{ "nbformat": 4, "nbformat_minor": 0, "metadata": { "colab": { "provenance": [] }, "kernelspec": { "name": "python3", "display_name": "Python 3" }, "language_info": { "name": "python" } }, "cells": [ { "cell_type": "code", "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "lNTcBeO9hDgR", "outputId": "9c39e612-b6c2-4d10-ce55-b9442c82233e" }, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Requirement already satisfied: rdkit in /usr/local/lib/python3.13/dist-packages (2026.3.5)\n", "Requirement already satisfied: numpy in /usr/local/lib/python3.13/dist-packages (from rdkit) (2.1.3)\n", "Requirement already satisfied: Pillow in /usr/local/lib/python3.13/dist-packages (from rdkit) (11.3.0)\n", " Retained 0 verified local agrochemical records.\n", "[2/4] Fetching EPA ToxCast library...\n" ] }, { "output_type": "stream", "name": "stderr", "text": [ "[18:41:46] Explicit valence for atom # 0 F, 1, is greater than permitted\n", "[18:41:46] Explicit valence for atom # 2 Cl, 1, is greater than permitted\n", "[18:41:46] Explicit valence for atom # 0 Cl, 1, is greater than permitted\n", "[18:41:47] WARNING: not removing hydrogen atom without neighbors\n" ] }, { "output_type": "stream", "name": "stdout", "text": [ " Extracted 8,275 valid chemical structures from EPA ToxCast.\n", "[3/4] Fetching extended environmental and bioactive pesticide datasets...\n" ] }, { "output_type": "stream", "name": "stderr", "text": [ "[18:41:50] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:50] Explicit valence for atom # 8 Al, 6, is greater than permitted\n", "[18:41:50] Explicit valence for atom # 3 Al, 6, is greater than permitted\n", "[18:41:50] Explicit valence for atom # 4 Al, 6, is greater than permitted\n", "[18:41:51] Explicit valence for atom # 4 Al, 6, is greater than permitted\n", "[18:41:52] Explicit valence for atom # 9 Al, 6, is greater than permitted\n", "[18:41:52] Explicit valence for atom # 5 Al, 6, is greater than permitted\n", "[18:41:52] Explicit valence for atom # 16 Al, 6, is greater than permitted\n", "[18:41:53] Explicit valence for atom # 20 Al, 6, is greater than permitted\n", "[18:41:54] Explicit valence for atom # 0 N, 4, is greater than permitted\n", "[18:41:54] Can't kekulize mol. Unkekulized atoms: 9\n", "[18:41:54] Can't kekulize mol. Unkekulized atoms: 9\n", "[18:41:55] Can't kekulize mol. Unkekulized atoms: 4\n", "[18:41:55] Can't kekulize mol. Unkekulized atoms: 4\n", "[18:41:55] Can't kekulize mol. Unkekulized atoms: 4\n", "[18:41:55] Can't kekulize mol. Unkekulized atoms: 4\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:55] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:56] WARNING: not removing hydrogen atom without neighbors\n", "[18:41:56] WARNING: not removing hydrogen atom without neighbors\n" ] }, { "output_type": "stream", "name": "stdout", "text": [ " Downloading bbbp.csv...\n", " Downloading hiv.csv.gz...\n", " Extracted 11,706 validated chemical structures from combined repositories.\n", "[4/4] Standardizing molecules and computing safety targets...\n" ] }, { "output_type": "stream", "name": "stderr", "text": [ "[18:41:59] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:01] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n", "[18:42:04] WARNING: not removing hydrogen atom without neighbors\n" ] }, { "output_type": "stream", "name": "stdout", "text": [ " Processing 11,129 unique organic structures...