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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This notebook outlines the steps for dataset creation of Astex Diverse Set.\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Background\n",
+    "\n",
+    "The Astex Diverse set is a well-established and commonly-used benchmark for evaluating docking methods. It was published in 2007 is a set of hand-picked, relevant, diverse, and high-quality protein–ligand complexes from the PDB. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest from the complexes before saving the proteins with the cofactors in PDB files and the ligands in SDF files.\n",
+    "\n",
+    "## Data source\n",
+    "- Reference: [Hartshorn  et al.](https://pubs.acs.org/doi/abs/10.1021/jm061277y)\n",
+    "- Orignial: https://zenodo.org/records/8278563\n",
+    "- Polaris: polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/astex_diverse_set\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "from pathlib import Path\n",
+    "import platformdirs\n",
+    "import os\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import datamol as dm\n",
+    "from polaris.dataset import DatasetFactory\n",
+    "from polaris.dataset.converters import SDFConverter, PDBConverter, ZarrConverter"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "DATA_ROOT = f\"{os.environ['HOME']}/sandbox/polaris_cache/posebusters_paper_data\"\n",
+    "dataset_name = \"astex_diverse_set\"\n",
+    "proteins = [Path(folder).name for folder in dm.fs.glob(f\"{DATA_ROOT}/{dataset_name}/*\")]\n",
+    "file_list = [\"ligand\", \"ligand_start_conf\", \"ligands\", \"protein\"]\n",
+    "\n",
+    "\n",
+    "SAVE_DIR = dm.fs.join(\n",
+    "    platformdirs.user_cache_dir(appname=\"polaris-recipes\"), \"posebusters\"\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ligands = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_ligands.sdf\")\n",
+    "    for protein in proteins\n",
+    "]\n",
+    "ligand_start_conf = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_ligand_start_conf.sdf\")\n",
+    "    for protein in proteins\n",
+    "]\n",
+    "ligand = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_ligand.sdf\")\n",
+    "    for protein in proteins\n",
+    "]\n",
+    "protein = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_protein.pdb\")\n",
+    "    for protein in proteins\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Preprocess sdf and add protein group\n",
+    "# This step is to facilitate the data aggregation later on\n",
+    "# It's neccessary for adding a list of ligands and conformers for one protein in a single row in the dataset\n",
+    "ligands_files = []\n",
+    "for sdf in ligands:\n",
+    "    mols = dm.read_sdf(sdf)\n",
+    "    protein_name = Path(sdf).parent.name\n",
+    "    for mol in mols:\n",
+    "        mol.SetProp(\"protein_group\", protein_name)\n",
+    "    url = dm.fs.join(SAVE_DIR, protein_name, Path(sdf).name)\n",
+    "    dm.to_sdf(mols, url)\n",
+    "    ligands_files.append(url)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create a new factory\n",
+    "\n",
+    "save_dst = dm.fs.join(SAVE_DIR, f\"{dataset_name}.zarr\")\n",
+    "factory = DatasetFactory(zarr_root_path=save_dst)\n",
+    "factory.reset(save_dst)\n",
+    "\n",
+    "converter = SDFConverter(\n",
+    "    smiles_column=f\"ligands_smiles\",\n",
+    "    mol_column=\"ligands\",\n",
+    ")\n",
+    "\n",
+    "factory.register_converter(\"sdf\", converter)\n",
+    "factory.add_from_files(paths=ligands_files, axis=0)\n",
+    "\n",
+    "# aggregate the table to map a list of ligands to one protein\n",
+    "agg_fn_ligands = lambda x: converter.get_pointer(\n",
+    "    converter.mol_column,\n",
+    "    f\"{x.index[0]}:{x.index[-1]}\" if len(x) > 1 else f\"{x.index[0]}\",\n",
+    ")\n",
+    "agg_fn_ligands_smiles = lambda x: str(np.unique(x).tolist())\n",
+    "factory._table = (\n",
+    "    factory._table.groupby(\"protein_group\")\n",
+    "    .agg({\"ligands\": agg_fn_ligands, \"ligands_smiles\": agg_fn_ligands_smiles})\n",
+    "    .reset_index()\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-06 21:40:51.305\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.dataset._factory\u001b[0m:\u001b[36mregister_converter\u001b[0m:\u001b[36m136\u001b[0m - \u001b[1mYou are overwriting the converter for the sdf extension.\u001b[0m\n",
+      "\u001b[32m2024-09-06 21:41:01.570\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.dataset._factory\u001b[0m:\u001b[36mregister_converter\u001b[0m:\u001b[36m136\u001b[0m - \u001b[1mYou are overwriting the converter for the sdf extension.\u001b[0m\n"
+     ]
+    }
+   ],
+   "source": [
+    "# add protein pdbs\n",
+    "factory.register_converter(\"pdb\", PDBConverter(pdb_column=\"protein\"))\n",
+    "factory.add_from_files(paths=protein, axis=0)\n",
+    "\n",
+    "# add ligand sdfs\n",
+    "factory.register_converter(\n",
+    "    \"sdf\",\n",
+    "    SDFConverter(\n",
+    "        smiles_column=\"ligand_smiles\", mol_column=\"ligand\", mol_prop_as_cols=False\n",
+    "    ),\n",
+    ")\n",
+    "factory.add_from_files(paths=ligand, axis=0)\n",
+    "\n",
+    "# add ligand start conformers\n",
+    "factory.register_converter(\n",
+    "    \"sdf\",\n",
+    "    SDFConverter(\n",
+    "        smiles_column=\"ligand_start_conf_smiles\",\n",
+    "        mol_column=\"ligand_start_conf\",\n",
+    "        mol_prop_as_cols=False,\n",
+    "    ),\n",
+    ")\n",
+    "factory.add_from_files(paths=ligand_start_conf, axis=0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Build the dataset through factory\n",
+    "dataset = factory.build()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-06 21:41:28.064\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.mixins._checksum\u001b[0m:\u001b[36mmd5sum\u001b[0m:\u001b[36m27\u001b[0m - \u001b[1mComputing the checksum. This can be slow for large datasets.\u001b[0m\n",
+      "Finding all files in the Zarr archive: 100%|██████████| 2796/2796 [00:05<00:00, 520.96it/s]\n"
+     ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "<table border=\"1\"><tr><th>name</th><td>None</td></tr><tr><th>description</th><td></td></tr><tr><th>tags</th><td></td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>owner</th><td>None</td></tr><tr><th>polaris_version</th><td>0.8.5.dev2+gf245e9e.d20240907</td></tr><tr><th>default_adapters</th><td><table border=\"1\"><tr><th>ligands</th><td>BYTES_TO_MOL</td></tr><tr><th>protein</th><td>ARRAY_TO_PDB</td></tr><tr><th>ligand</th><td>BYTES_TO_MOL</td></tr><tr><th>ligand_start_conf</th><td>BYTES_TO_MOL</td></tr></table></td></tr><tr><th>zarr_root_path</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/astex_diverse_set.zarr</td></tr><tr><th>readme</th><td></td></tr><tr><th>annotations</th><td><table border=\"1\"><tr><th>ligands_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>protein_group</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>UNKNOWN</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligands</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>protein</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>PROTEIN_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>PDB</td></tr></table></td></tr><tr><th>ligand_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligand_start_conf_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand_start_conf</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr></table></td></tr><tr><th>source</th><td>None</td></tr><tr><th>license</th><td>None</td></tr><tr><th>curation_reference</th><td>None</td></tr><tr><th>cache_dir</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/4f360014-690e-4195-8163-48c07c0f8549</td></tr><tr><th>md5sum</th><td>4c3021605382941ab4a9e90f38d23a48</td></tr><tr><th>artifact_id</th><td>None</td></tr><tr><th>n_rows</th><td>85</td></tr><tr><th>n_columns</th><td>8</td></tr></table>"
+      ],
+      "text/plain": [
+       "{\n",
+       "  \"name\": null,\n",
+       "  \"description\": \"\",\n",
+       "  \"tags\": [],\n",
+       "  \"user_attributes\": {},\n",
+       "  \"owner\": null,\n",
+       "  \"polaris_version\": \"0.8.5.dev2+gf245e9e.d20240907\",\n",
+       "  \"default_adapters\": {\n",
+       "    \"ligands\": \"BYTES_TO_MOL\",\n",
+       "    \"protein\": \"ARRAY_TO_PDB\",\n",
+       "    \"ligand\": \"BYTES_TO_MOL\",\n",
+       "    \"ligand_start_conf\": \"BYTES_TO_MOL\"\n",
+       "  },\n",
+       "  \"zarr_root_path\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/astex_diverse_set.zarr\",\n",
+       "  \"readme\": \"\",\n",
+       "  \"annotations\": {\n",
