{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import pickle, h5py\n", "import numpy as np\n", "import pandas as pd\n", "import matplotlib.pyplot as plt\n", "import os\n", "\n", "def load_from_HDF(fname):\n", " \"\"\"Load data from a HDF5 file to a dictionary.\"\"\"\n", " data = dict()\n", " with h5py.File(fname, 'r') as f:\n", " for key in f:\n", " data[key] = np.asarray(f[key])\n", " if isinstance(data[key][0], np.bytes_):\n", " data[key] = data[key].astype(str)\n", " return data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# get smiles txt" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "合并后的唯一 SMILES 数量: 66530\n" ] } ], "source": [ "# # 从 HDF5 文件加载数据\n", "BBBC036 = load_from_HDF('BBBC036_data.h5')\n", "cpg0016 = load_from_HDF('cpg0016_data.h5')\n", "\n", "BBBC036['canonical_smiles'] = BBBC036['canonical_smiles'].astype(str)\n", "\n", "# # 获取两个数据集的唯一 SMILES 并合并\n", "all_smiles = np.concatenate([cpg0016['canonical_smiles'], BBBC036['canonical_smiles']])\n", "unique_smiles = np.unique(all_smiles)\n", "\n", "print(f\"合并后的唯一 SMILES 数量: {len(unique_smiles)}\")" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "(1916, 14996)" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(np.unique(BBBC036['canonical_smiles'])), len(BBBC036['canonical_smiles'])" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "65119" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(np.unique(cpg0016['canonical_smiles']))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# 不要转成 UTF-8， 直接存。" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "66530 66530\n" ] } ], "source": [ "from rdkit import Chem\n", "\n", "def standardize_smiles(smiles_list):\n", " standardized = []\n", " for smiles in smiles_list:\n", " try:\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol is not None:\n", " canonical_smiles = Chem.MolToSmiles(mol)\n", " standardized.append(canonical_smiles)\n", " except:\n", " continue\n", " return standardized\n", "\n", "# 使用示例\n", "standardized_smiles = standardize_smiles(unique_smiles)\n", "print(len(standardized_smiles), len(unique_smiles))" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "✅ TXT 文件已保存，路径: image_all_unique_smiles.txt，包含 66530 个唯一 SMILES\n", "✅ CSV 文件已保存，路径: image_all_unique_smiles.csv\n" ] } ], "source": [ "txt_path='image_all_unique_smiles.txt'\n", "csv_path='image_all_unique_smiles.csv'\n", "\n", "# 假设 unique_smiles 是包含字节类型的列表\n", "# 先将所有元素转换为字符串\n", "# standardized_smiles = [s.decode('utf-8') if isinstance(s, bytes) else s for s in standardized_smiles]\n", "\n", "# 保存为 TXT 文件\n", "with open(txt_path, 'w', encoding='utf-8') as f:\n", " f.write('\\n'.join(standardized_smiles))\n", "print(f\"✅ TXT 文件已保存，路径: {txt_path}，包含 {len(standardized_smiles)} 个唯一 SMILES\")\n", "\n", "# 保存为 CSV 文件\n", "df = pd.DataFrame({'SMILES': standardized_smiles})\n", "df.to_csv(csv_path, index=False, encoding='utf-8')\n", "print(f\"✅ CSV 文件已保存，路径: {csv_path}\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate ECFP4 embedding for all smiles\n" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['BrC1C(Br)C(Br)C(Br)C(Br)C1Br', 'Brc1c(Br)c(Br)c2[nH]nnc2c1Br', 'Brc1c(NC2=NCCN2)ccc2nccnc12', 'Brc1cc2c(cc1C1Nc3ccccc3C3C=CCC31)OCO2', 'Brc1cc2c(cc1CN1CCN(c3ncccn3)CC1)OCCO2']\n" ] }, { "data": { "text/plain": [ "66530" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import numpy as np\n", "import pandas as pd\n", "\n", "# 使用合适的dtype参数以字符串形式加载数据\n", "# unique_smiles = pd.read_csv('CP_unique_smiles.csv')\n", "# print(len(unique_smiles))\n", "# unique_smiles = unique_smiles['SMILES'].tolist()\n", "# unique_smiles\n", "print(unique_smiles[0:5]) # 打印前5个SMILES以验证\n", "len(unique_smiles)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 统一转为标准的smiles" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "66530 66530\n" ] } ], "source": [ "# from rdkit import Chem\n", "\n", "# def standardize_smiles(smiles_list):\n", "# standardized = []\n", "# for smiles in smiles_list:\n", "# try:\n", "# mol = Chem.MolFromSmiles(smiles)\n", "# if mol is not None:\n", "# canonical_smiles = Chem.MolToSmiles(mol)\n", "# standardized.append(canonical_smiles)\n", "# except:\n", "# continue\n", "# return standardized\n", "\n", "# # 使用示例\n", "# standardized_smiles = standardize_smiles(unique_smiles)\n", "# print(len(standardized_smiles), len(unique_smiles))" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [], "source": [ "from rdkit import Chem\n", "from rdkit.Chem import AllChem\n", "import numpy as np\n", "import pickle\n", "\n", "def smiles_to_ecfp4(smiles_list, radius=2, n_bits=2048):\n", " \"\"\"\n", " 将SMILES列表转换为ECFP4特征向量。\n", "\n", " 参数:\n", " smiles_list (list): SMILES字符串列表。\n", " radius (int): ECFP的半径，默认为2（即ECFP4）。\n", " n_bits (int): 特征向量的长度，默认为2048。\n", "\n", " 返回:\n", " dict: 一个字典，键为SMILES字符串，值为对应的ECFP4特征向量。\n", " \"\"\"\n", " ecfp4_dict = {}\n", " new_smiles = []\n", " \n", " for smiles in smiles_list:\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol is not None:\n", " # 替换编码器\n", " new_smiles.append(smiles)\n", " ecfp4 = AllChem.GetMorganFingerprintAsBitVect(mol, radius=radius, nBits=n_bits)\n", " ecfp4_dict[smiles] = np.array(ecfp4, dtype=np.float32)\n", " else:\n", " print(\"Error in \", smiles)\n", " # 如果SMILES无法解析为分子，则填充一个全零的向量\n", " # ecfp4_dict[smiles] = np.zeros(n_bits, dtype=np.float32)\n", " \n", " return ecfp4_dict, new_smiles\n", "\n", "# 从字典中提取SMILES列表\n", "smiles_list = standardized_smiles\n", "\n", "# 计算ECFP4特征\n", "ecfp4_features_dict, new_smiles = smiles_to_ecfp4(smiles_list)" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "66530 66530 66530\n" ] } ], "source": [ "print(len(smiles_list), len(ecfp4_features_dict), len(new_smiles))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# 保存为 pickle 文件\n", "with open('/home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/ECFP4_emb2048.pickle', 'wb') as f:\n", " pickle.dump(ecfp4_features_dict, f)" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{'BrC1C(Br)C(Br)C(Br)C(Br)C1Br': array([0., 0., 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array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(C2CCCCC2)CC1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(CC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(CCC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(Cc2ccccc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2c(C)cccc2C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2cc(C)ccc2C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2cc(Cl)ccc2C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(C)cc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(C)cc2C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(F)cc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(OC)cc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2cccc(C)c2)C(C)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2cccc(C)c2)CC1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2cccc(Cl)c2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2ccccc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2ccccc2F)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCN(c2ccccc2OC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCN1CCc2ccccc2C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCOC1CCN(C(C)C)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCOC1CCN(Cc2ccccc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCc1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCc1nc2ccccc2[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCCn1cccn1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN(C)C1CCCCC1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN(C)Cc1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN(CC)Cc1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN(CCCC)Cc1cccs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN(Cc1cccs1)C(C)CC': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCC(Cc2ccccc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCCCC1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCCCC1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCN(c2cc(Cl)ccc2C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCN(c2ccc(OC)cc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCN(c2cccc(C)c2C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCN(c2cccc(Cl)c2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCN(c2ccccc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCN(c2ccccc2F)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCN1CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCOc1ccccc1OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCSCc1[nH]cnc1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCc1c(C)nn(C)c1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCc1c[nH]c2ccc(C)cc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCc1c[nH]c2ccc(OCc3ccccc3)cc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCc1c[nH]c2ccccc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCc1ccc(OCC)c(OCC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCc1csc(C)n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCCc1nc2cc(C)ccc2[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1c(C)n[nH]c1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1c(C)nn(CC)c1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1cc(F)cc(F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1cc(F)ccc1F': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1cc(OCC)c(OCC)c(OCC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(-c2nc(C)cs2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(-c2nc(CC)cs2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(=O)n(CC2CC2)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(=O)n(CCOC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(C(=O)N2CCOCC2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(F)cc1F': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(N(CC)CC)cc1': array([0., 0., 0., ..., 0., 0., 1.