    "    display_molecule(smiles)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<details><summary {style='color:beige;font-weight:bold'}> Click here to see a possible solution to Task 5 </summary>\n",
+    "\n",
+    "\n",
+    "```Python\n",
+    "molecule_smiles = ['C[C@@H]1CCO[C@@H]2N1C(=O)C3=C(C(=O)C(=CN3C2)C(=O)NCC4=C(C=C(C=C4)F)F)O',\n",
+    "'C1CC(CCC1C2=CC=C(C=C2)Cl)C3=C(C4=CC=CC=C4C(=O)C3=O)O',\n",
+    "'CC1=C2[C@H](C(=O)[C@@]3([C@H](C[C@@H]4[C@]([C@H]3[C@@H]([C@@](C2(C)C)(C[C@@H]1OC(=O)[C@@H]([C@H]>>>(C5=CC=CC=C5)NC(=O)C6=CC=CC=C6)O)O)OC(=O)C7=CC=CC=C7)(CO4)OC(=O)C)O)C)OC(=O)C']\n",
+    "\n",
+    "for smiles in molecule_smiles:\n",
+    "    display_molecule(smiles)\n",
+    "```"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {

lessons/basics/basics.md

@@ -0,0 +1,9 @@
+# Getting Started with Python
+
+Here, you will find how to start running Python.
+
+## What is Python
+
+[Python](https://en.wikipedia.org/wiki/Python_(programming_language)) is a high-level interpreted language that is widely used. This means it is written in a way that is close to standard English, reducing complexity for the programmer. 
+
+Due to this popularity there are many ways to install and to use it. In the following sections we will guide you on how to install and use Python