+       "    \"ligands_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"protein_group\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"UNKNOWN\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligands\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"protein\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"PROTEIN_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"PDB\"\n",
+       "    },\n",
+       "    \"ligand_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligand_start_conf_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand_start_conf\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    }\n",
+       "  },\n",
+       "  \"source\": null,\n",
+       "  \"license\": null,\n",
+       "  \"curation_reference\": null,\n",
+       "  \"cache_dir\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/4f360014-690e-4195-8163-48c07c0f8549\",\n",
+       "  \"md5sum\": \"4c3021605382941ab4a9e90f38d23a48\",\n",
+       "  \"artifact_id\": null,\n",
+       "  \"n_rows\": 85,\n",
+       "  \"n_columns\": 8\n",
+       "}"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Update the annotations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dataset.annotations[\n",
+    "    \"protein\"\n",
+    "].description = \"The protein structure without the ligand of interest without solvents and with all cofactors.\"\n",
+    "dataset.annotations[\n",
+    "    \"ligand\"\n",
+    "].description = \"One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.\"\n",
+    "\n",
+    "dataset.annotations[\"ligands\"].description = \"All instances of the ligand of interest.\"\n",
+    "dataset.annotations[\n",
+    "    \"ligand_start_conf\"\n",
+    "].description = \"One generated molecule conformation for the ligand of interest generated with RDKit's ETKDGv3 followed by an energy minimization with the UFF.\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from polaris.utils.types import HubOwner\n",
+    "\n",
+    "owner = HubOwner(slug=\"polaris\")\n",
+    "dataset.owner = HubOwner(slug=\"polaris\")\n",
+    "dataset.name = \"astex-diverse-set-v1\"\n",
+    "dataset.tags = [\"docking\"]\n",
+    "dataset.description = \"The Astex Diverse set is a well-established and commonly-used benchmark for evaluating docking methods.\"\n",
+    "dataset.license = \"CC-BY-4.0\"\n",
+    "dataset.user_attributes = {\"year\": \"2007\"}\n",
+    "dataset.source = \"https://pubs.acs.org/doi/abs/10.1021/jm061277y\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table border=\"1\"><tr><th>name</th><td>astex-diverse-set-v1</td></tr><tr><th>description</th><td>The Astex Diverse set is a well-established and commonly-used benchmark for evaluating docking methods.</td></tr><tr><th>tags</th><td><ul><li>docking</li></ul></td></tr><tr><th>user_attributes</th><td><table border=\"1\"><tr><th>year</th><td>2007</td></tr></table></td></tr><tr><th>owner</th><td>polaris</td></tr><tr><th>polaris_version</th><td>0.8.5.dev2+gf245e9e.d20240907</td></tr><tr><th>default_adapters</th><td><table border=\"1\"><tr><th>ligands</th><td>BYTES_TO_MOL</td></tr><tr><th>protein</th><td>ARRAY_TO_PDB</td></tr><tr><th>ligand</th><td>BYTES_TO_MOL</td></tr><tr><th>ligand_start_conf</th><td>BYTES_TO_MOL</td></tr></table></td></tr><tr><th>zarr_root_path</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/astex_diverse_set.zarr</td></tr><tr><th>readme</th><td></td></tr><tr><th>annotations</th><td><table border=\"1\"><tr><th>ligands_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>protein_group</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>UNKNOWN</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligands</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>All instances of the ligand of interest.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>protein</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>PROTEIN_3D</td></tr><tr><th>description</th><td>The protein structure without the ligand of interest without solvents and with all cofactors.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>PDB</td></tr></table></td></tr><tr><th>ligand_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligand_start_conf_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand_start_conf</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>One generated molecule conformation for the ligand of interest generated with RDKit&#x27;s ETKDGv3 followed by an energy minimization with the UFF.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr></table></td></tr><tr><th>source</th><td>https://pubs.acs.org/doi/abs/10.1021/jm061277y</td></tr><tr><th>license</th><td>CC-BY-4.0</td></tr><tr><th>curation_reference</th><td>None</td></tr><tr><th>cache_dir</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/4f360014-690e-4195-8163-48c07c0f8549</td></tr><tr><th>md5sum</th><td>4c3021605382941ab4a9e90f38d23a48</td></tr><tr><th>artifact_id</th><td>polaris/astex-diverse-set-v1</td></tr><tr><th>n_rows</th><td>85</td></tr><tr><th>n_columns</th><td>8</td></tr></table>"
+      ],
+      "text/plain": [
+       "{\n",
+       "  \"name\": \"astex-diverse-set-v1\",\n",
+       "  \"description\": \"The Astex Diverse set is a well-established and commonly-used benchmark for evaluating docking methods.\",\n",
+       "  \"tags\": [\n",
+       "    \"docking\"\n",
+       "  ],\n",
+       "  \"user_attributes\": {\n",
+       "    \"year\": \"2007\"\n",
+       "  },\n",
+       "  \"owner\": \"polaris\",\n",
+       "  \"polaris_version\": \"0.8.5.dev2+gf245e9e.d20240907\",\n",
+       "  \"default_adapters\": {\n",
+       "    \"ligands\": \"BYTES_TO_MOL\",\n",
+       "    \"protein\": \"ARRAY_TO_PDB\",\n",
+       "    \"ligand\": \"BYTES_TO_MOL\",\n",
+       "    \"ligand_start_conf\": \"BYTES_TO_MOL\"\n",
+       "  },\n",
+       "  \"zarr_root_path\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/astex_diverse_set.zarr\",\n",
+       "  \"readme\": \"\",\n",
+       "  \"annotations\": {\n",
+       "    \"ligands_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"protein_group\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"UNKNOWN\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligands\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"All instances of the ligand of interest.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"protein\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"PROTEIN_3D\",\n",
+       "      \"description\": \"The protein structure without the ligand of interest without solvents and with all cofactors.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"PDB\"\n",
+       "    },\n",
+       "    \"ligand_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligand_start_conf_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand_start_conf\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"One generated molecule conformation for the ligand of interest generated with RDKit's ETKDGv3 followed by an energy minimization with the UFF.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    }\n",
+       "  },\n",
+       "  \"source\": \"https://pubs.acs.org/doi/abs/10.1021/jm061277y\",\n",
+       "  \"license\": \"CC-BY-4.0\",\n",
+       "  \"curation_reference\": null,\n",
+       "  \"cache_dir\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/4f360014-690e-4195-8163-48c07c0f8549\",\n",
+       "  \"md5sum\": \"4c3021605382941ab4a9e90f38d23a48\",\n",
+       "  \"artifact_id\": \"polaris/astex-diverse-set-v1\",\n",
+       "  \"n_rows\": 85,\n",
+       "  \"n_columns\": 8\n",
+       "}"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "⠏ Uploading artifact... "
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-06 21:48:34.746\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.hub.client\u001b[0m:\u001b[36m_upload_dataset\u001b[0m:\u001b[36m697\u001b[0m - \u001b[1mCopying Zarr archive to the Hub. This may take a while.\u001b[0m\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "✅ SUCCESS: \u001b[1mYour standard dataset has been successfully uploaded to the Hub. View it here: https://polarishub.io/datasets/polaris/astex-diverse-set-v1\u001b[0m\n",
+      " \n"
+     ]
+    }
+   ],
+   "source": [
+    "dataset.upload_to_hub(timeout=20000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "po_datasets",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/org-Polaris/astex_diverse_set/dataset_readme.md b/org-Polaris/astex_diverse_set/dataset_readme.md
new file mode 100644
index 0000000..0589dd7
--- /dev/null
+++ b/org-Polaris/astex_diverse_set/dataset_readme.md
@@ -0,0 +1,8 @@
+## Background
+
+The Astex Diverse set is a well-established and commonly-used benchmark for evaluating docking methods. It was published in 2007 is a set of hand-picked, relevant, diverse, and high-quality protein–ligand complexes from the PDB. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest from the complexes before saving the proteins with the cofactors in PDB files and the ligands in SDF files.