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(N2CCC(C)CC2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(N2CCCC(C)C2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(N2CCCCC2C)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(OC(C)C)cc1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(OC(F)(F)F)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(OC)c(OC)c1OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc(OCC)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccc2nonc2c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1cccc(C(F)(F)F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1ccccn1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1cccn(C)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1cccn(CC2CC2)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)NCc1cccnc1-c1ccc(F)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(C)ccc1N=c1[nH]c(=Nc2cc(OC)ncc2C)[nH]cc1C(F)(F)F': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(N2CCN(CC)CC2)ccc1N=c1cc(N(C)C(=O)Nc2c(Cl)c(OC)cc(OC)c2Cl)[nH]cn1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3c[nH]c4ccccc34)cc[nH]2)c(OC)cc1N(C)CCN(C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3cn(C)c4ccccc34)c(C(=O)OC(C)C)c[nH]2)c(OC)cc1N(C)CCN(C)C': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3cn(C)c4ccccc34)cc[nH]2)c(OC)cc1N(C)CCN(C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3cn(C4CC4)c4ccccc34)cc[nH]2)c(OC)cc1N(C)CCN(C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(N=c2nc(-n3cc(CN(C)C)c(-c4ccccc4)n3)cc[nH]2)c(OC)cc1N1CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc(NC(=O)c2cnn(-c3ccccc3F)c2)ccc1F': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc2c(=Nc3ccc(F)c(Cl)c3)[nH]cnc2cc1C#CC(C)(C)N1CCN(C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cc2c(=Nc3ccc(F)c(Cl)c3)[nH]cnc2cc1OCCCN1CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1ccc(CN(C(=O)Nc2c(Cl)c(OC)cc(OC)c2Cl)c2cc(=Nc3ccc(N4CCN(C)CC4)cc3)[nH]cn2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1ccc(CN2C(=O)N(c3cc(OC)cc(OC)c3)Cc3c[nH]c(=Nc4ccc(N5CCN(C)CC5)cc4)nc32)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1ccc2[nH]c(=O)n(C3CCN(Cc4ccc(-c5nc6cc[nH]c(=O)c6cc5-c5ccccc5)cc4)CC3)c2c1': array([0., 0., 0., ..., 0., 1., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1ccc2[nH]cnc(=Nc3ccc(OCc4cccc(F)c4)c(Cl)c3)c2c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1ccc2[nH]cnc(=Nc3cccc(Br)c3)c2c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(C)c1N=c1nc2ccc(-c3c(Cl)c(OC)cc(OC)c3Cl)cc2c[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(N4CCN(C(C)=O)CC4)cc3OC)[nH]cc2C(F)(F)F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(NC4CN(CCF)C4)cc3OC)[nH]cc2C(F)(F)F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(OCCOC)cc3)[nH]cc2F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(Oc4ccnc(C(=O)NC)c4)cc3)[nH]cc2F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)c(F)c3)nc3[nH]ccc23)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)nc3ccsc23)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)ncc2Cl)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3OC)ncc2Cl)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(=O)Nc1cccc(Sc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)ncc2Cl)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(C)(C)c1[nH]c2cc(Br)ccc2c1CCNC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(C)(C)c1cc(C=CC(=O)c2ccc(O)cc2)c(OC)cc1O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(C)(C=Cc1ccc(O)cc1)CCC=C(C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(C)(O)CCC1C(C)(O)CCC2C(C)(C)CCCC21C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(C)(O)CCC=C(C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(C)(O)CCC=C(C)CCC=C(C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(C)(O)CN1CCN(Cc2nc(C(=O)NCC3CCCCC3)co2)CC1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(N)=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC(N)CCC(=O)O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1(C)CC(=O)C2(O)C(C)(O1)C(OC(C)=O)C(O)C1C(C)(C)CCC(O)C12C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1(C)CC(OC(=O)CO)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1(C)CC(OC(=O)CSC(C)(C)CNC(=O)C(N)C(C)C)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1(C)CC(OC(=O)CSC2CC3CCC(C2)N3C)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1(C)CC(OC(=O)CSCCN(CC)CC)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC12CN(C)C3C4COC(CC41)C1(C(=O)Nc4ccccc41)C32': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC12CN(C)C3CC14C(=Nc1ccccc14)C1CC2C3CO1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1=C(C(=O)O)N2C(=O)C(=NC(=O)C(NOCC(=O)O)c3csc(=N)[nH]3)C2SC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1=C(C(=O)O)N2C(=O)C(NC(=O)C(=NO)c3csc(=N)[nH]3)C2SC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1=C(C(=O)O)N2C(=O)[C@@H](NC(=O)/C(=N\\\\O)c3csc(N)n3)[C@H]2SC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1=C(C(=O)O)N2C(=O)[C@@H](NC(=O)/C(=N\\\\OCC(=O)O)c3csc(N)n3)[C@H]2SC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1C(OC2OC(CO)C(O)C(O)C2O)OC=C(C(=O)OC)C1CC(=O)O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1C(OC2OC(CO)C(O)C(O)C2O)OC=C2C(=O)OCCC21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1C(OC2OC(CO)C(O)C(O)C2O)OC=C2C(=O)OCCC21O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1C2=CCOC(=O)C2=COC1OC1OC(CO)C(O)C(O)C1O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CC1(NC(=O)C1CC(Oc2ncc(OC)c3ccc(Cl)cc23)CN1C(=O)C(NC(=O)OC(C)(C)C)C(C)(C)C)C(=O)NS(=O)(=O)C1CC1': array([1., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CC1(NC(=O)C1CC2CN1C(=O)C(C(C)(C)C)NC(=O)OC1CC1CCCCCc1nc3ccc(OC)cc3nc1O2)C(=O)NS(=O)(=O)C1CC1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2C(O)c1ccnc2ccc(OC)cc12': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2C(O)c1ccnc2ccccc12': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2CNC(=O)C1CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2CNC(=O)COc1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2CNC(=O)NCCC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2CNC(=O)Nc1ccc(OC(F)(F)F)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2CNC(=O)c1ccc2c(c1)OCO2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC1CN2CCC1CC2CNC(=O)c1ccc2ccccc2c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 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'C=CCC(O)(CC=C)C(C)NC(=O)C1CCCN1c1nc(C)c2cc(OC)ccc2n1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCC1(C(C)CCC)C(=O)N=C(S)NC1=O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCC1(O)CCC2C3=C(C=CC21C)C1=C(CC3)CC(=O)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCC1=CC(C)CC(C)CC(OC)C2OC(O)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C)=CC3CCC(O)C(OC)C3)C(C)C(O)CC1=O)C(C)CC2OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)N1CCC(N2c3ccccc3N(C)S2(=O)=O)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)N1CCC(Oc2nncs2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)N1CCCC(Oc2ncccn2)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)NC1CC(=O)N(CCc2cccc(Cl)c2)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)NC1CCN(c2ccc(C(F)(F)F)cn2)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)NCCc1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)NCc1ccc(-c2ccsc2)o1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)NCc1cn(-c2ccncc2)nn1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCC(=O)O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCCCCCCCC(=O)O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCCCCCCCC(=O)OC1CCC2C3CC=C4CC(=O)C=CC4(C)C3CCC12C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCCCCCCCCO': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCCCCCCCCc1n[nH]c(SCC(=O)O)n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)CC1c2ccccc2C=CN1C(C)=O)c1nc2c(s1)CCCC2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)CCc1nc(-c2ccsc2)no1)c1nc2ccccc2s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)CNc1ccccc1C(=O)NCCc1ccc(OC)cc1)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)COc1ccccc1)c1nnc(-c2ccncc2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)CSc1nc2ccsc2c(=O)n1Cc1ccccn1)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)Cn1c(C(=O)OC)cc2oc(C)cc21)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)Cn1ncc2c1-c1cc(C)ccc1OC2)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)Nc1ccc(OC)cc1)c1nnc(-c2ccncc2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)c1ccc2snnc2c1)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)c1ccccc1OCc1c(C)noc1C)c1nc2c(s1)CCCC2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C(=O)c1cnc2c(cnn2C(C)C)c1)c1nc(-c2ccccc2)cs1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C)C(=O)c1cncn1-c1cccc(-c2cccc(OC(F)(F)F)c2)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C)C(=O)c1cncn1-c1cccc(-c2ccccc2C(F)(F)F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(C)CCCCCCOc1ccc(C(=O)c2ccc(Br)cc2)c(F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC(=O)N1CCN(c2ccc(-c3ccccc3)nn2)CC1)C(=O)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC(=O)NC1CC1)S(=O)(=O)c1ccc(Cl)c(C(F)(F)F)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC=C)C(=O)CN1CC(C(N)=O)Oc2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC=C)C(=O)COC(=O)c1cc(-c2ccccc2)nc2onc(C)c12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC=C)C(=O)c1cc(N(C)C2CCCCC2)nc2ccccc12': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC=C)C(=O)c1ccc2c(c1)OCO2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC=C)C(=O)c1ccccc1NC(=O)c1ccccc1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(CC=C)S(=O)(=O)c1ccc2c(c1)CCCC(=O)N2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(Cc1ccc(Cl)s1)C(=O)Cc1csc(-c2ccc(OC)cc2)n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(Cc1cccs1)C(O)c1cc(C(N)=O)n(-c2ccccc2)n1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(Cc1cn(-c2cccc(C)c2)nc1-c1cccc(F)c1)C1CCS(=O)(=O)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(Cc1csc(COc2c(OC)cccc2OC)n1)C(=O)c1ccccc1F': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(Cc1csc(COc2ccc(OC)cc2)n1)C(=O)c1cccs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(c1ccc(C(=O)N(C)Cc2ccccc2)cc1)S(C)(=O)=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(c1ccc(C(=O)N2CCC(C)CC2)cc1)S(C)(=O)=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(c1ccccc1)S(=O)(=O)c1ccc2c(c1)NC(=O)C(C)S2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(c1ccccc1C(=O)NCC(=O)O)S(=O)(=O)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN(c1nc(C)c(Br)c(OC)n1)S(=O)(=O)c1ccc(C)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C(=c2sc3nc4ccccc4n3c2=O)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C(C)(C)COc2cc(NS(=O)(=O)c3cc(Cl)ccc3C)ccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C(C)(C)COc2ccc(NS(=O)(=O)c3cc(C)ccc3C)cc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C(C)(C)COc2ccc(NS(=O)(=O)c3ccc(F)c(Cl)c3)cc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccc(C)o2)c2cc(Br)ccc21': array([0., 