Update all plots, and use unique data caches with DynamicBind

BioinfoMachineLearning · Aug 17, 2024 · 662d147 · 662d147
1 parent 93ea040
commit 662d147
Show file tree

Hide file tree

Showing 35 changed files with 235 additions and 214 deletions.
diff --git a/configs/model/dynamicbind_inference.yaml b/configs/model/dynamicbind_inference.yaml
@@ -8,6 +8,7 @@ samples_per_complex: 40 # the number of samples to generate per complex
 savings_per_complex: 1 # the (top-N) number of sample visualizations to save per complex
 inference_steps: 20 # the number of inference steps to run for each complex
 batch_size: 5 # the batch size to use for inference
+cache_path: ${oc.env:PROJECT_ROOT}/data/dynamicbind_cache/cache # the cache directory to use for storing intermediate data files
 header: ${dataset} # name of the results directory to create
 num_workers: 1 # the number of workers to use for native relaxation during inference
 skip_existing: true # whether to skip existing predictions

diff --git a/docs/source/_static/PoseBench.png b/docs/source/_static/PoseBench.png
diff --git a/forks/DynamicBind/run_single_protein_inference.py b/forks/DynamicBind/run_single_protein_inference.py
@@ -22,6 +22,7 @@
 parser.add_argument('--savings_per_complex', type=int, default=1, help='num of samples data saved for movie generation.')
 parser.add_argument('--inference_steps', type=int, default=20, help='num of coordinate updates. (movie frames)')
 parser.add_argument('--batch_size', type=int, default=5, help='chunk size for inference batches.')
+parser.add_argument('--cache_path', type=str, default='data/cache', help='Folder from where to load/restore cached dataset')
 parser.add_argument('--header', type=str, default='test', help='informative name used to name result folder')
 parser.add_argument('--results', type=str, default='results', help='result folder.')
 parser.add_argument('--device', type=int, default=0, help='CUDA_VISIBLE_DEVICES')
@@ -302,7 +303,7 @@ def ref_filename_sort_key(filepath):
                 do(cmd)
                 cmd = f"CUDA_VISIBLE_DEVICES={args.device} {python} {script_folder}/esm/scripts/extract.py esm2_t33_650M_UR50D {os.path.join(outputs_dir, f'prepared_for_esm_{header}.fasta')} {os.path.join(outputs_dir, 'esm2_output' + unique_id)} --repr_layers 33 --include per_tok --truncation_seq_length 10000 --model_dir {script_folder}/esm_models"
                 do(cmd)
-                cmd = f"{python} {script_folder}/inference.py --seed {args.seed} --ckpt {ckpt} {protein_dynamic}"
+                cmd = f"{python} {script_folder}/inference.py --cache_path {args.cache_path} --seed {args.seed} --ckpt {ckpt} {protein_dynamic}"
                 cmd += f" --save_visualisation --model_dir {model_workdir}  --protein_ligand_csv {ligandFile_with_protein_path} "
                 cmd += f" --esm_embeddings_path {os.path.join(outputs_dir, 'esm2_output' + unique_id)} --out_dir {args.results}/{header} --inference_steps {args.inference_steps} --samples_per_complex {args.samples_per_complex} --savings_per_complex {args.savings_per_complex} --batch_size {args.batch_size} --actual_steps {args.inference_steps} --no_final_step_noise"
                 os.environ['CUDA_VISIBLE_DEVICES'] = str(args.device)
@@ -391,7 +392,7 @@ def ref_filename_sort_key(filepath):
             do(cmd)
             cmd = f"CUDA_VISIBLE_DEVICES={args.device} {python} {script_folder}/esm/scripts/extract.py esm2_t33_650M_UR50D {os.path.join(outputs_dir, f'prepared_for_esm_{header}.fasta')} {os.path.join(outputs_dir, 'esm2_output' + unique_id)} --repr_layers 33 --include per_tok --truncation_seq_length 10000 --model_dir {script_folder}/esm_models"
             do(cmd)
-            cmd = f"CUDA_VISIBLE_DEVICES={args.device} {python} {script_folder}/inference.py --seed {args.seed} --ckpt {ckpt} {protein_dynamic}"
+            cmd = f"CUDA_VISIBLE_DEVICES={args.device} {python} {script_folder}/inference.py --cache_path {args.cache_path} --seed {args.seed} --ckpt {ckpt} {protein_dynamic}"
             cmd += f" --save_visualisation --model_dir {model_workdir}  --protein_ligand_csv {ligandFile_with_protein_path} "