+
+## Data source
+- Reference: [Hartshorn  et al.](https://pubs.acs.org/doi/abs/10.1021/jm061277y)
+- Orignial: https://zenodo.org/records/8278563
+- Polaris: polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/astex_diverse_set
diff --git a/org-Polaris/astex_diverse_set/env.yml b/org-Polaris/astex_diverse_set/env.yml
new file mode 100644
index 0000000..7baa592
--- /dev/null
+++ b/org-Polaris/astex_diverse_set/env.yml
@@ -0,0 +1,21 @@
+channels:
+  - conda-forge
+
+dependencies:
+  # scientific
+  - rdkit == 2023.9.6
+  - auroris == 0.1.4
+  - polaris == 0.8.5
+
+  # visualization
+  - umap-learn==0.5.5
+  - seaborn==0.13.2
+
+  # notebooks
+  - jupyterlab==4.2.1
+
+  # utils
+  - gcsfs == 2024.6.1
+  - openpyxl == 3.1.2
+
+
diff --git a/org-Polaris/posebusters/01.dataset_creation.ipynb b/org-Polaris/posebusters/01.dataset_creation.ipynb
new file mode 100644
index 0000000..60fad78
--- /dev/null
+++ b/org-Polaris/posebusters/01.dataset_creation.ipynb
@@ -0,0 +1,509 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This notebook outlines the steps for dataset creation using PoseBusters.\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Background\n",
+    "The PoseBusters dataset set is a new set of carefully-selected publicly-available crystal complexes from the PDB. It is a diverse set of recent high-quality protein–ligand complexes which contain drug-like molecules. It only contains complexes released since 2021 and therefore does not contain any complexes present in the PDBbind General Set v2020 used to train many of the methods. \n",
+    "\n",
+    "\n",
+    "[Buttenschoen et al.](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a) lists the steps used to select the 308 unique proteins and 308 unique ligands in the PoseBusters dataset set. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest before saving the proteins with the cofactors in PDB files and the ligands in SDF files. \n",
+    "\n",
+    "\n",
+    "## Data source\n",
+    "- Orignial: https://zenodo.org/records/8278563\n",
+    "- Polaris: gs://polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/posebusters_benchmark_set\n",
+    "\n",
+    "## Other links\n",
+    "- Github: https://github.com/maabuu/posebusters/tree/main"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "from pathlib import Path\n",
+    "import platformdirs\n",
+    "import os\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import datamol as dm\n",
+    "from polaris.dataset import DatasetFactory\n",
+    "from polaris.dataset.converters import SDFConverter, PDBConverter, ZarrConverter"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "DATA_ROOT = f\"{os.environ['HOME']}/sandbox/polaris_cache/posebusters_paper_data\"\n",
+    "dataset_name = \"posebusters_benchmark_set\"\n",
+    "proteins = [Path(folder).name for folder in dm.fs.glob(f\"{DATA_ROOT}/{dataset_name}/*\")]\n",
+    "file_list = [\"ligand\", \"ligand_start_conf\", \"ligands\", \"protein\"]\n",
+    "\n",
+    "\n",
+    "SAVE_DIR = dm.fs.join(\n",
+    "    platformdirs.user_cache_dir(appname=\"polaris-recipes\"), \"posebusters\"\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ligands = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_ligands.sdf\")\n",
+    "    for protein in proteins\n",
+    "]\n",
+    "ligand_start_conf = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_ligand_start_conf.sdf\")\n",
+    "    for protein in proteins\n",
+    "]\n",
+    "ligand = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_ligand.sdf\")\n",
+    "    for protein in proteins\n",
+    "]\n",
+    "protein = [\n",
+    "    dm.fs.join(DATA_ROOT, dataset_name, protein, f\"{protein}_protein.pdb\")\n",
+    "    for protein in proteins\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Preprocess sdf and add protein group\n",
+    "# This step is to facilitate the data aggregation later on\n",
+    "# It's neccessary for adding a list of ligands and conformers for one protein in a single row in the dataset\n",
+    "ligands_files = []\n",
+    "for sdf in ligands:\n",
+    "    mols = dm.read_sdf(sdf)\n",
+    "    protein_name = Path(sdf).parent.name\n",
+    "    for mol in mols:\n",
+    "        mol.SetProp(\"protein_group\", protein_name)\n",
+    "    url = dm.fs.join(SAVE_DIR, protein_name, Path(sdf).name)\n",
+    "    dm.to_sdf(mols, url)\n",
+    "    ligands_files.append(url)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create a new factory\n",
+    "\n",
+    "save_dst = dm.fs.join(SAVE_DIR, f\"{dataset_name}.zarr\")\n",
+    "factory = DatasetFactory(zarr_root_path=save_dst)\n",
+    "factory.reset(save_dst)\n",
+    "\n",
+    "converter = SDFConverter(\n",
+    "    smiles_column=f\"ligands_smiles\",\n",
+    "    mol_column=\"ligands\",\n",
+    ")\n",
+    "\n",
+    "factory.register_converter(\"sdf\", converter)\n",
+    "factory.add_from_files(paths=ligands_files, axis=0)\n",
+    "\n",
+    "# aggregate the table to map a list of ligands to one protein\n",
+    "agg_fn_ligands = lambda x: converter.get_pointer(\n",
+    "    converter.mol_column,\n",
+    "    f\"{x.index[0]}:{x.index[-1]}\" if len(x) > 1 else f\"{x.index[0]}\",\n",
+    ")\n",
+    "agg_fn_ligands_smiles = lambda x: str(np.unique(x).tolist())\n",
+    "factory._table = (\n",
+    "    factory._table.groupby(\"protein_group\")\n",
+    "    .agg({\"ligands\": agg_fn_ligands, \"ligands_smiles\": agg_fn_ligands_smiles})\n",
+    "    .reset_index()\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-06 09:41:14.419\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.dataset._factory\u001b[0m:\u001b[36mregister_converter\u001b[0m:\u001b[36m136\u001b[0m - \u001b[1mYou are overwriting the converter for the sdf extension.\u001b[0m\n",
+      "\u001b[32m2024-09-06 09:43:11.238\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.dataset._factory\u001b[0m:\u001b[36mregister_converter\u001b[0m:\u001b[36m136\u001b[0m - \u001b[1mYou are overwriting the converter for the sdf extension.\u001b[0m\n"
+     ]
+    }
+   ],
+   "source": [
+    "# add protein pdbs\n",
+    "factory.register_converter(\"pdb\", PDBConverter(pdb_column=\"protein\"))\n",
+    "factory.add_from_files(paths=protein, axis=0)\n",
+    "\n",
+    "# add ligand sdfs\n",
+    "factory.register_converter(\n",
+    "    \"sdf\",\n",
+    "    SDFConverter(\n",
+    "        smiles_column=\"ligand_smiles\", mol_column=\"ligand\", mol_prop_as_cols=False\n",
+    "    ),\n",
+    ")\n",
+    "factory.add_from_files(paths=ligand, axis=0)\n",
+    "\n",
+    "# add ligand start conformers\n",
+    "factory.register_converter(\n",
+    "    \"sdf\",\n",
+    "    SDFConverter(\n",
+    "        smiles_column=\"ligand_start_conf_smiles\",\n",
+    "        mol_column=\"ligand_start_conf\",\n",
+    "        mol_prop_as_cols=False,\n",
+    "    ),\n",
+    ")\n",
+    "factory.add_from_files(paths=ligand_start_conf, axis=0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Build the dataset through factory\n",
+    "dataset = factory.build()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-06 09:45:55.864\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.mixins._checksum\u001b[0m:\u001b[36mmd5sum\u001b[0m:\u001b[36m27\u001b[0m - \u001b[1mComputing the checksum. This can be slow for large datasets.\u001b[0m\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Finding all files in the Zarr archive: 100%|██████████| 14057/14057 [00:31<00:00, 445.13it/s]\n"
+     ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "<table border=\"1\"><tr><th>name</th><td>None</td></tr><tr><th>description</th><td></td></tr><tr><th>tags</th><td></td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>owner</th><td>None</td></tr><tr><th>polaris_version</th><td>0.8.5.dev1+gc910f28.d20240906</td></tr><tr><th>default_adapters</th><td><table border=\"1\"><tr><th>ligands</th><td>BYTES_TO_MOL</td></tr><tr><th>protein</th><td>ARRAY_TO_PDB</td></tr><tr><th>ligand</th><td>BYTES_TO_MOL</td></tr><tr><th>ligand_start_conf</th><td>BYTES_TO_MOL</td></tr></table></td></tr><tr><th>zarr_root_path</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/posebusters_benchmark_set.zarr</td></tr><tr><th>readme</th><td></td></tr><tr><th>annotations</th><td><table border=\"1\"><tr><th>ligands_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>protein_group</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>UNKNOWN</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligands</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>protein</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>PROTEIN_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>PDB</td></tr></table></td></tr><tr><th>ligand_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligand_start_conf_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand_start_conf</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr></table></td></tr><tr><th>source</th><td>None</td></tr><tr><th>license</th><td>None</td></tr><tr><th>curation_reference</th><td>None</td></tr><tr><th>cache_dir</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/95416e57-ca9c-4a35-befe-ffd8747081f8</td></tr><tr><th>md5sum</th><td>3810e8268c3c9c89caf0193e1f97e35f</td></tr><tr><th>artifact_id</th><td>None</td></tr><tr><th>n_rows</th><td>428</td></tr><tr><th>n_columns</th><td>8</td></tr></table>"