0., 0., ..., 0., 0., 1.], dtype=float32),\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccc(OC)c([N+](=O)[O-])c2)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccccc2)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccco2)c2ccccc21': array([0., 0., 0., ..., 0., 0., 1.], dtype=float32),\n", " 'C=CCN1C(=O)C(c2c(C)[nH]c3ccccc23)(c2c(C)[nH]c3ccccc23)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C2(NC(C)c3c2c(O)n(Cc2ccccc2)c3O)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C2(NC(CC(C)C)c3c2c(O)n(C)c3O)c2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C2(NC(CCSC)c3c2c(O)n(C)c3O)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C2(c3ccccc31)C(C(=O)c1ccc(C)o1)C(=O)C(=O)N2CCCN1CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C2(c3ccccc31)C(C(=O)c1ccc(S(=O)(=O)N3CCCC3)cc1)C(=O)C(=O)N2CCCN(C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C2(c3ccccc31)C(C(=O)c1cccc(S(=O)(=O)N3CCCCC3)c1)C(=O)C(=O)N2CCN(C)C': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)C2=C(C(=O)Nc3cccc(OC)c3)C3CCC2(O3)C1C(=O)NC1CCCCC1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)COc2ccc(-c3csc(=NC(=O)CCCC)[nH]3)cc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)NC(c2ccc(F)cc2)c2c1cn(CCc1ccccc1)c2O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)NC(c2cccc(Oc3ccccc3)c2)c2c1cn(Cc1ccccc1)c2O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)SC(=Cc2ccc(N3CCCC3)o2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)c2ccccc2C1(O)Cc1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)c2ccccc2N2C(=O)CCC12C(=O)N(C)Cc1ccc(SC)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)c2ccccc2N2C(=O)CCC12C(=O)NC(C)c1ccccc1Cl': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)c2ccccc2NC12CCC(C)CC2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C(=O)c2ccccc2NC1c1cn(C)c(=O)n(C)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(C(=O)N(CCCN(C)C)C(=O)NCC)CC2c3cccc4[nH]cc(c34)CC21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(-c4cccc(OC)c4)c(C)c3n2)CC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(-c4ccccc4)c(C)c3n2)CC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(-c4ccccc4OC)c(C)c3n2)CC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(C)c(-c4ccccc4)c3n2)CC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(c2cc(=O)n3[nH]cc(-c4ccc(C)cc4)c3n2)CC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(c2cc(=O)n3[nH]cc(C(=O)Nc4ccccc4)c3n2)CC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC(c2nc3ccccc3n2Cc2ccc(C)cc2)CC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C(C)CN(C)CC)CC2': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C(N)CCSC)CC2': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C1CC13CCC3)CC2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C1CC=CCC1)CC2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C1Cc3ccccc3CN1CC)CC2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC2(CCC1=O)CCN(S(=O)(=O)C(C)CC)CC2': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCC2(CCC1=O)CN(C(=O)CCSC)CCN2C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCC2(CCC1=O)CN(Cc1cccc(SC)c1)CCN2C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCC23c4c5ccc(O)c4OC2C(=NNC(=O)c2ccccc2)CCC3(O)C1C5': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCC23c4c5ccc(O)c4OC2C(=O)CCC3(O)C1C5': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCCC1CNC(=O)c1cc(S(N)(=O)=O)cc(OC)c1OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCCC1CNC(=O)c1cc2[nH]nnc2cc1OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)C(CC)CC)C(Cc2ccccc2-c2ccncc2)C1=O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)C2CCC2)C(Cc2ccc(-c3ccncc3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)C2CCC2)C(Cc2cccc(-c3ccncc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2ccc(-c3cccnc3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2ccc(-c3ccncc3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2cccc(-c3cccnc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2ccccc2-c2ccncc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)CC(C)(C)C)C(Cc2ccccc2-c2ccncc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)CC(C)C)C(Cc2ccc(-c3cccnc3)cc2)C1=O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)CC(C)C)C(Cc2ccc(-c3ccncc3)cc2)C1=O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)CC(C)C)C(Cc2cccc(-c3cccnc3)c2)C1=O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)CNC(C)=O)C(Cc2cccc(-c3ccccc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)COC)C(Cc2ccc(-c3cccc(OC)c3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)COC)C(Cc2ccc(-c3cccs3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)COC)C(Cc2cccc(-c3ccccc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)Cc2cccnc2)C(Cc2ccc(-c3cccs3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)Cc2cccnc2)C(Cc2cccc(-c3ccncc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)Cn2nc(C)nc2C)C(Cc2ccc(-c3cccs3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2cc3c(s2)CCCC3)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccc(-c3ccccc3)cc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccc(C)s2)C(Cc2cccc(-c3cccnc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccc(F)cc2)c2cccnc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccc(OC)nc2)C(Cc2ccc(-c3cccnc3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccccc2)C(Cc2cccc(-c3ccncc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccccn2)C(Cc2ccc(-c3ccccc3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccccn2)C(Cc2ccc(-c3cccs3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccccn2)C(Cc2cccc(-c3ccncc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccncc2)C(Cc2ccc(-c3cccs3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2ccncc2)C(Cc2cccc(-c3ccncc3)c2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(C(=O)c2cnc(C)cn2)C(Cc2ccc(-c3cccs3)cc2)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(CCOC(=O)C(O)(c2ccccc2)c2ccccc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(c2nc3ccccc3nc2C#N)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCN(c2nccc(-n3nc(C)cc3C)n2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CC[C@]23c4c5ccc(O)c4O[C@H]2C(=O)CC[C@@]3(O)[C@H]1C5': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCc2c(cc(O)c(O)c2Br)[C@@H](c2ccccc2)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCc2c(cc(O)c(O)c2Cl)C(c2ccccc2)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCc2cc(O)c(O)cc2C(c2ccccc2)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCc2cccc3c2[C@H]1Cc1ccc(O)c(O)c1-3': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1CCc2nc(N)sc2CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C[C@H](C)N([C@@H](c2ccccc2)c2ccc(C(=O)N(CC)CC)cc2)C[C@H]1C': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C[C@H](C)N([C@H](c2ccc(C(=O)N(CC)CC)cc2)c2cccc(O)c2)C[C@H]1C': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN1C[C@H](C)N([C@H](c2ccc(C(=O)N(CC)CC)cc2)c2cccc(OC)c2)C[C@H]1C': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(-c2ccc(Cl)cc2)cs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(-c2ccc(OC)cc2OC)cs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(-c2sc(=NC(=O)CC)[nH]c2C)cs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(=NCc2ccc(Cl)cc2)c2cnn(C)c2[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(C(=O)OCC(=O)N2CCc3ccccc32)cs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(N)c(C(=O)N=c2cc(C)o[nH]2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(N)c(C(=O)c2ccc(OC)c(OC)c2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(N)c(C(=O)c2ccc(OC)cc2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(N2CCCC2)nc(=Nc2ccc([N+](=O)[O-])cc2)[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(OC)nc(=Nc2ccc(Cl)cc2)[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(OCC)nc(=Nc2ccc(OC)cc2)[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c(OCC)nc(=Nc2ccc([N+](=O)[O-])cc2)[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c2c(c(=O)[nH]c(=O)n2C)n1CCCCC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c2c(c(=O)[nH]c(=O)n2C)n1Cc1cccc(C)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c2c(c(=O)n(C)c(=O)n2C)n1CC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]c2c(c(=O)n(C)c(=O)n2C)n1Cc1ccc(F)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]cnc2c1cnn2-c1ccc(C)cc1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]cnc2ccc(Br)cc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]nc(-c2ccncc2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]nc(SCC(=O)c2cc(C)n(-c3cc(C)on3)c2C)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1[nH]nc(SCc2nc(Cc3ccccc3)no2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1cc(C)[nH]c2ccc(C)cc12': array([0., 0., 0., ..., 0., 0., 1.], dtype=float32),\n", " 