Add full dataset interaction notebook materials

notebooks/astex_posebusters_casp15_interaction_analysis_plotting.ipynb → notebooks/dataset_interaction_analysis_plotting.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Dataset Analysis Plotting"
+    "## Dataset Interaction Analysis Plotting"
    ]
   },
   {
@@ -67,19 +67,23 @@
    "source": [
     "ad_set_dir = os.path.join(\"..\", \"data\", \"astex_diverse_set\")\n",
     "pb_set_dir = os.path.join(\"..\", \"data\", \"posebusters_benchmark_set\")\n",
+    "dg_set_dir = os.path.join(\"..\", \"data\", \"dockgen_set\")\n",
     "casp15_set_dir = os.path.join(\n",
     "    \"..\",\n",
     "    \"data\",\n",
-    "    \"casp15_set\",\n",
+    "    \"casp15_set_public\",\n",
     "    \"targets\",\n",
-    ")\n",
+    ")  # NOTE: change to `casp15_set` directory as needed\n",
     "assert os.path.exists(\n",
     "    ad_set_dir\n",
     "), \"Please download the Astex Diverse set from `https://zenodo.org/records/11199233` before proceeding.\"\n",
     "assert os.path.exists(\n",
     "    pb_set_dir\n",
     "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/11199233` before proceeding.\"\n",
     "assert os.path.exists(\n",
+    "    dg_set_dir\n",
+    "), \"Please download the DockGen set from `https://zenodo.org/records/11199233` before proceeding.\"\n",
+    "assert os.path.exists(\n",
     "    casp15_set_dir\n",
     "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/11199233` before proceeding.\"\n",
     "\n",
@@ -248,6 +252,68 @@
     "                store.put(f\"df_{i}\", df)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### Analyze `DockGen` set interactions"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if not os.path.exists(\"dockgen_interaction_dataframes.h5\"):\n",
+    "    dockgen_test_ids_filepath = os.path.join(\n",
+    "        \"..\", \"data\", \"dockgen_set\", \"split_test.txt\"\n",
+    "    )  # NOTE: change as needed\n",
+    "    assert os.path.exists(\n",
+    "        dockgen_test_ids_filepath\n",
+    "    ), f\"Invalid test IDs filepath for DockGen: {os.path.exists(dockgen_test_ids_filepath)}.\"\n",
+    "    with open(dockgen_test_ids_filepath) as f:\n",
+    "        pdb_ids = {line.replace(\" \", \"-\") for line in f.read().splitlines()}\n",
+    "    dg_protein_ligand_filepath_pairs = []\n",
+    "    for item in os.listdir(dg_set_dir):\n",
+    "        if item not in pdb_ids:\n",
+    "            continue\n",
+    "        item_path = os.path.join(dg_set_dir, item)\n",
+    "        if os.path.isdir(item_path):\n",
+    "            protein_filepath = os.path.join(item_path, f\"{item}_protein_processed.pdb\")\n",
+    "            ligand_filepath = os.path.join(item_path, f\"{item}_ligand.pdb\")\n",
+    "            if os.path.exists(protein_filepath) and os.path.exists(ligand_filepath):\n",
+    "                dg_protein_ligand_filepath_pairs.append((protein_filepath, ligand_filepath))\n",
+    "\n",
+    "    pc = (\n",
+    "        PoseCheck()\n",
+    "    )  # NOTE: despite what `PoseCheck` might say, `reduce` should be available in the `PoseBench` environment\n",
+    "    dg_protein_ligand_interaction_dfs = []\n",
+    "    for protein_filepath, ligand_filepath in tqdm(\n",
+    "        dg_protein_ligand_filepath_pairs, desc=\"Processing DockGen set\"\n",
+    "    ):\n",
+    "        try:\n",
+    "            temp_protein_filepath = create_temp_pdb_with_only_molecule_type_residues(\n",
+    "                protein_filepath, molecule_type=\"protein\"\n",
+    "            )\n",
+    "            ligand_mol = Chem.MolFromPDBFile(ligand_filepath)\n",
+    "            if ligand_mol is None:\n",
+    "                ligand_mol = Chem.MolFromPDFile(ligand_filepath, sanitize=False)\n",
+    "            pc.load_protein_from_pdb(temp_protein_filepath)\n",
+    "            pc.load_ligands_from_mols([ligand_mol])\n",
+    "            dg_protein_ligand_interaction_dfs.append(pc.calculate_interactions())\n",
+    "        except Exception as e:\n",
+    "            print(\n",
+    "                f\"Error processing Dockgen filepath pari {temp_protein_filepath} and {ligand_filepath} due to: {e}. Skipping...\"\n",
+    "            )\n",
+    "            continue\n",
+    "\n",
+    "        # NOTE: we iteratively save the interaction dataframes to an HDF5 file\n",
+    "        with pd.HDFStore(\"dockgen_interaction_dataframes.h5\") as store:\n",
+    "            for i, df in enumerate(dg_protein_ligand_interaction_dfs):\n",
+    "                store.put(f\"df_{i}\", df)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -293,8 +359,7 @@
     "            pc.load_ligands_from_mols(\n",
     "                Chem.GetMolFrags(ligand_mol, asMols=True, sanitizeFrags=False)\n",
     "            )\n",
-    "            interactions = pc.calculate_interactions()\n",
-    "            casp15_protein_ligand_interaction_dfs.append(interactions)\n",
+    "            casp15_protein_ligand_interaction_dfs.append(pc.calculate_interactions())\n",
     "        except Exception as e:\n",
     "            print(\n",
     "                f\"Error processing CASP15 target {protein_ligand_complex_filepath} due to: {e}. Skipping...\"\n",
@@ -366,6 +431,9 @@
     "        process_dataset(\"posebusters_benchmark_interaction_dataframes.h5\", \"PoseBusters Benchmark\")\n",
     "    )\n",
     "\n",
+    "if os.path.exists(\"dockgen_interaction_dataframes.h5\"):\n",
+    "    dfs.append(process_dataset(\"dockgen_interaction_dataframes.h5\", \"DockGen\"))\n",
+    "\n",
     "if os.path.exists(\"casp15_interaction_dataframes.h5\"):\n",
     "    dfs.append(process_dataset(\"casp15_interaction_dataframes.h5\", \"CASP15\"))\n",
     "\n",
@@ -416,7 +484,7 @@
     "    ax.grid(True)\n",
     "\n",
     "plt.tight_layout()\n",
-    "plt.savefig(\"astex_posebusters_casp15_interaction_analysis.png\", dpi=300)\n",
+    "plt.savefig(\"dataset_interaction_analysis.png\", dpi=300)\n",
     "plt.show()"
    ]
   }