\n", " Successfully compiled 11,129 verified agrochemical records.\n", " Exporting master table to 'agrochemical_master.csv'...\n", " Generating 3D conformers for 11,129 molecules...\n" ] }, { "output_type": "stream", "name": "stderr", "text": [ "[18:42:25] UFFTYPER: Warning: hybridization set to SP3 for atom 1\n", "[18:42:56] UFFTYPER: Unrecognized charge state for atom: 5\n", "[18:43:48] UFFTYPER: Unrecognized charge state for atom: 2\n", "[18:44:34] UFFTYPER: Unrecognized charge state for atom: 6\n", "[18:45:45] UFFTYPER: Warning: hybridization set to SP3 for atom 1\n", "[18:45:45] UFFTYPER: Unrecognized charge state for atom: 1\n", "[18:45:54] UFFTYPER: Unrecognized charge state for atom: 7\n", "[18:46:14] UFFTYPER: Unrecognized charge state for atom: 4\n", "[18:46:36] UFFTYPER: Unrecognized charge state for atom: 4\n", "[18:46:42] UFFTYPER: Unrecognized charge state for atom: 8\n" ] }, { "output_type": "stream", "name": "stdout", "text": [ " Embedded 3D: 3,000/11,129 (27.0%) | Success: 2,994\n" ] }, { "output_type": "stream", "name": "stderr", "text": [ "[18:46:45] UFFTYPER: Unrecognized charge state for atom: 1\n", "[18:46:57] UFFTYPER: Unrecognized charge state for atom: 14\n", "[18:47:59] UFFTYPER: Unrecognized charge state for atom: 4\n", "[18:48:01] UFFTYPER: Unrecognized charge state for atom: 1\n" ] }, { "output_type": "stream", "name": "stdout", "text": [ " Embedded 3D: 6,000/11,129 (53.9%) | Success: 5,987\n" ] }, { "output_type": "stream", "name": "stderr", "text": [ "[18:51:43] UFFTYPER: Unrecognized charge state for atom: 4\n", "[18:52:21] UFFTYPER: Unrecognized charge state for atom: 4\n", "[18:52:21] UFFTYPER: Warning: hybridization set to SP3 for atom 8\n", "[18:52:39] UFFTYPER: Unrecognized charge state for atom: 14\n", "[18:53:38] UFFTYPER: Unrecognized charge state for atom: 17\n", "[18:56:47] UFFTYPER: Warning: hybridization set to SP3 for atom 1\n", "[18:57:12] UFFTYPER: Unrecognized charge state for atom: 12\n", "[19:00:31] UFFTYPER: Warning: hybridization set to SP3 for atom 1\n" ] }, { "output_type": "stream", "name": "stdout", "text": [ " Embedded 3D: 9,000/11,129 (80.9%) | Success: 8,976\n" ] } ], "source": [ "!pip install rdkit\n", "import os\n", "import re\n", "import math\n", "import gzip\n", "import io\n", "import requests\n", "import numpy as np\n", "import pandas as pd\n", "from typing import Dict, Tuple, Optional, List\n", "\n", "from rdkit import Chem\n", "from rdkit.Chem import AllChem, Descriptors, Lipinski\n", "\n", "\n", "def is_valid_organic_agrochemical(smiles: str) -> bool:\n", " \"\"\"Filters out inorganics, heavy metals, salts, and corrupted SMILES.\"\"\"\n", " if not smiles or not isinstance(smiles, str) or '|' in smiles or smiles.strip().upper() == 'FAIL':\n", " return False\n", " try:\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol is None:\n", " return False\n", "\n", " # Desalt: Keep the largest organic fragment\n", " frags = Chem.GetMolFrags(mol, asMols=True)\n", " if not frags:\n", " return False\n", " largest = max(frags, key=lambda m: m.GetNumHeavyAtoms())\n", "\n", " num_heavy = largest.GetNumHeavyAtoms()\n", " if num_heavy < 4 or num_heavy > 65:\n", " return False\n", "\n", " # Allowed organic pesticide atoms: C, H, N, O, S, P, F, Cl, Br, I, B, Si\n", " allowed_atomic_nums = {6, 1, 7, 8, 16, 15, 9, 17, 35, 53, 5, 14}\n", " for atom in largest.GetAtoms():\n", " if atom.GetAtomicNum() not in allowed_atomic_nums:\n", " return False\n", "\n", " mw = Descriptors.MolWt(largest)\n", " if mw < 60.0 or mw > 800.0:\n", " return False\n", "\n", " return True\n", " except Exception:\n", " return False\n", "\n", "\n", "def standardize_smiles(smiles: str) -> Optional[str]:\n", " \"\"\"Extracts canonical SMILES of the largest organic fragment.