'C=CCN=c1nc(-c2cn(CC)nc2C)cc(C(F)(F)F)[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCN=c1nc(N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)CC2)[nH]c(=NCC=C)[nH]1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C(=O)Nc1ccc2c(c1)CCCN2C(=O)c1cccs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)C(C)C)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)C2CCC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)CC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)c2cccnc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)c2ccncc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)c2cnccn2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccc(OC)c3)c2)CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3)c2)CCN(C(=O)C2CC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3)c2)CCN(C(=O)CC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3)c2)CCN(C(=O)c2cnccn2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3OC)c2)CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C(C)(C)C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C(C)C)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C2CC=CCC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C2CCC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)CC(C)(C)C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)CC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)c2ccncc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(CC2CC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)C(C)C)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)C2CC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)CC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)c2cccnc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)c2ccncc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)c2cnccn2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)C(C)(C)C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)C2CC=CCC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)C2CCCC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)CC(C)(C)C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)CC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(CC2CC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)C2CC2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)CC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)c2ccccn2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)c2cccnc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)c2ccncc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1(Cc2ccccc2-c2cccc(C(=O)NC3CC3)c2)CCOCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1CC1(c1ccccc1)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1CCCN(S(=O)(=O)c2ccc(Br)s2)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1CCN(S(=O)(=O)c2ccc3c(c2)OCCCO3)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1CCN(S(=O)(=O)c2cccs2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1CCN(c2cc3oc4ccccc4c3cc2OC)C1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)C1CCN(c2nccc(-n3nc(C)cc3C)n2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)CCNC(=O)N1CCN(C(=O)c2cc3ccccc3[nH]2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)CCn1cnc2c(-c3ccc(CC)cc3)noc2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)CN(Cc1ccccc1)S(=O)(=O)c1ccccc1': 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'C=CCNC(=O)c1cc(-c2ccc(C)c(C)c2)n(C2CCS(=O)(=O)C2)n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1cc(-c2cccc(Cl)c2)on1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1cc(N2CCN(c3cccc(C(F)(F)F)c3)CC2)nc2ccccc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1cc([N+](=O)[O-])cc2c(=O)[nH]c(Nc3ccc(Cl)c(Cl)c3)nc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1cc2ccccc2o1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1cc2sc(Br)cc2n1CC1CCCCO1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1ccc(-c2ccc(=O)[nH]c2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1ccc(Sc2ccc(NS(=O)(=O)CC)cc2)nc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1ccc2c(c1)N(Cc1c(F)cccc1Cl)C(=O)CS2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNC(=O)c1coc(COc2ccc3ccc(OC)cc3c2)n1': 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" 'C=CCNS(=O)(=O)c1ccc(OC)c(-c2noc(C3CCCCC3)n2)c1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNS(=O)(=O)c1ccc2[nH]c(=O)[nH]c2c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNS(=O)(=O)c1cccc(C(=O)N=c2[nH]c3ccccc3[nH]2)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNS(=O)(=O)c1nn(C)c2nc(C)c(Cl)c(C)c12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCNc1oc(-c2ccco2)nc1S(=O)(=O)c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOC(=O)C1=C(C)N=C2CC(C)(C)CC(=O)C2C1c1cc(Cl)c(O)c(OC)c1': array([0., 0., 0., ..., 1., 0., 0.], dtype=float32),\n", " 'C=CCOC(=O)C1C(=O)CC(C)(O)C(C(=O)OCC=C)C1c1ccc(OCC)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOC(=O)C1C(C)=NC(=O)NC1c1ccc(Cl)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOC(=O)C1C(c2ccccc2)c2c([nH][nH]c2=O)CC1(C)O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOC(=O)c1nnn(-c2no[nH]c2=N)c1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOC(Cn1ccnc1)c1ccc(Cl)cc1Cl': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOC(O)=c1ccccc1=C(O)Nc1ccc(NC(C)O)cc1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOCCN(CCOCC=C)C1=NS(=O)(=O)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCON=C1c2ccccc2-c2nc(C#N)c(C#N)nc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1c(Br)cc(C=c2c(=C)[nH]oc2=O)cc1OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1c(CNc2ccc3[nH]c(=O)[nH]c3c2)cccc1OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1c(OC)cccc1-c1cc(=O)[nH]c2c(-c3ccccc3)c(C(O)O)sc12': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccc(-c2c(C(=O)c3ccccc3)c(O)c(O)n2-c2nnc(C)s2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccc(-c2cc(C(F)(F)F)c3c(n2)sc2c(=O)cc(O)[nH]c23)cc1': 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'C=CCOc1ccc(NC(=O)C2CCCN(S(=O)(=O)c3cccs3)C2)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccc2c(C)cc(=O)oc2c1C(C)=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1cccc(-c2cc(=O)[nH]c3c(-c4ccc(F)cc4)c(C(O)O)sc23)c1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1cccc(C2Oc3nc(SCc4ccccc4Cl)nnc3-c3ccccc3N2C(C)=O)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1cccc2c1cc(C(=O)NCc1ccccc1)n2CC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccccc1-c1cc(=O)[nH]c2c(-c3ccc(F)cc3)c(C(O)O)sc12': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccccc1C1CC(=O)Nc2c(-c3ccc(Cl)cc3)csc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccccc1CN1CCN(Cc2ccsc2)C(CCO)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccccc1CNc1ccc2[nH]c(=O)[nH]c2c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccccc1NC(=O)c1nc2nc(C)cc(C)n2n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1ccccc1OCC(O)CNC(C)C': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1nc(N2CCCC2)nc(N2CCCC2)n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOc1nc2c(c(=O)n(C)c(=O)n2C)n1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCOn1c(=O)c(=O)n(OCc2ccccc2)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSCC(N)C(=O)O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSCC1Nc2cc(Cl)c(S(N)(=O)=O)cc2S(=O)(=O)N1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSCC=C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCS[S+]([O-])CC=C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1n[nH]c(=NC(=O)Cc2csc(-c3ccccc3)n2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1n[nH]c(=NC(=O)c2cc(=O)c3cc(CC)ccc3o2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1n[nH]c(=NC(=O)c2ccc3c(c2)CC(C)N3S(C)(=O)=O)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1n[nH]c(=NC(=O)c2cccc(S(=O)(=O)N(C)c3ccccc3)c2)s1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nc(-c2ccccc2)c2cc(Cl)ccc2n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nc(=O)c2c(C)c(C)sc2[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nc(=O)c2c([nH]1)N=C(C)C(C(=O)OC)C2c1sccc1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nc2ccccc2[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nc2ccccc2c(=O)n1CC(=C)C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1ncccc1C(=O)NCc1ccc(C)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc(-c2cccn(Cc3ccc(Cl)cc3Cl)c2=O)n1CC=C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc(-c2cccnc2)o1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc(CCCCCN2C(=O)c3cccc4cccc(c34)C2=O)o1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc(Cc2c(C)[nH]c3ccccc23)o1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc2c(n1)OC(c1c(C)nn(-c3ccccc3)c1Cl)N(C(C)=O)c1ccccc1-2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc2c(n1)OC(c1cc(Br)c(OCc3ccccc3)c(OC)c1)N(C(=O)CC)c1ccccc1-2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc2c(n1)OC(c1ccc(-c3cc(Cl)ccc3C)o1)Nc1ccccc1-2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc2c(n1)OC(c1ccccc1OCc1ccccc1)Nc1ccccc1-2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc2c(n1)OC(c1cn(C(C)=O)c3ccccc13)N(C(C)=O)c1ccccc1-2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc2c(n1)[nH]c1c(C)cccc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCSc1nnc2c(n1)[nH]c1ccc(CC)cc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC[N+]1(C2CC3C4CCC5CC(O)C(N6CCOCC6)CC5(C)C4CCC3(C)C2OC(C)=O)CCCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CC[S+]([O-])CC(N)C(=O)O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1c(C)nc2c(-c3ccccc3)cnn2c1N1CCCCC1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1cc(OC)c(O)c(C(=O)NCCO)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1cc(OC)c(OC)c(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1cc(OC)ccc1OCC(O)CN1CCN(c2ccc(OC)cc2)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1cc2c(oc(=O)c3ccccc32)c(C)c1O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(O)c(-c2cc(CC=C)ccc2O)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(O)c(-c2ccc(O)c(CC=C)c2)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(O)c(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(OC(C)=O)c(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(OC)c(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(OC)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(OCC(=O)N2CCCCC2CNS(C)(=O)=O)c(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(OCC(O)CN2CCCCC2)c(OC)c1': array([0., 1., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(OCc2ccc(C(=O)O)o2)c(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccc(OCc2ccc(C(=O)OC)o2)c(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1cccc(C=NNC(=O)CN2CCN(Cc3ccccc3)CC2)c1O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1cccc2cc(C(=O)Nc3ccc(F)cc3)c(=O)oc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccccc1OCC(O)CN1CCN(C(=O)OCC)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccccc1OCC(O)CN1CCN(c2ccc(F)cc2)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccccc1OCC(O)CN1CCN(c2ccccc2F)CC1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccccc1OCC(O)CNC(C)C': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccccc1OCCn1cnc2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCc1ccccc1OCc1nc2ccccc2[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(-c2cc(OC)c(OC)c(OC)c2)nc2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(-c2ccc(Cl)cc2)cnc1SCc1c(C)noc1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(-c2ccc(Cl)cc2)cnc1SCc1cc(=O)n2ccc(C)cc2n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(-c2cccc([N+](=O)[O-])c2)n[nH]c1=S': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(-c2cccs2)nc2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(-c2no[nH]c2=N)nc2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=N)c(C(=O)NCCCOC)cc2c(=O)n3cccc(C)c3nc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=N)c(C(=O)OCC)cc2c(=O)n3cc(C)ccc3nc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=N)c(C(=O)OCC)cc2c(=O)n3cccc(C)c3nc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=N)n(CC(O)C(C)(C)C)c2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=N)n(CC(O)COc2ccc(OC)cc2)c2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=N)n(CC(O)c2ccc(Cl)c(Cl)c2)c2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=NC(C)c2cc(Cl)ccc2O)[nH]c2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=NCc2cc(C)ccc2O)[nH]c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=NCc2ccc(N(C)C)cc2)[nH]c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=NCc2ccc(OC)cc2)[nH]c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)[nH]c(O)c(C2=NN(C(=O)CC)C(c3cc(OC)ccc3OC)C2)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)[nH]c2nc3cc(NC(C)=O)c(C)cc3nc2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)c(=O)n(C(C)C)c2ccc(C(F)(F)F)cc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)c(C(=O)NCCc2ccccc2)c(O)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)c(C(=O)Nc2c(C)cccc2C)c(O)c2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)c2c[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)nc2n1-c1cccc(C(C)(C)O)n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)c2ccc(C(=O)NCc3ccccc3)cc2n(Cc2ccc(C)cc2)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)c2ccccc2n2c(SCC(=O)N3c4ccccc4Sc4ccccc43)nnc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)n(C2CCCCC2)c(=O)c2cc(OC)c(OC)cc21': array([0., 0., 1., ..., 0., 1., 0.], dtype=float32),\n", " 'C=CCn1c(=O)n(C2OC(CO)C(O)C2O)c2nc(N)[nH]c(=O)c21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)oc2cc(NC(=O)Nc3ccc(C)c(Cl)c3)ccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)oc2cc(NC(=O)Nc3cccc(Cl)c3C)ccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=O)oc2ccc(C(=O)N3CCN(c4ccccn4)CC3)cc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(=S)[nH]c2c(c1=O)C1(CCCC1)Cc1ccccc1-2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(=O)NC(C)CCc2ccccc2)cc2cc(S(=O)(=O)N(C)C)ccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(=O)NCCC)cc2cc(S(=O)(=O)N(C)C)ccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(=O)NCCCOC(C)C)cc2cc(S(=O)(=O)N(C)C)ccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(=O)NCCCc2ccccc2)cc2cc(S(=O)(=O)N(C)C)ccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(=O)NCCc2ccc(Cl)cc2)cc2cc(S(=O)(=O)N(C)C)ccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(C)NC(=O)C(C)(C)C)nc2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(C)NC(=O)c2ccccc2)nc2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C(C)NC(C)=O)nc2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C)c(C(C)=O)c(N2CCN(c3ccccc3)CC2)nc1=S': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C)c(C(C)=O)cc(NC(=O)c2ccccc2)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C)cc(C(=O)COC(=O)c2ccccc2O)c1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C)cc(C(=O)COn2nnc3ccc(S(=O)(=O)N(C)C)cc32)c1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C)nc2c(sc3nc4c(cc32)COC(C)(C)C4)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C)nnc1SCC(=O)N=c1[nH]ccs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(C)nnc1SCC(=O)NC1CCCCC1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CC(=O)Nc2ccc(F)cc2)c(O)n(-c2ccc(Cl)cc2)c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CCC(=O)O)ccc1-c1ccc(OC)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CCCNC(=O)CCC)nc2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CCN2CCCCC2)nnc1SCc1cc(=O)n2cccc(C)c2n1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CCc2ccccc2)nnc1SCC(=O)OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CCc2ccccc2)nnc1SCC(N)=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CCc2ccccc2)nnc1SCc1cc(=O)n2ccsc2n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(COc2ccc(C)cc2)nnc1SCc1cc(=O)n2ccsc2n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(COc2ccc(OC)cc2)nc2ccccc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(COc2cccc3ccc(C)nc23)nnc1SCC(=O)OC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(COc2cccc3cccnc23)nnc1SCC(=O)O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(CSc2nc3ccccc3s2)nnc1SCC(=O)NCCO': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(Cc2cccc3ccccc23)n[nH]c1=S': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(Cc2cccs2)nnc1SCC(=O)NC1CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(N)c(-c2nc3ccccc3n2C)sc1=S': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(N)cc(=O)nc1SCC(=O)N1CCN(c2ccc(F)cc2)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(N)cc(=O)nc1SCC(=O)NC(C)c1ccccc1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(O)c(CC(=O)Nc2ccccc2)n(Cc2ccccn2)c1=S': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(Oc2cccc(C)c2)nc2c1c(=O)n(C)c(=O)n2C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SC(C)C(=O)Nc2ccccc2C#N)nc2ccccc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)N2CC(=O)Nc3ccccc32)nc2scc(-c3ccccc3)c2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)N2CCC(C)CC2)nc2sc3c(c2c1=O)CCCC3': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)N2CCN(CCO)CC2)nc2sc3c(c2c1=O)CCC3': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)N2CCN(c3ccc(F)cc3)CC2)nnc1-c1ccco1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)N2CCN(c3ccc(F)cc3)CC2)nnc1-c1cccs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)N2CCNC2=O)nnc1-c1ccc(OC)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)NC2CCCC2)nnc1-c1ccncc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)NC2CCCCC2)nnc1-c1ccc(OC)cc1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)NCc2ccc3c(c2)OCO3)nc2sc3c(c2c1=O)CCCC3': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)NCc2ccc3c(c2)OCO3)nc2scc(-c3ccccc3)c2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)Nc2ccc(-c3ccccc3)cc2)nc2sc3c(c2c1=O)CCCC3': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)Nc2ccc(-c3nc4ccc(C)cc4s3)cc2)nnc1-c1ccccc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)Nc2ccc(C(=O)OCC)cc2)nnc1-c1cccs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)Nc2ccc(C)cc2C)nnc1-c1ccc2ccccc2n1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)Nc2ccc(Cl)cc2)nnc1-c1cccs1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)Nc2sc3c(c2C#N)CCCCCC3)nnc1-c1ccncc1': array([0., 0., 1., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)O)nnc1-c1ccc([N+](=O)[O-])cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)O)nnc1-c1cccc(C)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)c2ccc(Br)cc2)nc2sc(CC)cc2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)c2ccc(CNC(C)=O)s2)nnc1-c1ccc(Cl)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)c2ccc([N+](=O)[O-])cc2)nc2ccccc2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)c2cccs2)nc2sc3c(c2c1=O)CCCC3': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCC(=O)c2cccs2)nnc1-c1cccc(OC)c1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCc2cc(=O)n3ccsc3n2)nnc1-c1ccccn1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCc2cc(=O)n3ccsc3n2)nnc1-c1ccncc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCc2cc(=O)n3ccsc3n2)nnc1C1CCCN(S(C)(=O)=O)C1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCc2ccc(C(=O)NCCO)cc2)nc2sc(C)c(C)c2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCc2cccc(OC)c2)nnc1-c1ccncc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(SCc2ccccc2Cl)nc2c1c(=O)[nH]c(=O)n2C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(Sc2nc(C)cs2)nc2c1c(=O)[nH]c(=O)n2C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c(Sc2ncc(Br)cc2[N+](=O)[O-])n[nH]c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c2ccccc2c2nnc(SC(CC)C(=O)N=c3[nH]c(C)c(C(=O)OCC)s3)nc21': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c2ccccc2c2nnc(SCC(=O)N=c3cc(C)o[nH]3)nc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1c2ccccc2n2c(C(=O)OC)c(C)nc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1ccc2c(OCC(=O)NC(C)C)cccc2c1=O': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1ccc2c(OCC(=O)Nc3ccc(C(N)=O)cc3)cccc2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1ccc2c(OCC(=O)Nc3ccccc3C)cccc2c1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1cnc2c(=NCc3ccccc3)[nH]cnc21': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CCn1nnc(=NCc2ccc(-c3ccccc3)cc2)[nH]1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CN1CCCC1=O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=CS(=O)(=O)NC1CCN(C(=O)CNc2cc(I)c(Cl)cc2OC)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=C[C@@]1(C)CC(=O)[C@]2(O)[C@@]3(C)[C@@H](O)CCC(C)(C)[C@@H]3[C@H](O)[C@H](OC(=O)CCCN3CCN(C)CC3)[C@@]2(C)O1': array([0., 