Update CASP15 notebooks

BioinfoMachineLearning · Aug 16, 2024 · ae8e1db · ae8e1db
1 parent d681388
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Showing 2 changed files with 2 additions and 37 deletions.
diff --git a/notebooks/casp15_inference_results_plotting.ipynb b/notebooks/casp15_inference_results_plotting.ipynb
@@ -68,11 +68,6 @@
    "outputs": [],
    "source": [
     "# General variables\n",
-    "SCALING_STUDY_RUN_COUNTS = [40, 1000]\n",
-    "SCALING_STUDY_REPEAT_INDICES = [1, 2, 3]\n",
-    "SCALING_STUDY_METHODS = [\"neuralplexer\"]\n",
-    "SCALING_STUDY_RANKING_METHODS = [\"l-plddt\", \"p-plddt\", \"pl-plddt\", \"consensus\"]\n",
-    "\n",
     "new_methods = [\n",
     "    \"diffdock\",\n",
     "    \"dynamicbind\",\n",
@@ -95,18 +90,6 @@
     "    \"consensus_ensemble\": \"Ensemble (Con)\",\n",
     "}\n",
     "\n",
-    "scaling_method_mapping = {\n",
-    "    \"neuralplexer_40\": \"NeuralPLexer (40)\",\n",
-    "    \"neuralplexer_1000\": \"NeuralPLexer (1000)\",\n",
-    "}\n",
-    "\n",
-    "scaling_ranking_method_mapping = {\n",
-    "    \"l-plddt\": \"Ligand plDDT\",\n",
-    "    \"p-plddt\": \"Protein plDDT\",\n",
-    "    \"pl-plddt\": \"Protein-Ligand plDDT\",\n",
-    "    \"consensus\": \"Consensus\",\n",
-    "}\n",
-    "\n",
     "method_category_mapping = {\n",
     "    \"diffdock\": \"DL-based blind\",\n",
     "    \"dynamicbind\": \"DL-based blind\",\n",
@@ -281,26 +264,6 @@
     "    return list(method_mapping.keys()).index(method)\n",
     "\n",
     "\n",
-    "def assign_scaling_method_index(method: str) -> str:\n",
-    "    \"\"\"\n",
-    "    Assign method index for plotting scaling experiment results.\n",
-    "\n",
-    "    :param method: Method name.\n",
-    "    :return: Method index.\n",
-    "    \"\"\"\n",
-    "    return list(scaling_method_mapping.keys()).index(method)\n",
-    "\n",
-    "\n",
-    "def assign_scaling_ranking_method_index(method: str) -> str:\n",
-    "    \"\"\"\n",
-    "    Assign ranking method index for plotting scaling experiment results.\n",
-    "\n",
-    "    :param method: Method name.\n",
-    "    :return: Method index.\n",
-    "    \"\"\"\n",
-    "    return list(scaling_ranking_method_mapping.keys()).index(method)\n",
-    "\n",
-    "\n",
     "def categorize_method(method: str) -> str:\n",
     "    \"\"\"\n",
     "    Categorize method for plotting.\n",

diff --git a/notebooks/casp15_method_interaction_analysis_plotting.ipynb b/notebooks/casp15_method_interaction_analysis_plotting.ipynb
@@ -76,6 +76,7 @@
     "    \"rfaa\",\n",
     "    \"tulip\",\n",
     "    \"vina_diffdock\",\n",
+    "    \"vina_p2rank\",\n",
     "    \"consensus_ensemble\",\n",
     "]\n",
     "max_num_repeats_per_method = (\n",
@@ -100,6 +101,7 @@
     "    \"rfaa\": \"RoseTTAFold-All-Atom\",\n",
     "    \"tulip\": \"TULIP\",\n",
     "    \"vina_diffdock\": \"DiffDock-L-Vina\",\n",
+    "    \"vina_p2rank\": \"P2Rank-Vina\",\n",
     "    \"consensus_ensemble\": \"Ensemble (Con)\",\n",
     "}\n",
     "\n",