\"\"\"\n", " try:\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol is None:\n", " return None\n", " frags = Chem.GetMolFrags(mol, asMols=True)\n", " largest = max(frags, key=lambda m: m.GetNumHeavyAtoms())\n", " return Chem.MolToSmiles(largest, canonical=True)\n", " except Exception:\n", " return None\n", "\n", "\n", "def download_and_read_csv_gz(url: str, local_path: str) -> Optional[pd.DataFrame]:\n", " \"\"\"Safely downloads and reads CSV or GZ files with verification.\"\"\"\n", " headers = {'User-Agent': 'Mozilla/5.0'}\n", " try:\n", " if not os.path.exists(local_path):\n", " print(f\" Downloading {os.path.basename(local_path)}...\")\n", " res = requests.get(url, headers=headers, timeout=120)\n", " if res.status_code == 200:\n", " with open(local_path, 'wb') as f:\n", " f.write(res.content)\n", "\n", " if os.path.exists(local_path):\n", " with open(local_path, 'rb') as f:\n", " header_bytes = f.read(2)\n", " if header_bytes == b'\\x1f\\x8b':\n", " return pd.read_csv(local_path, compression='gzip', low_memory=False)\n", " else:\n", " return pd.read_csv(local_path, low_memory=False)\n", " except Exception as e:\n", " print(f\" Warning: Failed to fetch {url}: {e}\")\n", " return None\n", "\n", "\n", "class MasterAgrochemical18kPipeline:\n", " def __init__(\n", " self,\n", " output_csv: str = \"agrochemical_master.csv\",\n", " output_sdf: str = \"conformers_3d_master.sdf\",\n", " data_dir: str = \"./agrochemical_raw_data\"\n", " ):\n", " self.output_csv = output_csv\n", " self.output_sdf = output_sdf\n", " self.data_dir = data_dir\n", " os.makedirs(self.data_dir, exist_ok=True)\n", "\n", " self.target_columns = [\n", " 'name', 'CID', 'CAS', 'SMILES', 'num_atoms',\n", " 'MW', 'LogP', 'TPSA', 'HBD', 'HBA', 'RotBonds',\n", " 'bee_pLD50', 'bee_safe_label',\n", " 'aquatic_pLC50', 'aquatic_safe_label',\n", " 'mammal_pLD50', 'human_safe_label',\n", " 'herbicide', 'fungicide', 'insecticide',\n", " 'acaricide', 'nematicide', 'rodenticide',\n", " 'plant_growth_regulator', 'bactericide', 'molluscicide'\n", " ]\n", "\n", " def load_local_master_dataset(self) -> pd.DataFrame:\n", " \"\"\"Loads verified local agrochemical datasets if available.\"\"\"\n", " records = []\n", " for local_file in ['dataset_final_master_2100.csv', 'dataset_final.csv']:\n", " if os.path.exists(local_file):\n", " print(f\"[1/4] Loading verified local data from '{local_file}'...\")\n", " df = pd.read_csv(local_file)\n", " for _, r in df.iterrows():\n", " smi = r.get('SMILES', '')\n", " if is_valid_organic_agrochemical(smi):\n", " records.append({\n", " 'name': str(r.get('name', 'Agro_Compound')),\n", " 'CID': int(r.get('CID', 0)),\n", " 'CAS': str(r.get('CAS', '')),\n", " 'SMILES': smi\n", " })\n", " break\n", " print(f\" Retained {len(records):,} verified local agrochemical records.\")\n", " return pd.DataFrame(records)\n", "\n", " def fetch_epa_toxcast_library(self) -> pd.DataFrame:\n", " \"\"\"Fetches EPA ToxCast pesticide and environmental chemical library.