+      ],
+      "text/plain": [
+       "{\n",
+       "  \"name\": null,\n",
+       "  \"description\": \"\",\n",
+       "  \"tags\": [],\n",
+       "  \"user_attributes\": {},\n",
+       "  \"owner\": null,\n",
+       "  \"polaris_version\": \"0.8.5.dev1+gc910f28.d20240906\",\n",
+       "  \"default_adapters\": {\n",
+       "    \"ligands\": \"BYTES_TO_MOL\",\n",
+       "    \"protein\": \"ARRAY_TO_PDB\",\n",
+       "    \"ligand\": \"BYTES_TO_MOL\",\n",
+       "    \"ligand_start_conf\": \"BYTES_TO_MOL\"\n",
+       "  },\n",
+       "  \"zarr_root_path\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/posebusters_benchmark_set.zarr\",\n",
+       "  \"readme\": \"\",\n",
+       "  \"annotations\": {\n",
+       "    \"ligands_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"protein_group\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"UNKNOWN\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligands\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"protein\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"PROTEIN_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"PDB\"\n",
+       "    },\n",
+       "    \"ligand_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligand_start_conf_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand_start_conf\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    }\n",
+       "  },\n",
+       "  \"source\": null,\n",
+       "  \"license\": null,\n",
+       "  \"curation_reference\": null,\n",
+       "  \"cache_dir\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/95416e57-ca9c-4a35-befe-ffd8747081f8\",\n",
+       "  \"md5sum\": \"3810e8268c3c9c89caf0193e1f97e35f\",\n",
+       "  \"artifact_id\": null,\n",
+       "  \"n_rows\": 428,\n",
+       "  \"n_columns\": 8\n",
+       "}"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Update the annotations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dataset.annotations[\n",
+    "    \"protein\"\n",
+    "].description = \"The protein structure without the ligand of interest without solvents and with all cofactors.\"\n",
+    "dataset.annotations[\n",
+    "    \"ligand\"\n",
+    "].description = \"One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.\"\n",
+    "\n",
+    "dataset.annotations[\"ligands\"].description = \"All instances of the ligand of interest.\"\n",
+    "dataset.annotations[\n",
+    "    \"ligand_start_conf\"\n",
+    "].description = \"One generated molecule conformation for the ligand of interest generated with RDKit's ETKDGv3 followed by an energy minimization with the UFF.\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from polaris.utils.types import HubOwner\n",
+    "\n",
+    "owner = HubOwner(slug=\"polaris\")\n",
+    "dataset.owner = owner\n",
+    "dataset.name = \"posebusters-v1\"\n",
+    "dataset.tags = [\"AI-based docking\"]\n",
+    "dataset.description = \"A diverse datasset of recent high-quality protein–ligand complexes which contain drug-like molecules for AI-based docking method evaluation.\"\n",
+    "dataset.license = \"CC-BY-4.0\"\n",
+    "dataset.user_attributes = {\"year\": \"2024\"}\n",
+    "dataset.source = \"https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table border=\"1\"><tr><th>name</th><td>posebusters-v1</td></tr><tr><th>description</th><td>A diverse datasset of recent high-quality protein–ligand complexes which contain drug-like molecules for AI-based docking method evaluation.</td></tr><tr><th>tags</th><td><ul><li>AI-based docking</li></ul></td></tr><tr><th>user_attributes</th><td><table border=\"1\"><tr><th>year</th><td>2024</td></tr></table></td></tr><tr><th>owner</th><td>polaris</td></tr><tr><th>polaris_version</th><td>0.8.5.dev1+gc910f28.d20240906</td></tr><tr><th>default_adapters</th><td><table border=\"1\"><tr><th>ligands</th><td>BYTES_TO_MOL</td></tr><tr><th>protein</th><td>ARRAY_TO_PDB</td></tr><tr><th>ligand</th><td>BYTES_TO_MOL</td></tr><tr><th>ligand_start_conf</th><td>BYTES_TO_MOL</td></tr></table></td></tr><tr><th>zarr_root_path</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/posebusters_benchmark_set.zarr</td></tr><tr><th>readme</th><td></td></tr><tr><th>annotations</th><td><table border=\"1\"><tr><th>ligands_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>protein_group</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>UNKNOWN</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligands</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>All instances of the ligand of interest.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>protein</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>PROTEIN_3D</td></tr><tr><th>description</th><td>The protein structure without the ligand of interest without solvents and with all cofactors.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>PDB</td></tr></table></td></tr><tr><th>ligand_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligand_start_conf_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td>None</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand_start_conf</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>One generated molecule conformation for the ligand of interest generated with RDKit&#x27;s ETKDGv3 followed by an energy minimization with the UFF.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr></table></td></tr><tr><th>source</th><td>https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a</td></tr><tr><th>license</th><td>CC-BY-4.0</td></tr><tr><th>curation_reference</th><td>None</td></tr><tr><th>cache_dir</th><td>/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/95416e57-ca9c-4a35-befe-ffd8747081f8</td></tr><tr><th>md5sum</th><td>3810e8268c3c9c89caf0193e1f97e35f</td></tr><tr><th>artifact_id</th><td>polaris/posebusters-v1</td></tr><tr><th>n_rows</th><td>428</td></tr><tr><th>n_columns</th><td>8</td></tr></table>"
+      ],
+      "text/plain": [
+       "{\n",
+       "  \"name\": \"posebusters-v1\",\n",
+       "  \"description\": \"A diverse datasset of recent high-quality protein\\u2013ligand complexes which contain drug-like molecules for AI-based docking method evaluation.\",\n",
+       "  \"tags\": [\n",
+       "    \"AI-based docking\"\n",
+       "  ],\n",
+       "  \"user_attributes\": {\n",
+       "    \"year\": \"2024\"\n",
+       "  },\n",
+       "  \"owner\": \"polaris\",\n",
+       "  \"polaris_version\": \"0.8.5.dev1+gc910f28.d20240906\",\n",
+       "  \"default_adapters\": {\n",
+       "    \"ligands\": \"BYTES_TO_MOL\",\n",
+       "    \"protein\": \"ARRAY_TO_PDB\",\n",
+       "    \"ligand\": \"BYTES_TO_MOL\",\n",
+       "    \"ligand_start_conf\": \"BYTES_TO_MOL\"\n",
+       "  },\n",
+       "  \"zarr_root_path\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris-recipes/posebusters/posebusters_benchmark_set.zarr\",\n",
+       "  \"readme\": \"\",\n",
+       "  \"annotations\": {\n",
+       "    \"ligands_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"protein_group\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"UNKNOWN\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligands\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"All instances of the ligand of interest.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"protein\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"PROTEIN_3D\",\n",
+       "      \"description\": \"The protein structure without the ligand of interest without solvents and with all cofactors.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"PDB\"\n",
+       "    },\n",
+       "    \"ligand_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligand_start_conf_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": null,\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand_start_conf\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"One generated molecule conformation for the ligand of interest generated with RDKit's ETKDGv3 followed by an energy minimization with the UFF.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    }\n",
+       "  },\n",
+       "  \"source\": \"https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a\",\n",
+       "  \"license\": \"CC-BY-4.0\",\n",
+       "  \"curation_reference\": null,\n",
+       "  \"cache_dir\": \"/mnt/ps/home/CORP/lu.zhu/.cache/polaris/datasets/95416e57-ca9c-4a35-befe-ffd8747081f8\",\n",
+       "  \"md5sum\": \"3810e8268c3c9c89caf0193e1f97e35f\",\n",
+       "  \"artifact_id\": \"polaris/posebusters-v1\",\n",
+       "  \"n_rows\": 428,\n",
+       "  \"n_columns\": 8\n",
+       "}"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dataset.upload_to_hub(timeout=20000)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "auroris",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/org-Polaris/posebusters/02.benchmark_creation.ipynb b/org-Polaris/posebusters/02.benchmark_creation.ipynb
new file mode 100644
index 0000000..9c1bd78
--- /dev/null
+++ b/org-Polaris/posebusters/02.benchmark_creation.ipynb
@@ -0,0 +1,1117 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "545099e3-0eb9-4a80-a0c6-0448c0674502",
+   "metadata": {},
+   "source": [
+    "# Dataset and Benchmark creation with `Polaris`\n",