             cmd += f" --esm_embeddings_path {os.path.join(outputs_dir, 'esm2_output' + unique_id)} --out_dir {args.results}/{header} --inference_steps {args.inference_steps} --samples_per_complex {args.samples_per_complex} --savings_per_complex {args.savings_per_complex} --batch_size {args.batch_size} --actual_steps {args.inference_steps} --no_final_step_noise"
             do(cmd)

diff --git a/img/PoseBench.png b/img/PoseBench.png
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_all_multi_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_all_multi_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_all_multi_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_all_multi_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_all_single_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_all_single_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_all_single_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_all_single_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/casp15_inference_results_plotting.ipynb b/notebooks/casp15_inference_results_plotting.ipynb
@@ -87,7 +87,7 @@
     "    \"dynamicbind\": \"DynamicBind\",\n",
     "    \"neuralplexer\": \"NeuralPLexer\",\n",
     "    \"neuralplexer_no_ilcl\": \"NeuralPLexer w/o ILCL\",\n",
-    "    \"rfaa\": \"RoseTTAFold-All-Atom\",\n",
+    "    \"rfaa\": \"RoseTTAFold-AA\",\n",
     "    \"tulip\": \"TULIP\",\n",
     "    \"vina_diffdock\": \"DiffDock-L-Vina\",\n",
     "    \"vina_p2rank\": \"P2Rank-Vina\",\n",
@@ -133,11 +133,11 @@
     "                \"casp15\",\n",
     "                f\"top_{method}{'' if 'ensemble' in method else '_ensemble'}_predictions_{repeat_index}\",\n",
     "            )\n",
-    "            globals()[\n",
-    "                f\"{method}{config}_scoring_results_csv_filepath_{repeat_index}\"\n",
-    "            ] = os.path.join(\n",
-    "                globals()[f\"{method}_output_dir_{repeat_index}\"] + config,\n",
-    "                \"scoring_results.csv\",\n",
+    "            globals()[f\"{method}{config}_scoring_results_csv_filepath_{repeat_index}\"] = (\n",
+    "                os.path.join(\n",
+    "                    globals()[f\"{method}_output_dir_{repeat_index}\"] + config,\n",
+    "                    \"scoring_results.csv\",\n",
+    "                )\n",
     "            )\n",
     "            globals()[f\"{method}{config}_bust_results_csv_filepath_{repeat_index}\"] = os.path.join(\n",
     "                globals()[f\"{method}_output_dir_{repeat_index}\"] + config,\n",
@@ -160,12 +160,6 @@
     "                .groupby([\"target\", \"mdl\"])[\"pose\"]\n",
     "                .transform(\"count\")\n",
     "            )\n",
-    "            grouped_num_target_ligands = (\n",
-    "                globals()[f\"{method}{config}_scoring_results_table_{repeat_index}\"]\n",
-    "                .groupby([\"target\", \"mdl\"])[\"num_target_ligands\"]\n",
-    "                .first()\n",
-    "            )\n",
-    "            num_ligands_per_complex = grouped_num_target_ligands.loc[(slice(None), 1)].tolist()\n",
     "            globals()[f\"{method}{config}_bust_results_table_{repeat_index}\"] = (\n",
     "                pd.read_csv(\n",
     "                    globals()[f\"{method}{config}_bust_results_csv_filepath_{repeat_index}\"]\n",
@@ -204,6 +198,13 @@
     "                <= 2\n",
     "            )\n",
     "\n",
+    "            grouped_num_target_ligands = (\n",
+    "                globals()[f\"{method}{config}_scoring_results_table_{repeat_index}\"]\n",
+    "                .groupby([\"target\", \"mdl\"])[\"num_target_ligands\"]\n",
+    "                .first()\n",
+    "            )\n",
+    "            num_ligands_per_complex = grouped_num_target_ligands.loc[(slice(None), 1)].tolist()\n",
+    "\n",
     "            print(\n",
     "                f\"{method_title}{config}_{repeat_index} CASP15 set average `lddt_pli`: {globals()[f'{method}{config}_scoring_results_table_{repeat_index}']['lddt_pli'].mean()}\"\n",
     "            )\n",
@@ -229,6 +230,16 @@
