Writes a small chapter on how to install foldx

Author: miguelgondu

docs/protein-optimization/understanding_foldx/00-installing-foldx.md

@@ -1,3 +1,26 @@
 # Installing `foldx`
 
-[TODO: write]
+One of the main subset of black-boxes of `poli` relates to [`foldx`](https://foldxsuite.crg.eu/), a suite for protein design that allows you to compute, among other things, the change in free energy $dG$. This software and metric have been used as a black-box for optimization in recent work {cite:p}`stanton2022accelerating,jain:multiobjective-gflownet:2023`.
+
+`poli` can't install `foldx` for you automatically, since the software is provided under an academic license. To install `foldx`,
+1. Go to https://foldxsuite.crg.eu/
+2. Download the academic license. You'll likely be downloading a zip file with the executable and auxiliary files.
+3. Create a folder in your home directory called `foldx`.
+4. Place your executable under `~/foldx/foldx`. You will need to rename it.
+5. (If you downloaded `foldx` version 4) Make sure you have the `rotabase.txt` at `~/foldx/rotabase.txt`
+
+If you installed everything correctly, you should be able to run
+```bash
+~/foldx/foldx --help
+```
+
+:::{warning}
+
+If you are using mac, it is likely that the operating system will raise a warning about `foldx` being an unverified executable. You can remove the quarantine with the following command:
+
+```bash
+# Use at your own risk! This removes the quarantine from foldx 
+xattr -d com.apple.quarantine ~/foldx/foldx
+```
+
+:::

docs/protein-optimization/using_poli/the_basics/defining_an_observer.ipynb

@@ -422,7 +422,13 @@
     "2. how `initialize_observer` is called, and\n",
     "3. how each query to the objective function is observed.\n",
     "\n",
-    "If you are interested in using more complex logic for your logging, you can check the `examples` folder in `poli`, as they include two observers using `mlflow` and `wandb`."
+    ":::{tip}\n",
+    "\n",
+    "If you are interested in using more complex logic for your logging, you can check the `examples` folder in `poli`, as they include two observers using `mlflow` and `wandb`.\n",
+    "\n",
+    "`poli` is also able to isolate observers, and the `examples` folder also includes a description of how.\n",
+    "\n",
+    ":::\n"
    ]
   }
  ],