+    "The first step of creating a benchmark is to set up a standard dataset which allows accessing the curated dataset (which has been demonstrated in <07_01_polaris_adme-fang-1_data_curation.ipynb>), and all necessary information about the dataset such as data source, description of endpoints, units etc. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "30138c1e",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "\n",
+    "import os\n",
+    "import sys\n",
+    "import pathlib\n",
+    "import numpy as np\n",
+    "\n",
+    "import datamol as dm\n",
+    "\n",
+    "# polaris benchmark\n",
+    "from polaris.benchmark import (\n",
+    "    SingleTaskBenchmarkSpecification,\n",
+    "    MultiTaskBenchmarkSpecification,\n",
+    ")\n",
+    "\n",
+    "# polaris hub\n",
+    "from polaris.utils.types import HubOwner\n",
+    "\n",
+    "# utils\n",
+    "root = pathlib.Path(\"__file__\").absolute().parents[2]\n",
+    "os.chdir(root)\n",
+    "sys.path.insert(0, str(root))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "9969540c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "org = \"polaris\"\n",
+    "gcp_root = f\"gs://polaris-public/polaris-recipes/org-{org}/posebusters\"\n",
+    "\n",
+    "owner = HubOwner(slug=\"polaris\", type=\"organization\")\n",
+    "\n",
+    "BENCHMARK_DIR = f\"{gcp_root}/benchmarks\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "345c2e61",
+   "metadata": {},
+   "source": [
+    "## Load existing dataset object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "e77724a0",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "⠋ Fetching artifact... {'status_code': 200, 'headers': Headers({'cache-control': 'public, max-age=0, must-revalidate', 'content-encoding': 'br', 'content-type': 'application/json', 'date': 'Thu, 26 Sep 2024 01:13:33 GMT', 'server': 'Vercel', 'strict-transport-security': 'max-age=63072000', 'vary': 'RSC, Next-Router-State-Tree, Next-Router-Prefetch', 'x-matched-path': '/api/v1/dataset/[owner]/[name]', 'x-vercel-cache': 'BYPASS', 'x-vercel-id': 'iad1::cle1::hh47m-1727313213276-1e75c762d047', 'content-length': '403246'}), '_request': <Request('GET', 'https://polarishub.io/api/v1/dataset/polaris/posebusters-v1')>, 'next_request': None, 'extensions': {'http_version': b'HTTP/1.1', 'reason_phrase': b'OK', 'network_stream': <httpcore._backends.sync.SyncStream object at 0x1698e9220>}, 'history': [], 'is_closed': True, 'is_stream_consumed': True, 'default_encoding': 'utf-8', 'stream': <httpx._client.BoundSyncStream object at 0x1698ea180>, '_num_bytes_downloaded': 403246, '_decoder': <httpx._decoders.BrotliDecoder object at 0x1698eb350>, '_elapsed': datetime.timedelta(seconds=1, microseconds=561971), '_content': b'{\"id\":\"Wno3Gp8meFYe8X3CZMlsJ\",\"createdAt\":\"2024-09-06T15:48:01.769Z\",\"deletedAt\":null,\"name\":\"posebusters-v1\",\"slug\":\"posebusters-v1\",\"description\":\"A diverse datasset of recent high-quality protein\\xe2\\x80\\x93ligand complexes which contain drug-like molecules for AI-based docking method evaluation.\",\"tags\":[\"docking\"],\"userAttributes\":{\"year\":\"2024\"},\"access\":\"private\",\"isCertified\":false,\"polarisVersion\":\"0.8.5.dev1+gc910f28.d20240906\",\"readme\":\"## Background\\\\nThe PoseBusters dataset set is a new set of carefully-selected publicly-available crystal complexes from the PDB. It is a diverse set of recent high-quality protein\\xe2\\x80\\x93ligand complexes which contain drug-like molecules. It only contains complexes released since 2021 and therefore does not contain any complexes present in the PDBbind General Set v2020 used to train many of the methods. \\\\n\\\\n\\\\n[Buttenschoen et al.](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a) lists the steps used to select the 308 unique proteins and 308 unique ligands in the PoseBusters dataset set. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest before saving the proteins with the cofactors in PDB files and the ligands in SDF files. \\\\n\\\\n\\\\n## Data source\\\\n- Orignial: https://zenodo.org/records/8278563\\\\n- Polaris: gs://polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/posebusters_benchmark_set\\\\n\\\\n## Other links\\\\n- Github: https://github.com/maabuu/posebusters/tree/main\",\"ownerId\":\"9qGUtJxWQ5MDZrK5op9jn\",\"creatorId\":\"NKnaHGybLqwSHcaMEHqfF\",\"state\":\"ready\",\"source\":\"https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a\",\"curationReference\":null,\"nRows\":428,\"nColumns\":8,\"license\":\"CC-BY-4.0\",\"md5Sum\":\"3810e8268c3c9c89caf0193e1f97e35f\",\"annotations\":{\"ligand\":{\"dtype\":\"object\",\"modality\":\"MOLECULE_3D\",\"isPointer\":true,\"description\":\"One of the instances of the ligand of interest. 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+      "⠹ Fetching artifact... "
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-25 21:13:35.756\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris._artifact\u001b[0m:\u001b[36m_validate_version\u001b[0m:\u001b[36m66\u001b[0m - \u001b[1mThe version of Polaris that was used to create the artifact (0.8.5.dev1+gc910f28.d20240906) is different from the currently installed version of Polaris (0.8.6.dev14+g870673b).\u001b[0m\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "✅ SUCCESS: \u001b[1mFetched artifact.\u001b[0m\n",
+      " \n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/lu.zhu/miniconda3/envs/po_dataset/lib/python3.12/site-packages/yaspin/core.py:228: UserWarning: color, on_color and attrs are not supported when running in jupyter\n",
+      "  self._color = self._set_color(value) if value else value\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Get the owner and organization\n",
+    "import polaris as po\n",
+    "\n",
+    "dataset = po.load_dataset(path=\"polaris/posebusters-v1\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "077fe9b3",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table border=\"1\"><tr><th>name</th><td>posebusters-v1</td></tr><tr><th>description</th><td>A diverse datasset of recent high-quality protein–ligand complexes which contain drug-like molecules for AI-based docking method evaluation.</td></tr><tr><th>tags</th><td><ul><li>docking</li></ul></td></tr><tr><th>user_attributes</th><td><table border=\"1\"><tr><th>year</th><td>2024</td></tr></table></td></tr><tr><th>owner</th><td>polaris</td></tr><tr><th>polaris_version</th><td>0.8.5.dev1+gc910f28.d20240906</td></tr><tr><th>default_adapters</th><td><table border=\"1\"><tr><th>ligand</th><td>BYTES_TO_MOL</td></tr><tr><th>ligands</th><td>BYTES_TO_MOL</td></tr><tr><th>protein</th><td>ARRAY_TO_PDB</td></tr><tr><th>ligand_start_conf</th><td>BYTES_TO_MOL</td></tr></table></td></tr><tr><th>zarr_root_path</th><td>polarisfs://data.zarr</td></tr><tr><th>readme</th><td>## Background\n",
+       "The PoseBusters dataset set is a new set of carefully-selected publicly-available crystal complexes from the PDB. It is a diverse set of recent high-quality protein–ligand complexes which contain drug-like molecules. It only contains complexes released since 2021 and therefore does not contain any complexes present in the PDBbind General Set v2020 used to train many of the methods. \n",
+       "\n",
+       "\n",
+       "[Buttenschoen et al.](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a) lists the steps used to select the 308 unique proteins and 308 unique ligands in the PoseBusters dataset set. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest before saving the proteins with the cofactors in PDB files and the ligands in SDF files. \n",
+       "\n",
+       "\n",
+       "## Data source\n",
+       "- Orignial: https://zenodo.org/records/8278563\n",
+       "- Polaris: gs://polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/posebusters_benchmark_set\n",
+       "\n",
+       "## Other links\n",
+       "- Github: https://github.com/maabuu/posebusters/tree/main</td></tr><tr><th>annotations</th><td><table border=\"1\"><tr><th>ligand</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligands</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>All instances of the ligand of interest.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>protein</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>PROTEIN_3D</td></tr><tr><th>description</th><td>The protein structure without the ligand of interest without solvents and with all cofactors.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>PDB</td></tr></table></td></tr><tr><th>ligand_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td></td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>protein_group</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>UNKNOWN</td></tr><tr><th>description</th><td></td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligands_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td></td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr><tr><th>ligand_start_conf</th><td><table border=\"1\"><tr><th>is_pointer</th><td>True</td></tr><tr><th>modality</th><td>MOLECULE_3D</td></tr><tr><th>description</th><td>One generated molecule conformation for the ligand of interest generated with RDKit&#x27;s ETKDGv3 followed by an energy minimization with the UFF.</td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>None</td></tr></table></td></tr><tr><th>ligand_start_conf_smiles</th><td><table border=\"1\"><tr><th>is_pointer</th><td>False</td></tr><tr><th>modality</th><td>MOLECULE</td></tr><tr><th>description</th><td></td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>dtype</th><td>object</td></tr><tr><th>content_type</th><td>SMILES</td></tr></table></td></tr></table></td></tr><tr><th>source</th><td>https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a</td></tr><tr><th>license</th><td>CC-BY-4.0</td></tr><tr><th>curation_reference</th><td>None</td></tr><tr><th>cache_dir</th><td>/Users/lu.zhu/Library/Caches/polaris/datasets/e5fa3d9a-be59-4df4-9b80-ec32f4a4f010</td></tr><tr><th>md5sum</th><td>3810e8268c3c9c89caf0193e1f97e35f</td></tr><tr><th>artifact_id</th><td>polaris/posebusters-v1</td></tr><tr><th>n_rows</th><td>428</td></tr><tr><th>n_columns</th><td>8</td></tr></table>"