     "                globals()[f\"{method}{config}_bust_results_table_{repeat_index}\"].loc[\n",
     "                    :, \"dataset\"\n",
     "                ] = \"casp15\"\n",
+    "                # filter bust results to only those for targets that were scoreable using the CASP scoring pipeline\n",
+    "                globals()[f\"{method}{config}_bust_results_table_{repeat_index}\"] = globals()[\n",
+    "                    f\"{method}{config}_bust_results_table_{repeat_index}\"\n",
+    "                ][\n",
+    "                    globals()[f\"{method}{config}_bust_results_table_{repeat_index}\"].target.isin(\n",
+    "                        globals()[\n",
+    "                            f\"{method}{config}_scoring_results_table_{repeat_index}\"\n",
+    "                        ].target.unique()\n",
+    "                    )\n",
+    "                ]\n",
     "                globals()[f\"{method}{config}_bust_results_table_{repeat_index}\"].loc[\n",
     "                    :, \"num_target_ligands\"\n",
     "                ] = num_ligands_per_complex\n",
@@ -357,7 +368,7 @@
     "        )\n",
     "    ]\n",
     "    combined_data_list.append(pd.concat([casp15_results_table, casp15_relaxed_results_table]))\n",
-    "combined_data = pd.concat(combined_data_list)\n",
+    "combined_data = pd.concat(combined_data_list).sort_values(\"method_assignment_index\")\n",
     "\n",
     "for complex_type in [\"single\", \"multi\"]:\n",
     "    for complex_license in [\"all\", \"public\"]:\n",
@@ -439,7 +450,7 @@
     "        )\n",
     "    ]\n",
     "    combined_data_list.append(pd.concat([casp15_results_table, casp15_relaxed_results_table]))\n",
-    "combined_data = pd.concat(combined_data_list)\n",
+    "combined_data = pd.concat(combined_data_list).sort_values(\"method_assignment_index\")\n",
     "\n",
     "for complex_type in [\"single\", \"multi\"]:\n",
     "    for complex_license in [\"all\", \"public\"]:\n",
@@ -453,7 +464,7 @@
     "            hue=\"post-processing\",\n",
     "            data=combined_data[\n",
     "                # ignore outliers\n",
-    "                (combined_data[\"rmsd\"] < 50)\n",
+    "                (combined_data[\"rmsd\"] < 150)\n",
     "                & (\n",
     "                    # filter the data based on the complex type and license\n",
     "                    combined_data[\"target\"].isin(\n",
@@ -724,7 +735,7 @@
     "                \"NeuralPLexer\",\n",
     "                \"DL-based blind\",\n",
     "                \"NeuralPLexer w/o ILCL\",\n",
-    "                \"RoseTTAFold-All-Atom\",\n",
+    "                \"RoseTTAFold-AA\",\n",
     "                \"TULIP\",\n",
     "                \"DiffDock-L-Vina\",\n",
     "                \"Conventional blind\",\n",
@@ -1042,7 +1053,7 @@
     "                \"NeuralPLexer\",\n",
     "                \"DL-based blind\",\n",
     "                \"NeuralPLexer w/o ILCL\",\n",
-    "                \"RoseTTAFold-All-Atom\",\n",
+    "                \"RoseTTAFold-AA\",\n",
     "                \"TULIP\",\n",
     "                \"DiffDock-L-Vina\",\n",
     "                \"Conventional blind\",\n",
@@ -1108,7 +1119,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/casp15_method_interaction_analysis.png b/notebooks/casp15_method_interaction_analysis.png
diff --git a/notebooks/casp15_method_interaction_analysis_plotting.ipynb b/notebooks/casp15_method_interaction_analysis_plotting.ipynb
@@ -98,7 +98,7 @@
     "    \"diffdock\": \"DiffDock-L\",\n",
     "    \"dynamicbind\": \"DynamicBind\",\n",
     "    \"neuralplexer\": \"NeuralPLexer\",\n",
-    "    \"rfaa\": \"RoseTTAFold-All-Atom\",\n",
+    "    \"rfaa\": \"RoseTTAFold-AA\",\n",
     "    \"tulip\": \"TULIP\",\n",
     "    \"vina_diffdock\": \"DiffDock-L-Vina\",\n",
     "    \"vina_p2rank\": \"P2Rank-Vina\",\n",