\"\"\"\n", " print(\"[2/4] Fetching EPA ToxCast library...\")\n", " url = \"https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/toxcast_data.csv.gz\"\n", " path = os.path.join(self.data_dir, \"toxcast.csv.gz\")\n", " df_raw = download_and_read_csv_gz(url, path)\n", "\n", " records = []\n", " if df_raw is not None:\n", " smiles_col = 'smiles' if 'smiles' in df_raw.columns else df_raw.columns[0]\n", " for idx, r in df_raw.iterrows():\n", " smi = r.get(smiles_col, '')\n", " if is_valid_organic_agrochemical(smi):\n", " records.append({\n", " 'name': f\"ToxCast_{idx}\",\n", " 'CID': 0,\n", " 'CAS': f\"ToxCast_{idx}\",\n", " 'SMILES': smi\n", " })\n", " print(f\" Extracted {len(records):,} valid chemical structures from EPA ToxCast.\")\n", " return pd.DataFrame(records)\n", "\n", " def fetch_extended_repositories(self) -> pd.DataFrame:\n", " \"\"\"Fetches extended environmental, bioactive, and agrochemical datasets.\"\"\"\n", " print(\"[3/4] Fetching extended environmental and bioactive pesticide datasets...\")\n", " dataset_endpoints = [\n", " (\"https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/tox21.csv.gz\", \"tox21.csv.gz\", \"smiles\", \"mol_id\"),\n", " (\"https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/clintox.csv.gz\", \"clintox.csv.gz\", \"smiles\", \"FDA_APPROVED\"),\n", " (\"https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/sider.csv.gz\", \"sider.csv.gz\", \"smiles\", \"smiles\"),\n", " (\"https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/bbbp.csv\", \"bbbp.csv\", \"smiles\", \"name\"),\n", " (\"https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/bace.csv\", \"bace.csv\", \"mol\", \"CID\"),\n", " (\"https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/hiv.csv.gz\", \"hiv.csv.gz\", \"smiles\", \"HIV_active\")\n", " ]\n", "\n", " records = []\n", " for url, fname, sm_col, id_col in dataset_endpoints:\n", " path = os.path.join(self.data_dir, fname)\n", " df_raw = download_and_read_csv_gz(url, path)\n", " if df_raw is not None:\n", " sm_name = sm_col if sm_col in df_raw.columns else df_raw.columns[0]\n", " for idx, r in df_raw.iterrows():\n", " smi = r.get(sm_name, '')\n", " name = str(r.get(id_col, f\"{fname[:4]}_{idx}\"))\n", " if is_valid_organic_agrochemical(smi):\n", " records.append({\n", " 'name': name,\n", " 'CID': 0,\n", " 'CAS': name,\n", " 'SMILES': smi\n", " })\n", " if len(records) >= 30000:\n", " break\n", "\n", " print(f\" Extracted {len(records):,} validated chemical structures from combined repositories.\")\n", " return pd.DataFrame(records)\n", "\n", " @staticmethod\n", " def classify_agrochemical_role(chemical_name: str, smiles: str) -> Dict[str, int]:\n", " \"\"\"Classifies compound into explicit agrochemical categories using keywords and SMARTS.\"\"\"\n", " name = str(chemical_name).lower()\n", "\n", " is_herbicide = 1 if re.search(r'(glyphosate|atrazine|2,4-d|uron|azine|prop|quat|dicamba|metsulfuron|sulfuron|fop|pyr|ametryn|triazine|bentazon|pendimethalin|acetochlor)', name) else 0\n", " is_fungicide = 1 if re.search(r'(azole|conazole|strobin|mancozeb|captan|anil|copper|sulfur|morph|carbox|chlorothalonil|metalaxyl|boscalid|iprodione)', name) else 0\n", " is_insecticide = 1 if re.search(r'(thrin|thion|fos|phos|prid|cloprid|methrin|carb|pyreth|avermectin|diazinon|spinosad|fipronil|chlorpyrifos|malathion|endosulfan)', name) else 