+      ],
+      "text/plain": [
+       "{\n",
+       "  \"name\": \"posebusters-v1\",\n",
+       "  \"description\": \"A diverse datasset of recent high-quality protein\\u2013ligand complexes which contain drug-like molecules for AI-based docking method evaluation.\",\n",
+       "  \"tags\": [\n",
+       "    \"docking\"\n",
+       "  ],\n",
+       "  \"user_attributes\": {\n",
+       "    \"year\": \"2024\"\n",
+       "  },\n",
+       "  \"owner\": \"polaris\",\n",
+       "  \"polaris_version\": \"0.8.5.dev1+gc910f28.d20240906\",\n",
+       "  \"default_adapters\": {\n",
+       "    \"ligand\": \"BYTES_TO_MOL\",\n",
+       "    \"ligands\": \"BYTES_TO_MOL\",\n",
+       "    \"protein\": \"ARRAY_TO_PDB\",\n",
+       "    \"ligand_start_conf\": \"BYTES_TO_MOL\"\n",
+       "  },\n",
+       "  \"zarr_root_path\": \"polarisfs://data.zarr\",\n",
+       "  \"readme\": \"## Background\\nThe PoseBusters dataset set is a new set of carefully-selected publicly-available crystal complexes from the PDB. It is a diverse set of recent high-quality protein\\u2013ligand complexes which contain drug-like molecules. It only contains complexes released since 2021 and therefore does not contain any complexes present in the PDBbind General Set v2020 used to train many of the methods. \\n\\n\\n[Buttenschoen et al.](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a) lists the steps used to select the 308 unique proteins and 308 unique ligands in the PoseBusters dataset set. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest before saving the proteins with the cofactors in PDB files and the ligands in SDF files. \\n\\n\\n## Data source\\n- Orignial: https://zenodo.org/records/8278563\\n- Polaris: gs://polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/posebusters_benchmark_set\\n\\n## Other links\\n- Github: https://github.com/maabuu/posebusters/tree/main\",\n",
+       "  \"annotations\": {\n",
+       "    \"ligand\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"One of the instances of the ligand of interest. This crystal pose marks the binding site for those docking methods that require a binding site.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligands\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"All instances of the ligand of interest.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"protein\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"PROTEIN_3D\",\n",
+       "      \"description\": \"The protein structure without the ligand of interest without solvents and with all cofactors.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"PDB\"\n",
+       "    },\n",
+       "    \"ligand_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": \"\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"protein_group\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"UNKNOWN\",\n",
+       "      \"description\": \"\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligands_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": \"\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    },\n",
+       "    \"ligand_start_conf\": {\n",
+       "      \"is_pointer\": true,\n",
+       "      \"modality\": \"MOLECULE_3D\",\n",
+       "      \"description\": \"One generated molecule conformation for the ligand of interest generated with RDKit's ETKDGv3 followed by an energy minimization with the UFF.\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": null\n",
+       "    },\n",
+       "    \"ligand_start_conf_smiles\": {\n",
+       "      \"is_pointer\": false,\n",
+       "      \"modality\": \"MOLECULE\",\n",
+       "      \"description\": \"\",\n",
+       "      \"user_attributes\": {},\n",
+       "      \"dtype\": \"object\",\n",
+       "      \"content_type\": \"SMILES\"\n",
+       "    }\n",
+       "  },\n",
+       "  \"source\": \"https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a\",\n",
+       "  \"license\": \"CC-BY-4.0\",\n",
+       "  \"curation_reference\": null,\n",
+       "  \"cache_dir\": \"/Users/lu.zhu/Library/Caches/polaris/datasets/e5fa3d9a-be59-4df4-9b80-ec32f4a4f010\",\n",
+       "  \"md5sum\": \"3810e8268c3c9c89caf0193e1f97e35f\",\n",
+       "  \"artifact_id\": \"polaris/posebusters-v1\",\n",
+       "  \"n_rows\": 428,\n",
+       "  \"n_columns\": 8\n",
+       "}"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "42c498f1",
+   "metadata": {},
+   "source": [
+    "## Benchmark creation with `Polaris`\n",
+    "PoseBuster dataset is a testset which is pre-defined in [paper](https://pubs.rsc.org/en/content/articlelanding/2024/sc/d3sc04185a). The training set is PDBbinder which cannot be added here due to license restriction.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "835197d1",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>protein_group</th>\n",
+       "      <th>ligands</th>\n",
+       "      <th>ligands_smiles</th>\n",
+       "      <th>protein</th>\n",
+       "      <th>ligand_smiles</th>\n",
+       "      <th>ligand</th>\n",
+       "      <th>ligand_start_conf_smiles</th>\n",
+       "      <th>ligand_start_conf</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>5S8I_2LY</td>\n",
+       "      <td>ligands#0</td>\n",
+       "      <td>['CNC(=O)C1=C2OCCOC2=CS1']</td>\n",
+       "      <td>protein/5S8I_2LY_protein</td>\n",
+       "      <td>CNC(=O)C1=C2OCCOC2=CS1</td>\n",
+       "      <td>ligand#0</td>\n",
+       "      <td>[H]C1=C2OC([H])([H])C([H])([H])OC2=C(C(=O)N([H...</td>\n",
+       "      <td>ligand_start_conf#0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>5SAK_ZRY</td>\n",
+       "      <td>ligands#1</td>\n",
+       "      <td>['N=C1N/C(=N\\\\NC2=CC=CC=C2)C2=CC=CC=C12']</td>\n",
+       "      <td>protein/5SAK_ZRY_protein</td>\n",
+       "      <td>N=C1N/C(=N\\NC2=CC=CC=C2)C2=CC=CC=C12</td>\n",
+       "      <td>ligand#1</td>\n",
+       "      <td>[H]/N=C1\\C2=C([H])C([H])=C([H])C([H])=C2/C(=N/...</td>\n",
+       "      <td>ligand_start_conf#1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>5SB2_1K2</td>\n",
+       "      <td>ligands#2</td>\n",
+       "      <td>['O=C(N[C@@H]1C[C@H]1C1=CC=CC=C1)C1=CC(Cl)=CC(...</td>\n",
+       "      <td>protein/5SB2_1K2_protein</td>\n",
+       "      <td>O=C(N[C@@H]1C[C@H]1C1=CC=CC=C1)C1=CC(Cl)=CC(CO...</td>\n",
+       "      <td>ligand#2</td>\n",
+       "      <td>[H]C1=NC2=C(C([H])=C1OC([H])([H])C1=C([H])C(C(...</td>\n",
+       "      <td>ligand_start_conf#2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>5SD5_HWI</td>\n",
+       "      <td>ligands#3</td>\n",
+       "      <td>['CCC1=C(OCCCOC2=CC(C)=CC=C2N2CC(C(=O)O)C2)C(N...</td>\n",
+       "      <td>protein/5SD5_HWI_protein</td>\n",
+       "      <td>CCC1=C(OCCCOC2=CC(C)=CC=C2N2CC(C(=O)O)C2)C(N)=...</td>\n",
+       "      <td>ligand#3</td>\n",
+       "      <td>[H]OC(=O)C1([H])C([H])([H])N(C2=C([H])C([H])=C...</td>\n",
+       "      <td>ligand_start_conf#3</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>5SIS_JSM</td>\n",
+       "      <td>ligands#4</td>\n",
+       "      <td>['CNCCN(C)C(=O)C1=C(C(=O)NC2=CC3=NC(C4=CC=CC=C...</td>\n",
+       "      <td>protein/5SIS_JSM_protein</td>\n",
+       "      <td>CNCCN(C)C(=O)C1=C(C(=O)NC2=CC3=NC(C4=CC=CC=C4)...</td>\n",
+       "      <td>ligand#4</td>\n",
+       "      <td>[H]C1=NN(C([H])([H])[H])C(C(=O)N([H])C2=C([H])...</td>\n",
+       "      <td>ligand_start_conf#4</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "  protein_group    ligands                                     ligands_smiles  \\\n",
+       "0      5S8I_2LY  ligands#0                         ['CNC(=O)C1=C2OCCOC2=CS1']   \n",
+       "1      5SAK_ZRY  ligands#1          ['N=C1N/C(=N\\\\NC2=CC=CC=C2)C2=CC=CC=C12']   \n",
+       "2      5SB2_1K2  ligands#2  ['O=C(N[C@@H]1C[C@H]1C1=CC=CC=C1)C1=CC(Cl)=CC(...   \n",
+       "3      5SD5_HWI  ligands#3  ['CCC1=C(OCCCOC2=CC(C)=CC=C2N2CC(C(=O)O)C2)C(N...   \n",
+       "4      5SIS_JSM  ligands#4  ['CNCCN(C)C(=O)C1=C(C(=O)NC2=CC3=NC(C4=CC=CC=C...   \n",
+       "\n",
+       "                    protein  \\\n",
+       "0  protein/5S8I_2LY_protein   \n",
+       "1  protein/5SAK_ZRY_protein   \n",
+       "2  protein/5SB2_1K2_protein   \n",
+       "3  protein/5SD5_HWI_protein   \n",
+       "4  protein/5SIS_JSM_protein   \n",
+       "\n",
+       "                                       ligand_smiles    ligand  \\\n",