@@ -482,7 +482,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/casp15_public_multi_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_public_multi_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_public_multi_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_public_multi_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_public_multi_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_public_multi_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_public_multi_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_public_multi_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_public_single_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_public_single_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_public_single_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_public_single_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/dockgen_inference_results_plotting.ipynb b/notebooks/dockgen_inference_results_plotting.ipynb
@@ -96,12 +96,12 @@
     "    )\n",
     "\n",
     "    # DiffDock (relaxed-protein) results\n",
-    "    globals()[\n",
-    "        f\"diffdock_relaxed_protein_dockgen_bust_results_csv_filepath_{repeat_index}\"\n",
-    "    ] = os.path.join(\n",
-    "        globals()[\"diffdock_output_dir\"],\n",
-    "        f\"diffdock_dockgen_output_{repeat_index}\",\n",
-    "        \"bust_results.csv\",\n",
+    "    globals()[f\"diffdock_relaxed_protein_dockgen_bust_results_csv_filepath_{repeat_index}\"] = (\n",
+    "        os.path.join(\n",
+    "            globals()[\"diffdock_output_dir\"],\n",
+    "            f\"diffdock_dockgen_output_{repeat_index}\",\n",
+    "            \"bust_results.csv\",\n",
+    "        )\n",
     "    )\n",
     "    globals()[\n",
     "        f\"diffdock_relaxed_protein_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"\n",
@@ -129,12 +129,12 @@
     "        f\"dockgen_{repeat_index}\",\n",
     "        \"bust_results.csv\",\n",
     "    )\n",
-    "    globals()[\n",
-    "        f\"dynamicbind_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"\n",
-    "    ] = os.path.join(\n",
-    "        globals()[\"dynamicbind_output_dir\"],\n",
-    "        f\"dockgen_{repeat_index}_relaxed\",\n",
-    "        \"bust_results.csv\",\n",
+    "    globals()[f\"dynamicbind_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"] = (\n",
+    "        os.path.join(\n",
+    "            globals()[\"dynamicbind_output_dir\"],\n",
+    "            f\"dockgen_{repeat_index}_relaxed\",\n",
+    "            \"bust_results.csv\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "    # NeuralPLexer results\n",
@@ -143,12 +143,12 @@
     "        f\"neuralplexer_dockgen_outputs_{repeat_index}\",\n",
     "        \"bust_results.csv\",\n",
     "    )\n",
-    "    globals()[\n",
-    "        f\"neuralplexer_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"\n",
-    "    ] = os.path.join(\n",
-    "        globals()[\"neuralplexer_output_dir\"],\n",
-    "        f\"neuralplexer_dockgen_outputs_{repeat_index}_relaxed\",\n",
-    "        \"bust_results.csv\",\n",
+    "    globals()[f\"neuralplexer_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"] = (\n",
+    "        os.path.join(\n",
+    "            globals()[\"neuralplexer_output_dir\"],\n",
+    "            f\"neuralplexer_dockgen_outputs_{repeat_index}_relaxed\",\n",
+    "            \"bust_results.csv\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "    # RoseTTAFold-All-Atom results\n",
@@ -169,12 +169,12 @@
     "        f\"vina_diffdock_dockgen_outputs_{repeat_index}\",\n",
     "        \"bust_results.csv\",\n",
     "    )\n",
-    "    globals()[\n",
-    "        f\"vina_diffdock_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"\n",
-    "    ] = os.path.join(\n",
-    "        globals()[\"vina_output_dir\"],\n",
-    "        f\"vina_diffdock_dockgen_outputs_{repeat_index}_relaxed\",\n",
-    "        \"bust_results.csv\",\n",
+    "    globals()[f\"vina_diffdock_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"] = (\n",
+    "        os.path.join(\n",
+    "            globals()[\"vina_output_dir\"],\n",
+    "            f\"vina_diffdock_dockgen_outputs_{repeat_index}_relaxed\",\n",
+    "            \"bust_results.csv\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "    # P2Rank-Vina results\n",
@@ -183,38 +183,38 @@
