Apply suggestions from code review

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

Author: IAlibay

cookbook/openfold3_to_openfe.ipynb

@@ -17,7 +17,7 @@
    "source": [
     "## Introduction\n",
     "\n",
-    "This notebook offers a brief preview of some of the steps one would need to go through to calculate binding affinities using [OpenFE](https://docs.openfree.energy/en/latest/) with [OpenFold3](https://openfold-3.readthedocs.io/en/latest/) generated structures.\n",
+    "This notebook offers a brief preview of some of the steps you may need to go through to calculate binding affinities using [OpenFE](https://docs.openfree.energy/en/latest/) with [OpenFold3](https://openfold-3.readthedocs.io/en/latest/) generated structures.\n",
     "\n",
     "Notably, we will demonstrate how to generate a set of predictions, clean them up for use in molecular dynamics simulations, and then apply them to both relative binding free energy (RBFE) and absolute binding free energy (ABFE) methods."
    ]
@@ -29,7 +29,7 @@
    "source": [
     "<div class=\"alert alert-block alert-danger\"> \n",
     "⚠️ <b>Important Note:</b>\n",
-    "    Please note that this notebook does not offer an exhaustive look into all everyone you may need to do when parsing OpenFold3 inputs into OpenFE. Where possible, we offer insights into some of the other hurdles you may face, but you are likely to encounter more in production settings.\n",
+    "    Please note that this notebook does not offer an exhaustive look into everything you may need to do when parsing OpenFold3 inputs into OpenFE. Where possible, we offer insights into some of the other hurdles you may face, but you are likely to encounter more in production settings.\n",
     "</div>"
    ]
   },
@@ -47,7 +47,7 @@
     "\n",
     "**The tutorial is broken into the following steps:**\n",
     "\n",
-    "1. Run cofolding with OpenFold3 on a set of TYK2 ligands\n",
+    "1. Running cofolding with OpenFold3 on a set of TYK2 ligands\n",
     "\n",
     "2. Processing the OpenFold3 output for use with OpenFE\n",
     "\n",
@@ -138,7 +138,7 @@
    "id": "80da7967-8046-44e4-aef7-c81ac6712f98",
    "metadata": {},
    "source": [
-    "We then create the json file that will be the OpenFold input."
+    "We then create the JSON file that will be the OpenFold input."
    ]
   },
   {
@@ -231,13 +231,11 @@
     "  - This is necessary for RBFE simulations, where a single structure must be kept constant throughout the transformations. Note that for ABFE simulations, this step can be avoided.\n",
     "  - For the sake of this demonstration, we will be choosing the predicted structure that is bound to the ligand occupying the largest volume. The idea here being that hopefully the binding site of that structure can accomodate all the other ligands. We note that in practice this is not always true.\n",
     "\n",
-    "2. Aligning all the structures to the chosen structure\n",
+    "2. Aligning the structures to the reference & extracting the necessary structures\n",
     "\n",
-    "  - This is so that we can extract the ligands and use them with the chosen structure.\n",
+    "  - This is so that we can extract the ligands and use them with the chosen structure.\n",.\n",
     "\n",
-    "3. Extracting the ligands to SDF files and the chosen protein structure to a PDB file.\n",
-    "\n",
-    "4. Fixing protonation & capping issues with the PDB file.\n",
+    "3. Fixing & protonating the reference protein structure.\n",
     "\n",
     "\n",
     "#### Choosing a reference protein structure\n",
@@ -324,7 +322,7 @@
     "import pathlib\n",
     "from rdkit.Chem.Descriptors3D import Asphericity\n",
     "\n",
-    "# gather all the complexes and align to a single structure which has the largest ligand by volume?\n",
+    "# gather all the complexes and align to a single structure which has the largest ligand by volume \n",
     "ligand_templates = {\n",
     "    \"lig_ejm_31\": \"CC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1\",\n",
     "    \"lig_ejm_42\": \"CCC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1\",\n",
@@ -500,7 +498,8 @@
    ],
    "source": [
     "# now run the reference protein through pdbfixer\n",
-    "! pdbfixer assets/of3_output/p_aligned/protein.pdb --add-atoms=all --add-residues --output=assets/of3_output/p_aligned/protein_fixed.pdb"
+    "%% bash\n"
+    "pdbfixer assets/of3_output/p_aligned/protein.pdb --add-atoms=all --add-residues --output=assets/of3_output/p_aligned/protein_fixed.pdb"
    ]
   },
   {