+       "0                             CNC(=O)C1=C2OCCOC2=CS1  ligand#0   \n",
+       "1               N=C1N/C(=N\\NC2=CC=CC=C2)C2=CC=CC=C12  ligand#1   \n",
+       "2  O=C(N[C@@H]1C[C@H]1C1=CC=CC=C1)C1=CC(Cl)=CC(CO...  ligand#2   \n",
+       "3  CCC1=C(OCCCOC2=CC(C)=CC=C2N2CC(C(=O)O)C2)C(N)=...  ligand#3   \n",
+       "4  CNCCN(C)C(=O)C1=C(C(=O)NC2=CC3=NC(C4=CC=CC=C4)...  ligand#4   \n",
+       "\n",
+       "                            ligand_start_conf_smiles    ligand_start_conf  \n",
+       "0  [H]C1=C2OC([H])([H])C([H])([H])OC2=C(C(=O)N([H...  ligand_start_conf#0  \n",
+       "1  [H]/N=C1\\C2=C([H])C([H])=C([H])C([H])=C2/C(=N/...  ligand_start_conf#1  \n",
+       "2  [H]C1=NC2=C(C([H])=C1OC([H])([H])C1=C([H])C(C(...  ligand_start_conf#2  \n",
+       "3  [H]OC(=O)C1([H])C([H])([H])N(C2=C([H])C([H])=C...  ligand_start_conf#3  \n",
+       "4  [H]C1=NN(C([H])([H])[H])C(C(=O)N([H])C2=C([H])...  ligand_start_conf#4  "
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dataset.table.head(5)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "03aa7204-c71f-4b46-9bf0-e4a57e82ff35",
+   "metadata": {},
+   "source": [
+    "## Create a Benchmark as in published paper\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "7b3dc13f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "train_split = []\n",
+    "test_split = list(range(dataset.table.shape[0]))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0676f308",
+   "metadata": {},
+   "source": [
+    "## Single task on ligand pose prediction"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "29de2f6d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-25 21:13:37.251\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.benchmark._base\u001b[0m:\u001b[36m_validate_split\u001b[0m:\u001b[36m189\u001b[0m - \u001b[1mThis benchmark only specifies a test set. It will return an empty train set in `get_train_test_split()`\u001b[0m\n"
+     ]
+    }
+   ],
+   "source": [
+    "benchmark_name = \"posebusters_v1\"\n",
+    "\n",
+    "benchmark = SingleTaskBenchmarkSpecification(\n",
+    "    name=benchmark_name,\n",
+    "    dataset=dataset,\n",
+    "    target_cols=[\"ligand\"],\n",
+    "    target_types={\"ligand\": \"docking\"},\n",
+    "    input_cols=[\"protein\"],\n",
+    "    split=(train_split, test_split),\n",
+    "    main_metric=\"rmsd_coverage\",\n",
+    "    metrics=[\"rmsd_coverage\"],\n",
+    "    tags=[\"Docking\", \"SingleTask\"],\n",
+    "    owner=\"polaris\",\n",
+    "    description=f\"Docking task benchmark for 428 proteins and ligands.\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dfd5a4c3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "benchmark"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "1b31ab0c",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
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+       "  'externalId': 'org_2gtoaJIVrgRqiIR8Qm5BnpFCbxu',\n",
+       "  'type': 'organization'},\n",
+       " 'creator': {'slug': 'lu-valencelabs',\n",
+       "  'externalId': 'user_2gtYwEALU6nz7YYhVOTrlJmkWtN',\n",
+       "  'type': 'user'},\n",
+       " 'dataset': {'access': 'private',\n",
+       "  'createdAt': '2024-09-06T15:48:01.769Z',\n",
+       "  'description': 'A diverse datasset of recent high-quality protein–ligand complexes which contain drug-like molecules for AI-based docking method evaluation.',\n",
+       "  'isCertified': False,\n",
+       "  'name': 'posebusters-v1',\n",
+       "  'artifactId': 'polaris/posebusters-v1',\n",
+       "  'owner': {'slug': 'polaris'}},\n",
+       " 'results': [],\n",
+       " 'review': None}"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Upload to polaris hub\n",
+    "benchmark.upload_to_hub(owner=owner, access=\"private\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f78854c2",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "id": "61b9aad3",
+   "metadata": {},
+   "source": [
+    "### Code example for evaluation with "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "833278e0",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "⠹ Fetching artifact... {'status_code': 200, 'headers': Headers({'cache-control': 'public, max-age=0, must-revalidate', 'content-encoding': 'br', 'content-type': 'application/json', 'date': 'Thu, 26 Sep 2024 02:37:15 GMT', 'server': 'Vercel', 'strict-transport-security': 'max-age=63072000', 'vary': 'RSC, Next-Router-State-Tree, Next-Router-Prefetch', 'x-matched-path': '/api/v1/benchmark/[owner]/[name]', 'x-vercel-cache': 'BYPASS', 'x-vercel-id': 'iad1::cle1::r8566-1727318235029-357e4dd09bc0', 'content-length': '1701'}), '_request': <Request('GET', 'https://polarishub.io/api/v1/benchmark/polaris/posebusters_v1')>, 'next_request': None, 'extensions': {'http_version': b'HTTP/1.1', 'reason_phrase': b'OK', 'network_stream': <httpcore._backends.sync.SyncStream object at 0x16dd69550>}, 'history': [], 'is_closed': True, 'is_stream_consumed': True, 'default_encoding': 'utf-8', 'stream': <httpx._client.BoundSyncStream object at 0x16e4a7e60>, '_num_bytes_downloaded': 1701, '_decoder': <httpx._decoders.BrotliDecoder object at 0x16e529b20>, '_elapsed': datetime.timedelta(microseconds=227182), '_content': b'{\"id\":\"8tEKzKfGATSxzc3rNMA64\",\"createdAt\":\"2024-09-26T01:14:06.951Z\",\"deletedAt\":null,\"name\":\"posebusters_v1\",\"slug\":\"posebusters-v1\",\"description\":\"Docking task benchmark for 428 proteins and ligands.\",\"tags\":[\"Docking\",\"SingleTask\"],\"userAttributes\":{},\"access\":\"private\",\"isCertified\":false,\"polarisVersion\":\"0.8.6.dev14+g870673b\",\"readme\":\"\",\"state\":\"ready\",\"ownerId\":\"9qGUtJxWQ5MDZrK5op9jn\",\"creatorId\":\"NKnaHGybLqwSHcaMEHqfF\",\"targetCols\":[\"ligand\"],\"inputCols\":[\"protein\"],\"md5Sum\":\"f60faeb65123fd59d315828e0202e28a\",\"metrics\":[\"rmsd_coverage\"],\"mainMetric\":\"rmsd_coverage\",\"split\":[[],[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427]],\"taskType\":\"single_task\",\"targetTypes\":{\"ligand\":\"docking\"},\"nTestSets\":1,\"nTestDatapoints\":{\"test\":428},\"nTrainDatapoints\":0,\"nClasses\":{},\"datasetId\":\"Wno3Gp8meFYe8X3CZMlsJ\",\"artifactId\":\"polaris/posebusters-v1\",\"owner\":{\"slug\":\"polaris\",\"externalId\":\"org_2gtoaJIVrgRqiIR8Qm5BnpFCbxu\",\"type\":\"organization\"},\"creator\":{\"slug\":\"lu-valencelabs\",\"externalId\":\"user_2gtYwEALU6nz7YYhVOTrlJmkWtN\",\"type\":\"user\"},\"dataset\":{\"access\":\"private\",\"createdAt\":\"2024-09-06T15:48:01.769Z\",\"description\":\"A diverse datasset of recent high-quality protein\\xe2\\x80\\x93ligand complexes which contain drug-like molecules for AI-based docking method evaluation.\",\"isCertified\":false,\"name\":\"posebusters-v1\",\"artifactId\":\"polaris/posebusters-v1\",\"owner\":{\"slug\":\"polaris\"}},\"results\":[],\"review\":null}'}\n",
+      "⠴ Fetching artifact... {'status_code': 200, 'headers': Headers({'cache-control': 'public, max-age=0, must-revalidate', 'content-encoding': 'br', 'content-type': 'application/json', 'date': 'Thu, 26 Sep 2024 02:37:15 GMT', 'server': 'Vercel', 'strict-transport-security': 'max-age=63072000', 'vary': 'RSC, Next-Router-State-Tree, Next-Router-Prefetch', 'x-matched-path': '/api/v1/dataset/[owner]/[name]', 'x-vercel-cache': 'BYPASS', 'x-vercel-id': 'iad1::cle1::r8566-1727318235176-90dee289afaa', 'content-length': '398361'}), '_request': <Request('GET', 'https://polarishub.io/api/v1/dataset/polaris/posebusters-v1')>, 'next_request': None, 'extensions': {'http_version': b'HTTP/1.1', 'reason_phrase': b'OK', 'network_stream': <httpcore._backends.sync.SyncStream object at 0x16dd69550>}, 'history': [], 'is_closed': True, 'is_stream_consumed': True, 'default_encoding': 'utf-8', 'stream': <httpx._client.BoundSyncStream object at 0x16e360440>, '_num_bytes_downloaded': 398361, '_decoder': <httpx._decoders.BrotliDecoder object at 0x16e528740>, '_elapsed': datetime.timedelta(seconds=1, microseconds=80693), '_content': b'{\"id\":\"Wno3Gp8meFYe8X3CZMlsJ\",\"createdAt\":\"2024-09-06T15:48:01.769Z\",\"deletedAt\":null,\"name\":\"posebusters-v1\",\"slug\":\"posebusters-v1\",\"description\":\"A diverse datasset of recent high-quality protein\\xe2\\x80\\x93ligand complexes which contain drug-like molecules for AI-based docking method evaluation.\",\"tags\":[\"docking\"],\"userAttributes\":{\"year\":\"2024\"},\"access\":\"private\",\"isCertified\":false,\"polarisVersion\":\"0.8.5.dev1+gc910f28.d20240906\",\"readme\":\"## Background\\\\nThe PoseBusters dataset set is a new set of carefully-selected publicly-available crystal complexes from the PDB. It is a diverse set of recent high-quality protein\\xe2\\x80\\x93ligand complexes which contain drug-like molecules. It only contains complexes released since 2021 and therefore does not contain any complexes present in the PDBbind General Set v2020 used to train many of the methods. \\\\n\\\\n\\\\n[Buttenschoen et al.](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a) lists the steps used to select the 308 unique proteins and 308 unique ligands in the PoseBusters dataset set. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest before saving the proteins with the cofactors in PDB files and the ligands in SDF files. \\\\n\\\\n\\\\n## Data source\\\\n- Orignial: https://zenodo.org/records/8278563\\\\n- Polaris: gs://polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/posebusters_benchmark_set\\\\n\\\\n## Other links\\\\n- Github: https://github.com/maabuu/posebusters/tree/main\",\"ownerId\":\"9qGUtJxWQ5MDZrK5op9jn\",\"creatorId\":\"NKnaHGybLqwSHcaMEHqfF\",\"state\":\"ready\",\"source\":\"https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a\",\"curationReference\":null,\"nRows\":428,\"nColumns\":8,\"license\":\"CC-BY-4.0\",\"md5Sum\":\"3810e8268c3c9c89caf0193e1f97e35f\",\"annotations\":{\"ligand\":{\"dtype\":\"object\",\"modality\":\"MOLECULE_3D\",\"isPointer\":true,\"description\":\"One of the instances of the ligand of interest. 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task benchmark for 428 proteins and ligands.\",\"name\":\"posebusters_v1\",\"artifactId\":\"polaris/posebusters-v1\",\"owner\":{\"slug\":\"polaris\"}}],\"review\":null}'}\n",