0., 0., ..., 1., 0., 0.], dtype=float32),\n", " 'C=C[C@@]12CN(C)[C@H]3[C@H]1[C@@]1(C(=O)Nc4ccccc41)C1CC2[C@@H]3CO1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=C[C@H]1CN2CC[C@H]1C[C@@H]2[C@@H](O)c1ccnc2ccc(OC)cc12': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1c(C)c2[nH]c1=Cc1[nH]c(c(C=CC(=O)O)c1C)C=c1[nH]c(c(C)c1C=CC(=O)O)=Cc1[nH]c(c(CC)c1C)C=2': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1c(O)[nH]c(=Cc2[nH]c(=Cc3[nH]c(C=c4[nH]c(O)c(C)c4=CC)c(C)c3CCC(=O)O)c(=CCC(=O)O)c2C)c1=C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1cc(O)cc2nc(-c3ccc(O)c(F)c3)oc12': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1ccc(CN2C(=O)N(Cc3ccc(OC)cc3)S(=O)(=O)c3ccccc32)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1ccc(Cn2c(=O)c3cnc(-c4cccnc4)nc3n(C)c2=O)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1ccc(Cn2c(=O)n(CC3CCC(C(=O)NC(C)C)CC3)c(=O)c3sccc32)cc1': array([0., 1., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1ccc(Cn2c(C(=O)O)c(CNC3CCCC3)c3ccc(C)cc32)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1ccc(Cn2ccn3nc(-c4ccc(C)c(C)c4)cc3c2=O)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cc1ccc(Cn2nc(-c3nc(C(C)(C)C)no3)ccc2=O)cc1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=Cn1cnc2c1c(=O)n(C)c(=O)n2C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccc(S(=O)(=O)Cc4c(Cl)cccc4Cl)cc23)c(C)c1C(=O)N1CCCC1CN1CCCC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccc(S(=O)(=O)N(C)c4cccc(Cl)c4)cc23)c(C)c1C(=O)N1CCN(C)CC1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccccc23)c(C)c1C(=O)OCC': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccccc23)c(C)c1CCC(=O)O': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=c1[nH]c(=Cc2cc(F)c(O)c(F)c2)c(=O)n1C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=c1[nH]n(-c2ccc(C(=O)O)cc2)c(=O)c1=Cc1ccc(-c2cc(C)c(C)cc2[N+](=O)[O-])o1': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " 'C=c1[nH]n(-c2ccc(C)c(C)c2)c(=O)c1=Cc1ccc2c(c1)n(C)c(=O)n2C': array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),\n", " ...}" ] }, "execution_count": 25, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import pickle, h5py\n", "import numpy as np\n", "import pandas as pd\n", "\n", "with open('/home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/ECFP4_emb2048.pickle', 'rb') as f:\n", " KPGT_emb2304 = pickle.load(f)\n", "KPGT_emb2304" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate KGPT embedding for all smiles" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "import pickle, h5py\n", "import numpy as np\n", "import pandas as pd\n", "\n", "with open('./smiles_emb/KPGT_emb2304.pickle', 'rb') as f:\n", " KPGT_emb2304 = pickle.load(f)\n", "KPGT_emb2304" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate InfoAlign embedding for all smiles" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# pip install infoalign\n", "\n", "infoalign_predict --input image_all_unique_smiles.csv \\\n", " --output InfoAlign_output.npy \\\n", " --output-to-input-column # Adds the representation as an additional column in the input CSV\n", "\n", "# 是否存在数据泄露，因为这个是基于表征学习的" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [], "source": [ "import csv\n", "import numpy as np\n", "import pickle\n", "\n", "# CSV文件路径\n", "csv_path = 'image_all_unique_smiles.csv'\n", "# NPY文件路径\n", "npy_path = 'InfoAlign_output.npy'\n", "\n", "# 初始化一个空字典来存储SMILES和对应的表征\n", "smiles_to_representation = {}\n", "\n", "# 读取NPY文件\n", "info_align_output = np.load(npy_path)\n", "\n", "# 读取CSV文件并同时替换字典中的值\n", "with open(csv_path, mode='r', newline='', encoding='utf-8') as csvfile:\n", " reader = csv.DictReader(csvfile)\n", " for idx, row in enumerate(reader):\n", " smiles = row['SMILES']\n", " # 直接从info_align_output中获取对应的数值\n", " representation = info_align_output[idx]\n", " smiles_to_representation[smiles] = representation\n" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "66530" ] }, "execution_count": 28, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(smiles_to_representation)" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "字典已成功保存到 /home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/InfoAlign_emb300.pickle\n" ] } ], "source": [ "# 保存字典为pickle文件\n", "pickle_path = '/home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/InfoAlign_emb300.pickle'\n", "with open(pickle_path, 'wb') as pickle_file:\n", " pickle.dump(smiles_to_representation, pickle_file)\n", "\n", "print(f\"字典已成功保存到 {pickle_path}\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate ChemBERTa-2 embedding for all smiles" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Some weights of RobertaModel were not initialized from the model checkpoint at DeepChem/ChemBERTa-77M-MLM and are newly initialized: ['roberta.pooler.dense.bias', 'roberta.pooler.dense.weight']\n", "You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.\n" ] } ], "source": [ "from transformers import AutoModel, AutoTokenizer\n", "model = AutoModel.from_pretrained(\"DeepChem/ChemBERTa-77M-MLM\") # 77M SMILES（完整PubChem数据集)\n", "tokenizer = AutoTokenizer.from_pretrained(\"DeepChem/ChemBERTa-77M-MLM\")\n", "inputs = tokenizer(\"CCO\", return_tensors=\"pt\")\n", "outputs = model(**inputs) # 嵌入位于 outputs.last_hidden_state" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "torch.Size([1, 5, 384])" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "outputs.last_hidden_state.shape" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Some weights of RobertaModel were not initialized from the model checkpoint at DeepChem/ChemBERTa-77M-MLM and are newly initialized: ['roberta.pooler.dense.bias', 'roberta.pooler.dense.weight']\n", "You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.\n", "100%|██████████| 2080/2080 [00:11<00:00, 183.83it/s]\n" ] } ], "source": [ "import pickle\n", "from transformers import AutoModel, AutoTokenizer\n", "import torch\n", "import numpy as np\n", "from rdkit import Chem\n", "from tqdm import tqdm # 可选：用于进度条\n", "\n", "def smiles_to_chemberta2(smiles_list, model_name=\"DeepChem/ChemBERTa-77M-MLM\", batch_size=32):\n", " \"\"\"\n", " 将SMILES列表转换为ChemBERTa-2的嵌入向量（CLS token的隐藏状态）。\n", " \n", " 参数:\n", " smiles_list (list): SMILES字符串列表\n", " model_name (str): Hugging Face模型ID，默认为ChemBERTa-2的MLM版本\n", " batch_size (int): 批处理大小，根据GPU内存调整\n", " \n", " 返回:\n", " dict: 键为SMILES，值为768维嵌入向量（numpy数组）\n", " \"\"\"\n", " # 加载模型和tokenizer\n", " tokenizer = AutoTokenizer.from_pretrained(model_name)\n", " model = AutoModel.from_pretrained(model_name)\n", " model.eval() # 切换到推理模式\n", " \n", " # 检查CUDA可用性\n", " device = torch.device(\"cuda\" if torch.cuda.is_available() else \"cpu\")\n", " model.to(device)\n", " \n", " chemberta2_dict = {}\n", " \n", " # 分批处理SMILES\n", " for i in tqdm(range(0, len(smiles_list), batch_size)):\n", " batch_smiles = smiles_list[i:i+batch_size]\n", " valid_indices = []\n", " batch_inputs = []\n", " \n", " # 过滤无效SMILES并生成输入\n", " for idx, smiles in enumerate(batch_smiles):\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol is not None:\n", " valid_indices.append(idx)\n", " batch_inputs.append(smiles)\n", " else:\n", " print(f\"Invalid SMILES: {smiles}\")\n", " \n", " if not batch_inputs:\n", " continue\n", " \n", " # Tokenize并移动到设备\n", " inputs = tokenizer(\n", " batch_inputs, \n", " return_tensors=\"pt\", \n", " padding=True, \n", " truncation=True, \n", " max_length=512\n", " ).to(device)\n", " \n", " # 生成嵌入\n", " with torch.no_grad():\n", " outputs = model(**inputs)\n", " embeddings = outputs.last_hidden_state[:, 0, :] # 取CLS token的嵌入\n", " \n", " # 将有效结果存入字典\n", " for j, idx in enumerate(valid_indices):\n", " chemberta2_dict[batch_smiles[idx]] = embeddings[j].cpu().numpy()\n", " \n", " # 处理无效SMILES（填充零向量）\n", " for idx, smiles in enumerate(batch_smiles):\n", " if idx not in valid_indices:\n", " chemberta2_dict[smiles] = np.zeros(768, dtype=np.float32)\n", " \n", " return chemberta2_dict\n", "\n", "# 使用示例\n", "smiles_list = standardized_smiles # 假设idx2smi是SMILES字典\n", "chemberta2_features_dict = smiles_to_chemberta2(smiles_list)" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['BrC1C(Br)C(Br)C(Br)C(Br)C1Br',\n", " 'Brc1c(Br)c(Br)c2[nH]nnc2c1Br',\n", " 'Brc1c(NC2=NCCN2)ccc2nccnc12',\n", " 'Brc1cc2c(cc1C1Nc3ccccc3C3C=CCC31)OCO2',\n", " 'Brc1cc2c(cc1CN1CCN(c3ncccn3)CC1)OCCO2',\n", " 'Brc1cc2c(cc1CN1CCc3ccccc3C1)OCO2',\n", " 'Brc1cc2c(cc1CSc1nnc(C3CC3)n1Cc1ccccc1)OCO2',\n", " 'Brc1ccc(-c2cc3ccccn3c2)cc1',\n", " 'Brc1ccc(-c2ccc(CNCc3ccccn3)o2)cc1',\n", " 'Brc1ccc(-c2cn3ccccc3n2)cc1',\n", " 'Brc1ccc(-c2csc(N3CCc4ccccc4C3)n2)cc1',\n", " 'Brc1ccc(-c2csc3c4ncnc-4ncn23)cc1',\n", " 'Brc1ccc(-c2nc(-c3ccccc3)no2)o1',\n", " 'Brc1ccc(-c2nc(-c3ccncc3)no2)o1',\n", " 'Brc1ccc(-c2ncc3ccccn23)cc1',\n", " 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'C=CC(=O)NCCCN1CCCCCC1',\n", " 'C=CC(=O)NCCCN1CCCc2ccccc21',\n", " 'C=CC(=O)NCCCN1CCN(C)CC1',\n", " 'C=CC(=O)NCCCN1CCN(C2CCCCC2)CC1',\n", " 'C=CC(=O)NCCCN1CCN(CC)CC1',\n", " 'C=CC(=O)NCCCN1CCN(CCC)CC1',\n", " 'C=CC(=O)NCCCN1CCN(Cc2ccccc2)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2c(C)cccc2C)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2cc(C)ccc2C)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2cc(Cl)ccc2C)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(C)cc2)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(C)cc2C)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(F)cc2)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2ccc(OC)cc2)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2cccc(C)c2)C(C)C1',\n", " 'C=CC(=O)NCCCN1CCN(c2cccc(C)c2)CC1C',\n", " 