Add all PoseBusters Benchmark method interaction analyses in bulk

Author: amorehead

notebooks/posebusters_benchmark_method_interaction_analysis.png

@@ -329,12 +329,9 @@
     "                    ) + glob.glob(ligand_item_path)\n",
     "                elif os.path.isdir(ligand_item_path) and \"_relaxed\" not in item:\n",
     "                    protein_pdb_filepath, ligand_sdf_filepath = None, None\n",
-    "                    complex_filepaths = (\n",
-    "                        glob.glob(os.path.join(protein_item_path, \"*rank1*.pdb\"))\n",
-    "                        + glob.glob(os.path.join(protein_item_path, \"*idx_0*.pdb\"))\n",
-    "                        + glob.glob(os.path.join(ligand_item_path, \"*rank1.sdf\"))\n",
-    "                        + glob.glob(os.path.join(ligand_item_path, \"*idx_0*.sdf\"))\n",
-    "                    )\n",
+    "                    complex_filepaths = glob.glob(\n",
+    "                        os.path.join(protein_item_path, \"*rank1*.pdb\")\n",
+    "                    ) + glob.glob(os.path.join(ligand_item_path, \"*rank1.sdf\"))\n",
     "                    if not len(complex_filepaths) == 2:\n",
     "                        # NOTE: this handles DiffDock and TULIP's output formats\n",
     "                        complex_filepaths = glob.glob(f\"{protein_item_path}.pdb\") + glob.glob(\n",
@@ -350,7 +347,37 @@
     "                        complex_filepaths = glob.glob(f\"{protein_item_path}.pdb\") + glob.glob(\n",
     "                            os.path.join(ligand_item_path, f\"{item}.sdf\")\n",
     "                        )\n",
-    "                    if method == \"consensus_ensemble\":\n",
+    "\n",
+    "                    if method == \"neuralplexer\":\n",
+    "                        # NOTE: this handles NeuralPlexer's output formats\n",
+    "                        complex_filepaths = [\n",
+    "                            p\n",
+    "                            for p in glob.glob(\n",
+    "                                os.path.join(protein_item_path.removesuffix(\"*\"), \"*rank1_*.pdb\")\n",
+    "                            )\n",
+    "                            + glob.glob(\n",
+    "                                os.path.join(ligand_item_path.removesuffix(\"*\"), \"*rank1_*.sdf\")\n",
+    "                            )\n",
+    "                            if \"relaxed\" not in p and \"aligned\" not in p\n",
+    "                        ]\n",
+    "                    elif method == \"chai-lab\":\n",
+    "                        # NOTE: this handles Chai-1's output formats\n",
+    "                        complex_filepaths = [\n",
+    "                            p\n",
+    "                            for p in glob.glob(\n",
+    "                                os.path.join(\n",
+    "                                    protein_item_path.removesuffix(\"*\"),\n",
+    "                                    \"pred.model_idx_0_protein.pdb\",\n",
+    "                                )\n",
+    "                            )\n",
+    "                            + glob.glob(\n",
+    "                                os.path.join(\n",
+    "                                    ligand_item_path.removesuffix(\"*\"),\n",
+    "                                    \"pred.model_idx_0_ligand.sdf\",\n",
+    "                                )\n",
+    "                            )\n",
+    "                        ]\n",
+    "                    elif method == \"consensus_ensemble\":\n",
     "                        # NOTE: this handles the Consensus Ensemble's output formats\n",
     "                        complex_filepaths = glob.glob(\n",
     "                            os.path.join(protein_item_path.removesuffix(\"*\"), \"*.pdb\")\n",