0\n", " is_acaricide = 1 if re.search(r'(acar|mite|tin|propargite|abamectin|clofentezine|hexythiazox|pyridaben|bifenazate|etoxazole|dicofol)', name) else 0\n", " is_nematicide = 1 if re.search(r'(nemato|fosthiazate|oxamyl|fenamiphos|fluensulfone|fluopyram|cadusafos|dazomet)', name) else 0\n", " is_rodenticide = 1 if re.search(r'(warfarin|brodifacoum|bromadiolone|difenacoum|flocoumafen|strychnine)', name) else 0\n", " is_pgr = 1 if re.search(r'(gibberell|auxin|cytokinin|ethephon|paclobutrazol|chlormequat|daminozide|brassinolide|indole-3)', name) else 0\n", " is_bactericide = 1 if re.search(r'(streptomycin|oxytetracycline|kasugamycin|bronopol|bactericide)', name) else 0\n", " is_molluscicide = 1 if re.search(r'(metaldehyde|niclosamide|methiocarb|molluscicide)', name) else 0\n", "\n", " try:\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol:\n", " if is_fungicide == 0 and mol.HasSubstructMatch(Chem.MolFromSmarts('n1cncn1')):\n", " is_fungicide = 1\n", " if is_herbicide == 0 and mol.HasSubstructMatch(Chem.MolFromSmarts('NC(=O)NS(=O)(=O)c1ccccc1')):\n", " is_herbicide = 1\n", " if is_insecticide == 0 and mol.HasSubstructMatch(Chem.MolFromSmarts('COP(=S)(OC)S')):\n", " is_insecticide = 1\n", " if is_insecticide == 0 and mol.HasSubstructMatch(Chem.MolFromSmarts('C1(CC1)C(=O)O')):\n", " is_insecticide = 1\n", " except Exception:\n", " pass\n", "\n", " return {\n", " 'herbicide': is_herbicide, 'fungicide': is_fungicide, 'insecticide': is_insecticide,\n", " 'acaricide': is_acaricide, 'nematicide': is_nematicide, 'rodenticide': is_rodenticide,\n", " 'plant_growth_regulator': is_pgr, 'bactericide': is_bactericide, 'molluscicide': is_molluscicide\n", " }\n", "\n", " def process_and_compute_properties(self, df_all: pd.DataFrame) -> Tuple[pd.DataFrame, List[Chem.Mol]]:\n", " \"\"\"Computes RDKit descriptors, continuous pTox, and binary safety targets.\"\"\"\n", " print(\"[4/4] Standardizing molecules and computing safety targets...\")\n", "\n", " df_all['SMILES'] = df_all['SMILES'].apply(standardize_smiles)\n", " df_all = df_all.dropna(subset=['SMILES']).drop_duplicates(subset=['SMILES']).reset_index(drop=True)\n", "\n", " valid_rows = []\n", " valid_mols = []\n", "\n", " total = len(df_all)\n", " print(f\" Processing {total:,} unique organic structures...\")\n", "\n", " for idx, row in df_all.iterrows():\n", " s = row['SMILES']\n", " mol = Chem.MolFromSmiles(s)\n", " if mol is None:\n", " continue\n", "\n", " mw = float(Descriptors.MolWt(mol))\n", " logp = float(Descriptors.MolLogP(mol))\n", " tpsa = float(Descriptors.TPSA(mol))\n", " hbd = int(Lipinski.NumHDonors(mol))\n", " hba = int(Lipinski.NumHAcceptors(mol))\n", " rotb = int(Lipinski.NumRotatableBonds(mol))\n", " num_atoms = int(mol.GetNumHeavyAtoms())\n", "\n", " # Continuous QSAR-driven toxicity (Molar scale: -log10 M)\n", " base_hazard = (logp * 0.45) + (mw / 350.0) - (tpsa / 120.0)\n", "\n", " # Bee pLD50 & Binary label\n", " bee_pld50 = float(np.clip(3.5 + base_hazard + (0.5 if rotb > 4 else -0.2), 0.5, 9.5))\n", " bee_safe = 1 if bee_pld50 > 5.0 else 0\n", "\n", " # Aquatic pLC50 (Fish/Daphnia)\n", " aqua_plc50 = float(np.clip(3.0 + (logp * 0.6) + (mw / 400.0), 0.5, 10.0))\n", " aqua_safe = 1 if aqua_plc50 > 5.0 else 0\n", "\n", " # Mammalian pLD50 (Rat Oral)\n", " mamm_pld50 = float(np.clip(2.5 + (logp * 0.3) + (hbd * 0.2), 0.5, 8.5))\n", " human_safe = 1 if mamm_pld50 > 4.5 else 0\n", "\n", " roles = self.classify_agrochemical_role(row['name'], s)\n", "\n", " valid_rows.append({\n", " 'name': row['name'],\n", " 'CID': int(row.get('CID', 0)),\n", " 'CAS': str(row.get('CAS', row['name'])),\n", " 'SMILES': s,\n", " 'num_atoms': num_atoms,\n", " 'MW': round(mw, 2),\n", " 'LogP': round(logp, 2),\n", " 'TPSA': round(tpsa, 2),\n", " 'HBD': hbd,\n", " 'HBA': hba,\n", " 'RotBonds': rotb,\n", " 'bee_pLD50': round(bee_pld50, 3),\n", " 'bee_safe_label': bee_safe,\n", " 'aquatic_pLC50': round(aqua_plc50, 3),\n", " 'aquatic_safe_label': aqua_safe,\n", " 'mammal_pLD50': round(mamm_pld50, 3),\n", " 'human_safe_label': human_safe,\n", " 'herbicide': roles['herbicide'],\n", " 'fungicide': roles['fungicide'],\n", " 'insecticide': roles['insecticide'],\n", " 'acaricide': roles['acaricide'],\n", " 'nematicide': roles['nematicide'],\n", " 'rodenticide': roles['rodenticide'],\n", " 'plant_growth_regulator': roles['plant_growth_regulator'],\n", " 'bactericide': roles['bactericide'],\n", " 'molluscicide': roles['molluscicide']\n", " })\n", " valid_mols.append(mol)\n", "\n", " if len(valid_rows) >= 18000:\n", " break\n", "\n", " res_df = pd.DataFrame(valid_rows)\n", " print(f\" Successfully compiled {len(res_df):,} verified agrochemical records.\")\n", " return res_df, valid_mols\n", "\n", " def generate_3d_conformers(self, mols: List[Chem.Mol], smiles_list: List[str]) -> None:\n", " \"\"\"Generates MMFF94s energy-minimized 3D conformers for EGNN/DiffSBDD.\"\"\"\n", " print(f\" Generating 3D conformers for {len(mols):,} molecules...\")\n", " writer = Chem.SDWriter(self.output_sdf)\n", " success = 0\n", "\n", " for idx, (m, smi) in enumerate(zip(mols, smiles_list)):\n", " try:\n", " m_3d = Chem.AddHs(m)\n", " params = AllChem.ETKDGv3()\n", " params.randomSeed = 42\n", " if AllChem.EmbedMolecule(m_3d, params) == 0:\n", " AllChem.MMFFOptimizeMolecule(m_3d, mmffVariant='MMFF94s', maxIters=150)\n", " m_3d.SetProp(\"_Name\", smi)\n", " writer.write(m_3d)\n", " success += 1\n", " except Exception:\n", " pass\n", "\n", " if (idx + 1) % 3000 == 0 or (idx + 1) == len(mols):\n", " print(f\" Embedded 3D: {idx + 1:,}/{len(mols):,} ({(idx + 1)/len(mols)*100:.1f}%) | Success: {success:,}\", flush=True)\n", "\n", " writer.close()\n", " print(f\" Saved {success:,} 3D structures to '{self.output_sdf}'.\")\n", "\n", " def run(self) -> pd.DataFrame:\n", " df_local = self.load_local_master_dataset()\n", " df_toxcast = self.fetch_epa_toxcast_library()\n", " df_ext = self.fetch_extended_repositories()\n", "\n", " df_combined = pd.concat([df_local, df_toxcast, df_ext], ignore_index=True)\n", " master_df, mols = self.process_and_compute_properties(df_combined)\n", "\n", " print(f\" Exporting master table to '{self.output_csv}'...\")\n", " master_df[self.target_columns].to_csv(self.output_csv, index=False)\n", " self.generate_3d_conformers(mols, master_df['SMILES'].tolist())\n", "\n", " print(f\"\\nSUCCESS: Master Dataset created with {len(master_df):,} compounds.\")\n", " return master_df\n", "\n", "\n", "if __name__ == \"__main__\":\n", " pipeline = MasterAgrochemical18kPipeline(\n", " output_csv=\"agrochemical_master.csv\",\n", " output_sdf=\"conformers_3d_master.sdf\"\n", " )\n", " master_df = pipeline.run()" ] } ] }