'C=CC(=O)NCCCN1CCN(c2cccc(Cl)c2)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2ccccc2)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2ccccc2F)CC1',\n", " 'C=CC(=O)NCCCN1CCN(c2ccccc2OC)CC1',\n", " 'C=CC(=O)NCCCN1CCOCC1',\n", " 'C=CC(=O)NCCCN1CCc2ccccc2C1',\n", " 'C=CC(=O)NCCCOC1CCN(C(C)C)CC1',\n", " 'C=CC(=O)NCCCOC1CCN(Cc2ccccc2)CC1',\n", " 'C=CC(=O)NCCCc1ccccc1',\n", " 'C=CC(=O)NCCCc1nc2ccccc2[nH]1',\n", " 'C=CC(=O)NCCCn1cccn1',\n", " 'C=CC(=O)NCCN(C)C1CCCCC1',\n", " 'C=CC(=O)NCCN(C)Cc1ccccc1',\n", " 'C=CC(=O)NCCN(CC)Cc1ccccc1',\n", " 'C=CC(=O)NCCN(CCCC)Cc1cccs1',\n", " 'C=CC(=O)NCCN(Cc1cccs1)C(C)CC',\n", " 'C=CC(=O)NCCN1CCC(Cc2ccccc2)CC1',\n", " 'C=CC(=O)NCCN1CCCC1',\n", " 'C=CC(=O)NCCN1CCCCC1',\n", " 'C=CC(=O)NCCN1CCCCC1C',\n", " 'C=CC(=O)NCCN1CCN(c2cc(Cl)ccc2C)CC1',\n", " 'C=CC(=O)NCCN1CCN(c2ccc(OC)cc2)CC1',\n", " 'C=CC(=O)NCCN1CCN(c2cccc(C)c2C)CC1',\n", " 'C=CC(=O)NCCN1CCN(c2cccc(Cl)c2)CC1',\n", " 'C=CC(=O)NCCN1CCN(c2ccccc2)CC1',\n", " 'C=CC(=O)NCCN1CCN(c2ccccc2F)CC1',\n", " 'C=CC(=O)NCCN1CCOCC1',\n", " 'C=CC(=O)NCCOc1ccccc1OC',\n", " 'C=CC(=O)NCCSCc1[nH]cnc1C',\n", " 'C=CC(=O)NCCc1c(C)nn(C)c1C',\n", " 'C=CC(=O)NCCc1c[nH]c2ccc(C)cc12',\n", " 'C=CC(=O)NCCc1c[nH]c2ccc(OCc3ccccc3)cc12',\n", " 'C=CC(=O)NCCc1c[nH]c2ccccc12',\n", " 'C=CC(=O)NCCc1ccc(OCC)c(OCC)c1',\n", " 'C=CC(=O)NCCc1csc(C)n1',\n", " 'C=CC(=O)NCCc1nc2cc(C)ccc2[nH]1',\n", " 'C=CC(=O)NCc1c(C)n[nH]c1C',\n", " 'C=CC(=O)NCc1c(C)nn(CC)c1C',\n", " 'C=CC(=O)NCc1cc(F)cc(F)c1',\n", " 'C=CC(=O)NCc1cc(F)ccc1F',\n", " 'C=CC(=O)NCc1cc(OCC)c(OCC)c(OCC)c1',\n", " 'C=CC(=O)NCc1ccc(-c2nc(C)cs2)cc1',\n", " 'C=CC(=O)NCc1ccc(-c2nc(CC)cs2)cc1',\n", " 'C=CC(=O)NCc1ccc(=O)n(CC2CC2)c1',\n", " 'C=CC(=O)NCc1ccc(=O)n(CCOC)c1',\n", " 'C=CC(=O)NCc1ccc(C(=O)N2CCOCC2)cc1',\n", " 'C=CC(=O)NCc1ccc(F)cc1F',\n", " 'C=CC(=O)NCc1ccc(N(CC)CC)cc1',\n", " 'C=CC(=O)NCc1ccc(N2CCC(C)CC2)cc1',\n", " 'C=CC(=O)NCc1ccc(N2CCCC(C)C2)cc1',\n", " 'C=CC(=O)NCc1ccc(N2CCCCC2C)cc1',\n", " 'C=CC(=O)NCc1ccc(OC(C)C)cc1',\n", " 'C=CC(=O)NCc1ccc(OC(F)(F)F)cc1',\n", " 'C=CC(=O)NCc1ccc(OC)c(OC)c1OC',\n", " 'C=CC(=O)NCc1ccc(OCC)cc1',\n", " 'C=CC(=O)NCc1ccc2nonc2c1',\n", " 'C=CC(=O)NCc1cccc(C(F)(F)F)c1',\n", " 'C=CC(=O)NCc1ccccn1',\n", " 'C=CC(=O)NCc1cccn(C)c1=O',\n", " 'C=CC(=O)NCc1cccn(CC2CC2)c1=O',\n", " 'C=CC(=O)NCc1cccnc1-c1ccc(F)cc1',\n", " 'C=CC(=O)Nc1cc(C)ccc1N=c1[nH]c(=Nc2cc(OC)ncc2C)[nH]cc1C(F)(F)F',\n", " 'C=CC(=O)Nc1cc(N2CCN(CC)CC2)ccc1N=c1cc(N(C)C(=O)Nc2c(Cl)c(OC)cc(OC)c2Cl)[nH]cn1',\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3c[nH]c4ccccc34)cc[nH]2)c(OC)cc1N(C)CCN(C)C',\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3cn(C)c4ccccc34)c(C(=O)OC(C)C)c[nH]2)c(OC)cc1N(C)CCN(C)C',\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3cn(C)c4ccccc34)cc[nH]2)c(OC)cc1N(C)CCN(C)C',\n", " 'C=CC(=O)Nc1cc(N=c2nc(-c3cn(C4CC4)c4ccccc34)cc[nH]2)c(OC)cc1N(C)CCN(C)C',\n", " 'C=CC(=O)Nc1cc(N=c2nc(-n3cc(CN(C)C)c(-c4ccccc4)n3)cc[nH]2)c(OC)cc1N1CCOCC1',\n", " 'C=CC(=O)Nc1cc(NC(=O)c2cnn(-c3ccccc3F)c2)ccc1F',\n", " 'C=CC(=O)Nc1cc2c(=Nc3ccc(F)c(Cl)c3)[nH]cnc2cc1C#CC(C)(C)N1CCN(C)CC1',\n", " 'C=CC(=O)Nc1cc2c(=Nc3ccc(F)c(Cl)c3)[nH]cnc2cc1OCCCN1CCOCC1',\n", " 'C=CC(=O)Nc1ccc(CN(C(=O)Nc2c(Cl)c(OC)cc(OC)c2Cl)c2cc(=Nc3ccc(N4CCN(C)CC4)cc3)[nH]cn2)cc1',\n", " 'C=CC(=O)Nc1ccc(CN2C(=O)N(c3cc(OC)cc(OC)c3)Cc3c[nH]c(=Nc4ccc(N5CCN(C)CC5)cc4)nc32)cc1',\n", " 'C=CC(=O)Nc1ccc2[nH]c(=O)n(C3CCN(Cc4ccc(-c5nc6cc[nH]c(=O)c6cc5-c5ccccc5)cc4)CC3)c2c1',\n", " 'C=CC(=O)Nc1ccc2[nH]cnc(=Nc3ccc(OCc4cccc(F)c4)c(Cl)c3)c2c1',\n", " 'C=CC(=O)Nc1ccc2[nH]cnc(=Nc3cccc(Br)c3)c2c1',\n", " 'C=CC(=O)Nc1cccc(C)c1N=c1nc2ccc(-c3c(Cl)c(OC)cc(OC)c3Cl)cc2c[nH]1',\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(N4CCN(C(C)=O)CC4)cc3OC)[nH]cc2C(F)(F)F)c1',\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(NC4CN(CCF)C4)cc3OC)[nH]cc2C(F)(F)F)c1',\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(OCCOC)cc3)[nH]cc2F)c1',\n", " 'C=CC(=O)Nc1cccc(N=c2[nH]c(=Nc3ccc(Oc4ccnc(C(=O)NC)c4)cc3)[nH]cc2F)c1',\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)c(F)c3)nc3[nH]ccc23)c1',\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)nc3ccsc23)c1',\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)ncc2Cl)c1',\n", " 'C=CC(=O)Nc1cccc(Oc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3OC)ncc2Cl)c1',\n", " 'C=CC(=O)Nc1cccc(Sc2[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)ncc2Cl)c1',\n", " 'C=CC(C)(C)c1[nH]c2cc(Br)ccc2c1CCNC',\n", " 'C=CC(C)(C)c1cc(C=CC(=O)c2ccc(O)cc2)c(OC)cc1O',\n", " 'C=CC(C)(C=Cc1ccc(O)cc1)CCC=C(C)C',\n", " 'C=CC(C)(O)CCC1C(C)(O)CCC2C(C)(C)CCCC21C',\n", " 'C=CC(C)(O)CCC=C(C)C',\n", " 'C=CC(C)(O)CCC=C(C)CCC=C(C)C',\n", " 'C=CC(C)(O)CN1CCN(Cc2nc(C(=O)NCC3CCCCC3)co2)CC1',\n", " 'C=CC(N)=O',\n", " 'C=CC(N)CCC(=O)O',\n", " 'C=CC1(C)CC(=O)C2(O)C(C)(O1)C(OC(C)=O)C(O)C1C(C)(C)CCC(O)C12C',\n", " 'C=CC1(C)CC(OC(=O)CO)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O',\n", " 'C=CC1(C)CC(OC(=O)CSC(C)(C)CNC(=O)C(N)C(C)C)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O',\n", " 'C=CC1(C)CC(OC(=O)CSC2CC3CCC(C2)N3C)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O',\n", " 'C=CC1(C)CC(OC(=O)CSCCN(CC)CC)C2(C)C(C)CCC3(CCC(=O)C32)C(C)C1O',\n", " 'C=CC12CN(C)C3C4COC(CC41)C1(C(=O)Nc4ccccc41)C32',\n", " 'C=CC12CN(C)C3CC14C(=Nc1ccccc14)C1CC2C3CO1',\n", " 'C=CC1=C(C(=O)O)N2C(=O)C(=NC(=O)C(NOCC(=O)O)c3csc(=N)[nH]3)C2SC1',\n", " 'C=CC1=C(C(=O)O)N2C(=O)C(NC(=O)C(=NO)c3csc(=N)[nH]3)C2SC1',\n", " 'C=CC1=C(C(=O)O)N2C(=O)[C@@H](NC(=O)/C(=N\\\\O)c3csc(N)n3)[C@H]2SC1',\n", " 'C=CC1=C(C(=O)O)N2C(=O)[C@@H](NC(=O)/C(=N\\\\OCC(=O)O)c3csc(N)n3)[C@H]2SC1',\n", " 'C=CC1C(OC2OC(CO)C(O)C(O)C2O)OC=C(C(=O)OC)C1CC(=O)O',\n", " 'C=CC1C(OC2OC(CO)C(O)C(O)C2O)OC=C2C(=O)OCCC21',\n", " 'C=CC1C(OC2OC(CO)C(O)C(O)C2O)OC=C2C(=O)OCCC21O',\n", " 'C=CC1C2=CCOC(=O)C2=COC1OC1OC(CO)C(O)C(O)C1O',\n", " 'C=CC1CC1(NC(=O)C1CC(Oc2ncc(OC)c3ccc(Cl)cc23)CN1C(=O)C(NC(=O)OC(C)(C)C)C(C)(C)C)C(=O)NS(=O)(=O)C1CC1',\n", " 'C=CC1CC1(NC(=O)C1CC2CN1C(=O)C(C(C)(C)C)NC(=O)OC1CC1CCCCCc1nc3ccc(OC)cc3nc1O2)C(=O)NS(=O)(=O)C1CC1',\n", " 'C=CC1CN2CCC1CC2C(O)c1ccnc2ccc(OC)cc12',\n", " 'C=CC1CN2CCC1CC2C(O)c1ccnc2ccccc12',\n", " 'C=CC1CN2CCC1CC2CNC(=O)C1CC1',\n", " 'C=CC1CN2CCC1CC2CNC(=O)COc1ccccc1',\n", " 'C=CC1CN2CCC1CC2CNC(=O)NCCC',\n", " 'C=CC1CN2CCC1CC2CNC(=O)Nc1ccc(OC(F)(F)F)cc1',\n", " 'C=CC1CN2CCC1CC2CNC(=O)c1ccc2c(c1)OCO2',\n", " 'C=CC1CN2CCC1CC2CNC(=O)c1ccc2ccccc2c1',\n", " 'C=CC1CN2CCC1CC2CNS(=O)(=O)c1ccc(C)cc1',\n", " 'C=CC1CN2CCC1CC2CNS(=O)(=O)c1ccc(NC(C)=O)cc1',\n", " 'C=CC1CN2CCC1CC2CNS(=O)(=O)c1cccc(F)c1',\n", " 'C=CC1CN2CCC1CC2CNS(=O)(=O)c1cccc2cccnc12',\n", " 'C=CC1CN2CCC1CC2CNS(=O)(=O)c1cccs1',\n", " 'C=CC1CN2CCC3(C(=O)Nc4ccccc43)C2CC1C(=COC)C(=O)OC',\n", " 'C=CC1CNC(=S)O1',\n", " 'C=CCC(=NOS(=O)(=O)O)SC1OC(CO)C(O)C(O)C1O',\n", " 'C=CCC(C(=O)NC(N)=O)C(C)C',\n", " 'C=CCC(C)C(=O)O',\n", " 'C=CCC(O)(CC=C)C(C)NC(=O)C1CCCN1c1nc(C)c2cc(OC)ccc2n1',\n", " 'C=CCC1(C(C)CCC)C(=O)N=C(S)NC1=O',\n", " 'C=CCC1(O)CCC2C3=C(C=CC21C)C1=C(CC3)CC(=O)CC1',\n", " 'C=CCC1=CC(C)CC(C)CC(OC)C2OC(O)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C)=CC3CCC(O)C(OC)C3)C(C)C(O)CC1=O)C(C)CC2OC',\n", " 'C=CCCC(=O)N1CCC(N2c3ccccc3N(C)S2(=O)=O)CC1',\n", " 'C=CCCC(=O)N1CCC(Oc2nncs2)CC1',\n", " 'C=CCCC(=O)N1CCCC(Oc2ncccn2)C1',\n", " 'C=CCCC(=O)NC1CC(=O)N(CCc2cccc(Cl)c2)C1',\n", " 'C=CCCC(=O)NC1CCN(c2ccc(C(F)(F)F)cn2)C1',\n", " 'C=CCCC(=O)NCCc1ccccc1',\n", " 'C=CCCC(=O)NCc1ccc(-c2ccsc2)o1',\n", " 'C=CCCC(=O)NCc1cn(-c2ccncc2)nn1',\n", " 'C=CCCC(=O)O',\n", " 'C=CCCCCCCCCC(=O)O',\n", " 'C=CCCCCCCCCC(=O)OC1CCC2C3CC=C4CC(=O)C=CC4(C)C3CCC12C',\n", " 'C=CCCCCCCCCCO',\n", " 'C=CCCCCCCCCc1n[nH]c(SCC(=O)O)n1',\n", " 'C=CCN(C(=O)CC1c2ccccc2C=CN1C(C)=O)c1nc2c(s1)CCCC2',\n", " 'C=CCN(C(=O)CCc1nc(-c2ccsc2)no1)c1nc2ccccc2s1',\n", " 'C=CCN(C(=O)CNc1ccccc1C(=O)NCCc1ccc(OC)cc1)c1ccccc1',\n", " 'C=CCN(C(=O)COc1ccccc1)c1nnc(-c2ccncc2)s1',\n", " 'C=CCN(C(=O)CSc1nc2ccsc2c(=O)n1Cc1ccccn1)c1ccccc1',\n", " 'C=CCN(C(=O)Cn1c(C(=O)OC)cc2oc(C)cc21)c1ccccc1',\n", " 'C=CCN(C(=O)Cn1ncc2c1-c1cc(C)ccc1OC2)c1ccccc1',\n", " 'C=CCN(C(=O)Nc1ccc(OC)cc1)c1nnc(-c2ccncc2)s1',\n", " 'C=CCN(C(=O)c1ccc2snnc2c1)c1ccccc1',\n", " 'C=CCN(C(=O)c1ccccc1OCc1c(C)noc1C)c1nc2c(s1)CCCC2',\n", " 'C=CCN(C(=O)c1cnc2c(cnn2C(C)C)c1)c1nc(-c2ccccc2)cs1',\n", " 'C=CCN(C)C(=O)c1cncn1-c1cccc(-c2cccc(OC(F)(F)F)c2)c1',\n", " 'C=CCN(C)C(=O)c1cncn1-c1cccc(-c2ccccc2C(F)(F)F)c1',\n", " 'C=CCN(C)CCCCCCOc1ccc(C(=O)c2ccc(Br)cc2)c(F)c1',\n", " 'C=CCN(CC(=O)N1CCN(c2ccc(-c3ccccc3)nn2)CC1)C(=O)c1ccccc1',\n", " 'C=CCN(CC(=O)NC1CC1)S(=O)(=O)c1ccc(Cl)c(C(F)(F)F)c1',\n", " 'C=CCN(CC=C)C(=O)CN1CC(C(N)=O)Oc2ccccc21',\n", " 'C=CCN(CC=C)C(=O)COC(=O)c1cc(-c2ccccc2)nc2onc(C)c12',\n", " 'C=CCN(CC=C)C(=O)c1cc(N(C)C2CCCCC2)nc2ccccc12',\n", " 'C=CCN(CC=C)C(=O)c1ccc2c(c1)OCO2',\n", " 'C=CCN(CC=C)C(=O)c1ccccc1NC(=O)c1ccccc1C',\n", " 'C=CCN(CC=C)S(=O)(=O)c1ccc2c(c1)CCCC(=O)N2',\n", " 'C=CCN(Cc1ccc(Cl)s1)C(=O)Cc1csc(-c2ccc(OC)cc2)n1',\n", " 'C=CCN(Cc1cccs1)C(O)c1cc(C(N)=O)n(-c2ccccc2)n1',\n", " 'C=CCN(Cc1cn(-c2cccc(C)c2)nc1-c1cccc(F)c1)C1CCS(=O)(=O)C1',\n", " 'C=CCN(Cc1csc(COc2c(OC)cccc2OC)n1)C(=O)c1ccccc1F',\n", " 'C=CCN(Cc1csc(COc2ccc(OC)cc2)n1)C(=O)c1cccs1',\n", " 'C=CCN(c1ccc(C(=O)N(C)Cc2ccccc2)cc1)S(C)(=O)=O',\n", " 'C=CCN(c1ccc(C(=O)N2CCC(C)CC2)cc1)S(C)(=O)=O',\n", " 'C=CCN(c1ccccc1)S(=O)(=O)c1ccc2c(c1)NC(=O)C(C)S2',\n", " 'C=CCN(c1ccccc1C(=O)NCC(=O)O)S(=O)(=O)c1ccccc1',\n", " 'C=CCN(c1nc(C)c(Br)c(OC)n1)S(=O)(=O)c1ccc(C)cc1',\n", " 'C=CCN1C(=O)C(=c2sc3nc4ccccc4n3c2=O)c2ccccc21',\n", " 'C=CCN1C(=O)C(C)(C)COc2cc(NS(=O)(=O)c3cc(Cl)ccc3C)ccc21',\n", " 'C=CCN1C(=O)C(C)(C)COc2ccc(NS(=O)(=O)c3cc(C)ccc3C)cc21',\n", " 'C=CCN1C(=O)C(C)(C)COc2ccc(NS(=O)(=O)c3ccc(F)c(Cl)c3)cc21',\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccc(C)o2)c2cc(Br)ccc21',\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccc(OC)c([N+](=O)[O-])c2)c2ccccc21',\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccccc2)c2ccccc21',\n", " 'C=CCN1C(=O)C(O)(CC(=O)c2ccco2)c2ccccc21',\n", " 'C=CCN1C(=O)C(c2c(C)[nH]c3ccccc23)(c2c(C)[nH]c3ccccc23)c2ccccc21',\n", " 