+      "⠴ Fetching artifact... "
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m2024-09-25 22:37:17.061\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris._artifact\u001b[0m:\u001b[36m_validate_version\u001b[0m:\u001b[36m66\u001b[0m - \u001b[1mThe version of Polaris that was used to create the artifact (0.8.5.dev1+gc910f28.d20240906) is different from the currently installed version of Polaris (0.8.6.dev14+g870673b).\u001b[0m\n",
+      "/Users/lu.zhu/miniconda3/envs/po_dataset/lib/python3.12/site-packages/yaspin/core.py:228: UserWarning: color, on_color and attrs are not supported when running in jupyter\n",
+      "  self._color = self._set_color(value) if value else value\n",
+      "\u001b[32m2024-09-25 22:37:17.080\u001b[0m | \u001b[1mINFO    \u001b[0m | \u001b[36mpolaris.benchmark._base\u001b[0m:\u001b[36m_validate_split\u001b[0m:\u001b[36m189\u001b[0m - \u001b[1mThis benchmark only specifies a test set. It will return an empty train set in `get_train_test_split()`\u001b[0m\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "✅ SUCCESS: \u001b[1mFetched artifact.\u001b[0m\n",
+      " \n",
+      "✅ SUCCESS: \u001b[1mFetched artifact.\u001b[0m\n",
+      " \n"
+     ]
+    }
+   ],
+   "source": [
+    "# load the benchmark\n",
+    "benchmark = po.load_benchmark(\"polaris/posebusters_v1\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "id": "f4d9ef93",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# make predictions\n",
+    "# each data point is the docked ligand conformer\n",
+    "# here we use same ligand in dataset for demonstration purpose\n",
+    "predictions = np.array(\n",
+    "    [\n",
+    "        benchmark.dataset.get_data(row=i, col=\"ligand\")\n",
+    "        for i in range(benchmark.dataset.n_rows)\n",
+    "    ]\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "id": "91777eff",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table border=\"1\"><tr><th>name</th><td>None</td></tr><tr><th>description</th><td></td></tr><tr><th>tags</th><td></td></tr><tr><th>user_attributes</th><td></td></tr><tr><th>owner</th><td>None</td></tr><tr><th>polaris_version</th><td>0.8.6.dev14+g870673b</td></tr><tr><th>github_url</th><td>None</td></tr><tr><th>paper_url</th><td>None</td></tr><tr><th>contributors</th><td>None</td></tr><tr><th>benchmark_name</th><td>posebusters_v1</td></tr><tr><th>benchmark_owner</th><td><table border=\"1\"><tr><th>slug</th><td>polaris</td></tr><tr><th>external_id</th><td>org_2gtoaJIVrgRqiIR8Qm5BnpFCbxu</td></tr><tr><th>type</th><td>organization</td></tr></table></td></tr><tr><th>artifact_id</th><td>None</td></tr><tr><th>benchmark_artifact_id</th><td>polaris/posebusters-v1</td></tr><tr><th>results</th><td><table border=\"1\"><thead><tr><th>Test set</th><th>Target label</th><th>Metric</th><th>Score</th></tr></thead><tbody><tr><td>test</td><td>ligand</td><td>rmsd_coverage</td><td>1.0</td></tr></tbody></table></td></tr></table>"
+      ],
+      "text/plain": [
+       "{\n",
+       "  \"name\": null,\n",
+       "  \"description\": \"\",\n",
+       "  \"tags\": [],\n",
+       "  \"user_attributes\": {},\n",
+       "  \"owner\": null,\n",
+       "  \"polaris_version\": \"0.8.6.dev14+g870673b\",\n",
+       "  \"github_url\": null,\n",
+       "  \"paper_url\": null,\n",
+       "  \"contributors\": null,\n",
+       "  \"benchmark_name\": \"posebusters_v1\",\n",
+       "  \"benchmark_owner\": {\n",
+       "    \"slug\": \"polaris\",\n",
+       "    \"external_id\": \"org_2gtoaJIVrgRqiIR8Qm5BnpFCbxu\",\n",
+       "    \"type\": \"organization\"\n",
+       "  },\n",
+       "  \"artifact_id\": null,\n",
+       "  \"benchmark_artifact_id\": \"polaris/posebusters-v1\",\n",
+       "  \"results\": [\n",
+       "    {\n",
+       "      \"Test set\": \"test\",\n",
+       "      \"Target label\": \"ligand\",\n",
+       "      \"Metric\": \"rmsd_coverage\",\n",
+       "      \"Score\": 1.0\n",
+       "    }\n",
+       "  ]\n",
+       "}"
+      ]
+     },
+     "execution_count": 29,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# perform evaluation\n",
+    "res = benchmark.evaluate(predictions)\n",
+    "res"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/org-Polaris/posebusters/benchmark_readme.md b/org-Polaris/posebusters/benchmark_readme.md
new file mode 100644
index 0000000..9acc312
--- /dev/null
+++ b/org-Polaris/posebusters/benchmark_readme.md
@@ -0,0 +1,25 @@
+![logo](https://posebusters.readthedocs.io/en/latest/_static/logo_square.png)
+## Background
+The PoseBusters dataset set is a new set of carefully-selected publicly-available crystal complexes from the PDB. It is a diverse set of recent high-quality protein–ligand complexes which contain drug-like molecules. It only contains complexes released since 2021 and therefore does not contain any complexes present in the PDBbind General Set v2020 used to train many of the methods. 
+
+
+[Buttenschoen et al.](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a) outlines the steps used to select the 308 unique proteins and 308 unique ligands in the PoseBusters dataset. The complexes were downloaded from the PDB as MMTF files, and PyMOL was used to remove solvents and all occurrences of the ligand of interest. The proteins were saved with their cofactors in PDB format, while the ligands were saved in SDF format.
+
+## Benchmark description
+
+This is a zero-shot benchmark that contains only a test set of 308 proteisn and ligands for evaluation.
+
+Posebusters offers a series of ligand checkers, known as 'Posebuster Checkers,' to filter out undesired docked ligand conformers. It is recommended to apply these filters before uploading results to the Polaris Hub.
+
+Only the extracted ligand from the docking output should be uploaded for evaluation, ensuring that the receptor (protein) coordinates have been aligned with the original crystal structure.
+
+This benchmark uses the metric RMSD coverage (≤2Å), which calculates the percentage of molecules with an RMSD of less than 2Å compared to the reference. For more details, see the documentation on [polaris](https://github.com/polaris-hub/polaris/blob/6e402f9d58d80d0ffe0b499cfef69a0c28c0427c/polaris/evaluate/metrics/docking_metrics.py#L39). .
+
+
+## Data source
+- Orignial: https://zenodo.org/records/8278563
+- Polaris: gs://polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/posebusters_benchmark_set
+
+## Other links
+- Paper: https://pubs.rsc.org/en/content/articlelanding/2024/sc/d3sc04185a
+- Github: https://github.com/maabuu/posebusters/tree/main
\ No newline at end of file
diff --git a/org-Polaris/posebusters/dataset_readme.md b/org-Polaris/posebusters/dataset_readme.md
new file mode 100644
index 0000000..fb9e603
--- /dev/null
+++ b/org-Polaris/posebusters/dataset_readme.md
@@ -0,0 +1,13 @@
+## Background
+The PoseBusters dataset set is a new set of carefully-selected publicly-available crystal complexes from the PDB. It is a diverse set of recent high-quality protein–ligand complexes which contain drug-like molecules. It only contains complexes released since 2021 and therefore does not contain any complexes present in the PDBbind General Set v2020 used to train many of the methods. 
+
+
+[Buttenschoen et al.](https://pubs.rsc.org/en/content/articlehtml/2024/sc/d3sc04185a) lists the steps used to select the 308 unique proteins and 308 unique ligands in the PoseBusters dataset set. The complexes were downloaded from the PDB as MMTF files and PyMOL was used to remove solvents and all occurrences of the ligand of interest before saving the proteins with the cofactors in PDB files and the ligands in SDF files. 
+
+
+## Data source
+- Orignial: https://zenodo.org/records/8278563
+- Polaris: gs://polaris-public/polaris-recipes/org-polaris/posebusters/posebusters_paper_data/posebusters_benchmark_set
+
+## Other links
+- Github: https://github.com/maabuu/posebusters/tree/main
\ No newline at end of file
diff --git a/org-Polaris/posebusters/env.yml b/org-Polaris/posebusters/env.yml
new file mode 100644
index 0000000..e785382
--- /dev/null
+++ b/org-Polaris/posebusters/env.yml
@@ -0,0 +1,21 @@
+channels:
+  - conda-forge
+
+dependencies:
+  # scientific
+  - rdkit == 2023.9.6
+  - auroris == 0.1.4
+  - polaris == 0.8.0
+
+  # visualization
+  - umap-learn==0.5.5
+  - seaborn==0.13.2
+
+  # notebooks
+  - jupyterlab==4.2.1
+
+  # utils
+  - gcsfs == 2024.6.1
+  - openpyxl == 3.1.2
+
+