Updates the foldx example

Author: miguelgondu

docs/protein-optimization/_toc.yml

@@ -10,11 +10,7 @@ parts:
   - caption: The basics
     chapters:
       - file: using_poli/the_basics/intro_to_poli.ipynb
-      - file: using_poli/the_basics/registering_an_objective_function.md
       - file: using_poli/the_basics/defining_an_observer.ipynb
-      - file: using_poli/the_basics/defining_a_problem_solver.md
-      - file: using_poli/the_basics/optimizing_an_objective_function.md
-      - file: using_poli/the_basics/diving_deeper.md
   - caption: Examples
     chapters:
       - file: using_poli/optimization_examples/protein-stability-foldx/optimizing_protein_stability.ipynb

docs/protein-optimization/using_poli/optimization_examples/protein-stability-foldx/optimizing_protein_stability.ipynb

@@ -30,13 +30,21 @@
      "data": {
       "text/plain": [
        "['aloha',\n",
+       " 'dockstring',\n",
+       " 'drd3_docking',\n",
        " 'foldx_rfp_lambo',\n",
        " 'foldx_sasa',\n",
        " 'foldx_stability',\n",
        " 'foldx_stability_and_sasa',\n",
+       " 'gfp_cbas',\n",
+       " 'gfp_select',\n",
+       " 'penalized_logp_lambo',\n",
+       " 'rasp',\n",
        " 'rdkit_logp',\n",
        " 'rdkit_qed',\n",
+       " 'sa_tdc',\n",
        " 'super_mario_bros',\n",
+       " 'toy_continuous_problem',\n",
        " 'white_noise']"
       ]
      },
@@ -81,7 +89,7 @@
    "source": [
     "In this example, we will focus on optimizing [`mRouge`, also known as `3NED`](https://www.rcsb.org/structure/3NED), one of the red fluorescent proteins explored in `LaMBO` {cite:p}`stanton2022accelerating`. Before optimization, we need to download the file and \"repair\" it (see [single mutations using foldx](../../understanding_foldx/01-single-mutation-using-foldx/index.ipynb)).\n",
     "\n",
-    "We assume that the file is already here: [TODO: expand/automate the process of repair]."
+    "We assume that the repaired file is already here."
    ]
   },
   {
@@ -227,9 +235,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "`objective_factory.create` returns four things:\n",
+    "`objective_factory.create` returns five things:\n",
     "\n",
-    "1. a `problem_info` with a description of the problem, including useful attributes like `alphabet` or `max_sequence_length`. (See more [here (TODO: ADD API REFERENCE)]()).\n",
+    "1. a `problem_info` with a description of the problem, including useful attributes like `alphabet` or `max_sequence_length`.\n",
     "2. a black-box function `f: AbstractBlackBox` from `poli`.\n",
     "3. an initial design `x0: np.ndarray`, and\n",
     "4. an initial evaluation `y0: np.ndarray`.\n",

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

@@ -145,17 +145,6 @@
     "### Using a solver, or creating your own"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    ":::{warning}\n",
-    "\n",
-    "`poli-baselines` is still in alpha, and the interface might change in the future.\n",
-    "\n",
-    ":::"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},