     "        f\"vina_p2rank_dockgen_outputs_{repeat_index}\",\n",
     "        \"bust_results.csv\",\n",
     "    )\n",
-    "    globals()[\n",
-    "        f\"vina_p2rank_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"\n",
-    "    ] = os.path.join(\n",
-    "        globals()[\"vina_output_dir\"],\n",
-    "        f\"vina_p2rank_dockgen_outputs_{repeat_index}_relaxed\",\n",
-    "        \"bust_results.csv\",\n",
+    "    globals()[f\"vina_p2rank_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"] = (\n",
+    "        os.path.join(\n",
+    "            globals()[\"vina_output_dir\"],\n",
+    "            f\"vina_p2rank_dockgen_outputs_{repeat_index}_relaxed\",\n",
+    "            \"bust_results.csv\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "    # Consensus ensemble results\n",
-    "    globals()[\n",
-    "        f\"consensus_ensemble_dockgen_bust_results_csv_filepath_{repeat_index}\"\n",
-    "    ] = os.path.join(\n",
-    "        os.path.join(\"..\", \"data\", \"test_cases\", \"dockgen\"),\n",
-    "        f\"top_consensus_ensemble_predictions_{repeat_index}\",\n",
-    "        \"bust_results.csv\",\n",
+    "    globals()[f\"consensus_ensemble_dockgen_bust_results_csv_filepath_{repeat_index}\"] = (\n",
+    "        os.path.join(\n",
+    "            os.path.join(\"..\", \"data\", \"test_cases\", \"dockgen\"),\n",
+    "            f\"top_consensus_ensemble_predictions_{repeat_index}\",\n",
+    "            \"bust_results.csv\",\n",
+    "        )\n",
     "    )\n",
-    "    globals()[\n",
-    "        f\"consensus_ensemble_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"\n",
-    "    ] = os.path.join(\n",
-    "        os.path.join(\"..\", \"data\", \"test_cases\", \"dockgen\"),\n",
-    "        f\"top_consensus_ensemble_predictions_{repeat_index}_relaxed\",\n",
-    "        \"bust_results.csv\",\n",
+    "    globals()[f\"consensus_ensemble_dockgen_relaxed_bust_results_csv_filepath_{repeat_index}\"] = (\n",
+    "        os.path.join(\n",
+    "            os.path.join(\"..\", \"data\", \"test_cases\", \"dockgen\"),\n",
+    "            f\"top_consensus_ensemble_predictions_{repeat_index}_relaxed\",\n",
+    "            \"bust_results.csv\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "# Mappings\n",
     "method_mapping = {\n",
     "    \"diffdock\": \"DiffDock-L\",\n",
-    "    \"diffdock_relaxed_protein\": \"DiffDock-L (Relaxed-Protein)\",\n",
+    "    \"diffdock_relaxed_protein\": \"DiffDock-L-Relax-Prot\",\n",
     "    \"fabind\": \"FABind\",\n",
     "    \"dynamicbind\": \"DynamicBind\",\n",
     "    \"neuralplexer\": \"NeuralPLexer\",\n",
-    "    \"rfaa\": \"RoseTTAFold-All-Atom\",\n",
+    "    \"rfaa\": \"RoseTTAFold-AA\",\n",
     "    \"vina_diffdock\": \"DiffDock-L-Vina\",\n",
     "    \"vina_p2rank\": \"P2Rank-Vina\",\n",
     "    \"consensus_ensemble\": \"Ensemble (Con)\",\n",
@@ -429,7 +429,7 @@
     "    x=\"method\",\n",
     "    y=\"rmsd\",\n",
     "    hue=\"post-processing\",\n",
-    "    data=combined_relaxed_data[combined_relaxed_data[\"rmsd\"] < 50],\n",
+    "    data=combined_relaxed_data[combined_relaxed_data[\"rmsd\"] < 150],  # ignore outliers\n",
     "    split=True,\n",
     "    inner=\"quartile\",\n",
     "    palette=colors,\n",
@@ -724,12 +724,12 @@
     "axis.set_xticklabels(\n",
     "    [\n",
     "        \"DiffDock-L\",\n",
-    "        \"DiffDock-L (Relax-P)\",\n",
+    "        \"DiffDock-L-Relax-Prot\",\n",
     "        \"FABind\",\n",
     "        \"DL-based blind\",\n",
     "        \"DynamicBind\",\n",
     "        \"NeuralPLexer\",\n",
-    "        \"RoseTTAFold-All-Atom\",\n",
+    "        \"RoseTTAFold-AA\",\n",
     "        \"DiffDock-L-Vina\",\n",
     "        \"Conventional blind\",\n",
     "        \"P2Rank-Vina\",\n",
@@ -791,7 +791,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/dockgen_single_ligand_relaxed_bar_chart.png b/notebooks/dockgen_single_ligand_relaxed_bar_chart.png
diff --git a/notebooks/dockgen_single_ligand_relaxed_rmsd_violin_plot.png b/notebooks/dockgen_single_ligand_relaxed_rmsd_violin_plot.png