'C=CCN1C(=O)C2(NC(C)c3c2c(O)n(Cc2ccccc2)c3O)c2ccccc21',\n", " 'C=CCN1C(=O)C2(NC(CC(C)C)c3c2c(O)n(C)c3O)c2ccccc21',\n", " 'C=CCN1C(=O)C2(NC(CCSC)c3c2c(O)n(C)c3O)c2ccccc21',\n", " 'C=CCN1C(=O)C2(c3ccccc31)C(C(=O)c1ccc(C)o1)C(=O)C(=O)N2CCCN1CCOCC1',\n", " 'C=CCN1C(=O)C2(c3ccccc31)C(C(=O)c1ccc(S(=O)(=O)N3CCCC3)cc1)C(=O)C(=O)N2CCCN(C)C',\n", " 'C=CCN1C(=O)C2(c3ccccc31)C(C(=O)c1cccc(S(=O)(=O)N3CCCCC3)c1)C(=O)C(=O)N2CCN(C)C',\n", " 'C=CCN1C(=O)C2=C(C(=O)Nc3cccc(OC)c3)C3CCC2(O3)C1C(=O)NC1CCCCC1C',\n", " 'C=CCN1C(=O)COc2ccc(-c3csc(=NC(=O)CCCC)[nH]3)cc21',\n", " 'C=CCN1C(=O)NC(c2ccc(F)cc2)c2c1cn(CCc1ccccc1)c2O',\n", " 'C=CCN1C(=O)NC(c2cccc(Oc3ccccc3)c2)c2c1cn(Cc1ccccc1)c2O',\n", " 'C=CCN1C(=O)SC(=Cc2ccc(N3CCCC3)o2)C1=O',\n", " 'C=CCN1C(=O)c2ccccc2C1(O)Cc1ccccc1',\n", " 'C=CCN1C(=O)c2ccccc2N2C(=O)CCC12C(=O)N(C)Cc1ccc(SC)cc1',\n", " 'C=CCN1C(=O)c2ccccc2N2C(=O)CCC12C(=O)NC(C)c1ccccc1Cl',\n", " 'C=CCN1C(=O)c2ccccc2NC12CCC(C)CC2',\n", " 'C=CCN1C(=O)c2ccccc2NC1c1cn(C)c(=O)n(C)c1=O',\n", " 'C=CCN1CC(C(=O)N(CCCN(C)C)C(=O)NCC)CC2c3cccc4[nH]cc(c34)CC21',\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(-c4cccc(OC)c4)c(C)c3n2)CC1=O',\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(-c4ccccc4)c(C)c3n2)CC1=O',\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(-c4ccccc4OC)c(C)c3n2)CC1=O',\n", " 'C=CCN1CC(c2cc(=O)n3[nH]c(C)c(-c4ccccc4)c3n2)CC1=O',\n", " 'C=CCN1CC(c2cc(=O)n3[nH]cc(-c4ccc(C)cc4)c3n2)CC1=O',\n", " 'C=CCN1CC(c2cc(=O)n3[nH]cc(C(=O)Nc4ccccc4)c3n2)CC1=O',\n", " 'C=CCN1CC(c2nc3ccccc3n2Cc2ccc(C)cc2)CC1=O',\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C(C)CN(C)CC)CC2',\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C(N)CCSC)CC2',\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C1CC13CCC3)CC2',\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C1CC=CCC1)CC2',\n", " 'C=CCN1CC2(CCC1=O)CCN(C(=O)C1Cc3ccccc3CN1CC)CC2',\n", " 'C=CCN1CC2(CCC1=O)CCN(S(=O)(=O)C(C)CC)CC2',\n", " 'C=CCN1CCC2(CCC1=O)CN(C(=O)CCSC)CCN2C',\n", " 'C=CCN1CCC2(CCC1=O)CN(Cc1cccc(SC)c1)CCN2C',\n", " 'C=CCN1CCC23c4c5ccc(O)c4OC2C(=NNC(=O)c2ccccc2)CCC3(O)C1C5',\n", " 'C=CCN1CCC23c4c5ccc(O)c4OC2C(=O)CCC3(O)C1C5',\n", " 'C=CCN1CCCC1CNC(=O)c1cc(S(N)(=O)=O)cc(OC)c1OC',\n", " 'C=CCN1CCCC1CNC(=O)c1cc2[nH]nnc2cc1OC',\n", " 'C=CCN1CCN(C(=O)C(CC)CC)C(Cc2ccccc2-c2ccncc2)C1=O',\n", " 'C=CCN1CCN(C(=O)C2CCC2)C(Cc2ccc(-c3ccncc3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)C2CCC2)C(Cc2cccc(-c3ccncc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2ccc(-c3cccnc3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2ccc(-c3ccncc3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2cccc(-c3cccnc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)C2CCCC2)C(Cc2ccccc2-c2ccncc2)C1=O',\n", " 'C=CCN1CCN(C(=O)CC(C)(C)C)C(Cc2ccccc2-c2ccncc2)C1=O',\n", " 'C=CCN1CCN(C(=O)CC(C)C)C(Cc2ccc(-c3cccnc3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)CC(C)C)C(Cc2ccc(-c3ccncc3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)CC(C)C)C(Cc2cccc(-c3cccnc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)CNC(C)=O)C(Cc2cccc(-c3ccccc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)COC)C(Cc2ccc(-c3cccc(OC)c3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)COC)C(Cc2ccc(-c3cccs3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)COC)C(Cc2cccc(-c3ccccc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)Cc2cccnc2)C(Cc2ccc(-c3cccs3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)Cc2cccnc2)C(Cc2cccc(-c3ccncc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)Cn2nc(C)nc2C)C(Cc2ccc(-c3cccs3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2cc3c(s2)CCCC3)CC1',\n", " 'C=CCN1CCN(C(=O)c2ccc(-c3ccccc3)cc2)CC1',\n", " 'C=CCN1CCN(C(=O)c2ccc(C)s2)C(Cc2cccc(-c3cccnc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2ccc(F)cc2)c2cccnc21',\n", " 'C=CCN1CCN(C(=O)c2ccc(OC)nc2)C(Cc2ccc(-c3cccnc3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2ccccc2)C(Cc2cccc(-c3ccncc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2ccccn2)C(Cc2ccc(-c3ccccc3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2ccccn2)C(Cc2ccc(-c3cccs3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2ccccn2)C(Cc2cccc(-c3ccncc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2ccncc2)C(Cc2ccc(-c3cccs3)cc2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2ccncc2)C(Cc2cccc(-c3ccncc3)c2)C1=O',\n", " 'C=CCN1CCN(C(=O)c2cnc(C)cn2)C(Cc2ccc(-c3cccs3)cc2)C1=O',\n", " 'C=CCN1CCN(CCOC(=O)C(O)(c2ccccc2)c2ccccc2)CC1',\n", " 'C=CCN1CCN(c2nc3ccccc3nc2C#N)CC1',\n", " 'C=CCN1CCN(c2nccc(-n3nc(C)cc3C)n2)CC1',\n", " 'C=CCN1CC[C@]23c4c5ccc(O)c4O[C@H]2C(=O)CC[C@@]3(O)[C@H]1C5',\n", " 'C=CCN1CCc2c(cc(O)c(O)c2Br)[C@@H](c2ccccc2)C1',\n", " 'C=CCN1CCc2c(cc(O)c(O)c2Cl)C(c2ccccc2)C1',\n", " 'C=CCN1CCc2cc(O)c(O)cc2C(c2ccccc2)C1',\n", " 'C=CCN1CCc2cccc3c2[C@H]1Cc1ccc(O)c(O)c1-3',\n", " 'C=CCN1CCc2nc(N)sc2CC1',\n", " 'C=CCN1C[C@H](C)N([C@@H](c2ccccc2)c2ccc(C(=O)N(CC)CC)cc2)C[C@H]1C',\n", " 'C=CCN1C[C@H](C)N([C@H](c2ccc(C(=O)N(CC)CC)cc2)c2cccc(O)c2)C[C@H]1C',\n", " 'C=CCN1C[C@H](C)N([C@H](c2ccc(C(=O)N(CC)CC)cc2)c2cccc(OC)c2)C[C@H]1C',\n", " 'C=CCN=c1[nH]c(-c2ccc(Cl)cc2)cs1',\n", " 'C=CCN=c1[nH]c(-c2ccc(OC)cc2OC)cs1',\n", " 'C=CCN=c1[nH]c(-c2sc(=NC(=O)CC)[nH]c2C)cs1',\n", " 'C=CCN=c1[nH]c(=NCc2ccc(Cl)cc2)c2cnn(C)c2[nH]1',\n", " 'C=CCN=c1[nH]c(C(=O)OCC(=O)N2CCc3ccccc32)cs1',\n", " 'C=CCN=c1[nH]c(N)c(C(=O)N=c2cc(C)o[nH]2)s1',\n", " 'C=CCN=c1[nH]c(N)c(C(=O)c2ccc(OC)c(OC)c2)s1',\n", " 'C=CCN=c1[nH]c(N)c(C(=O)c2ccc(OC)cc2)s1',\n", " 'C=CCN=c1[nH]c(N2CCCC2)nc(=Nc2ccc([N+](=O)[O-])cc2)[nH]1',\n", " 'C=CCN=c1[nH]c(OC)nc(=Nc2ccc(Cl)cc2)[nH]1',\n", " 'C=CCN=c1[nH]c(OCC)nc(=Nc2ccc(OC)cc2)[nH]1',\n", " 'C=CCN=c1[nH]c(OCC)nc(=Nc2ccc([N+](=O)[O-])cc2)[nH]1',\n", " 'C=CCN=c1[nH]c2c(c(=O)[nH]c(=O)n2C)n1CCCCC',\n", " 'C=CCN=c1[nH]c2c(c(=O)[nH]c(=O)n2C)n1Cc1cccc(C)c1',\n", " 'C=CCN=c1[nH]c2c(c(=O)n(C)c(=O)n2C)n1CC',\n", " 'C=CCN=c1[nH]c2c(c(=O)n(C)c(=O)n2C)n1Cc1ccc(F)cc1',\n", " 'C=CCN=c1[nH]cnc2c1cnn2-c1ccc(C)cc1C',\n", " 'C=CCN=c1[nH]cnc2ccc(Br)cc12',\n", " 'C=CCN=c1[nH]nc(-c2ccncc2)s1',\n", " 'C=CCN=c1[nH]nc(SCC(=O)c2cc(C)n(-c3cc(C)on3)c2C)s1',\n", " 'C=CCN=c1[nH]nc(SCc2nc(Cc3ccccc3)no2)s1',\n", " 'C=CCN=c1cc(C)[nH]c2ccc(C)cc12',\n", " 'C=CCN=c1nc(-c2cn(CC)nc2C)cc(C(F)(F)F)[nH]1',\n", " 'C=CCN=c1nc(N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)CC2)[nH]c(=NCC=C)[nH]1',\n", " 'C=CCNC(=O)C(=O)Nc1ccc2c(c1)CCCN2C(=O)c1cccs1',\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)C(C)C)CC1',\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)C2CCC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)CC)CC1',\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)c2cccnc2)CC1',\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)c2ccncc2)CC1',\n", " 'C=CCNC(=O)C1(Cc2ccc(-c3cccs3)cc2)CCN(C(=O)c2cnccn2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccc(OC)c3)c2)CCOCC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3)c2)CCN(C(=O)C2CC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3)c2)CCN(C(=O)CC)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3)c2)CCN(C(=O)c2cnccn2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccccc3OC)c2)CCOCC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C(C)(C)C)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C(C)C)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C2CC=CCC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)C2CCC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)CC(C)(C)C)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)CC)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(C(=O)c2ccncc2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccnc3)c2)CCN(CC2CC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)C(C)C)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)C2CC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)CC)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)c2cccnc2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)c2ccncc2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cccs3)c2)CCN(C(=O)c2cnccn2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)C(C)(C)C)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)C2CC=CCC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)C2CCCC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)CC(C)(C)C)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(C(=O)CC)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCN(CC2CC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3ccncc3)c2)CCOCC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)C2CC2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)CC)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)c2ccccn2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)c2cccnc2)CC1',\n", " 'C=CCNC(=O)C1(Cc2cccc(-c3cncnc3)c2)CCN(C(=O)c2ccncc2)CC1',\n", " 'C=CCNC(=O)C1(Cc2ccccc2-c2cccc(C(=O)NC3CC3)c2)CCOCC1',\n", " 'C=CCNC(=O)C1CC1(c1ccccc1)c1ccccc1',\n", " 'C=CCNC(=O)C1CCCN(S(=O)(=O)c2ccc(Br)s2)C1',\n", " 'C=CCNC(=O)C1CCN(S(=O)(=O)c2ccc3c(c2)OCCCO3)CC1',\n", " 'C=CCNC(=O)C1CCN(S(=O)(=O)c2cccs2)CC1',\n", " 'C=CCNC(=O)C1CCN(c2cc3oc4ccccc4c3cc2OC)C1=O',\n", " 'C=CCNC(=O)C1CCN(c2nccc(-n3nc(C)cc3C)n2)CC1',\n", " 'C=CCNC(=O)CCNC(=O)N1CCN(C(=O)c2cc3ccccc3[nH]2)CC1',\n", " 'C=CCNC(=O)CCn1cnc2c(-c3ccc(CC)cc3)noc2c1=O',\n", " 'C=CCNC(=O)CN(Cc1ccccc1)S(=O)(=O)c1ccccc1',\n", " 'C=CCNC(=O)CN1N=C(c2ccc(C)cc2)CCC1=O',\n", " 'C=CCNC(=O)CSc1ccc(C(=O)Nc2ccc(Cl)cc2F)cc1[N+](=O)[O-]',\n", " 'C=CCNC(=O)Cc1c(C)n(C(=O)c2ccc(Cl)cc2)c2ccc(OC)cc12',\n", " 'C=CCNC(=O)Cc1cc(-c2cccc(OC)c2)on1',\n", " 'C=CCNC(=O)Cc1sc(C)nc1-c1cccs1',\n", " 'C=CCNC(=O)Cn1nc(C)c2cnn(-c3ccc(F)cc3)c2c1=O',\n", " 'C=CCNC(=O)N1CCC(c2nc(C)ccc2C(=O)Nc2ccccc2)CC1',\n", " 'C=CCNC(=O)NCc1cccnc1N1CCN(c2ccccn2)CC1',\n", " 'C=CCNC(=O)Nc1cc(C)ccc1N1CCCN(Cc2ccccc2)C1=O',\n", " 'C=CCNC(=O)c1cc(-c2ccc(C)c(C)c2)n(C2CCS(=O)(=O)C2)n1',\n", " 'C=CCNC(=O)c1cc(-c2cccc(Cl)c2)on1',\n", " 'C=CCNC(=O)c1cc(N2CCN(c3cccc(C(F)(F)F)c3)CC2)nc2ccccc12',\n", " 'C=CCNC(=O)c1cc([N+](=O)[O-])cc2c(=O)[nH]c(Nc3ccc(Cl)c(Cl)c3)nc12',\n", " 'C=CCNC(=O)c1cc2ccccc2o1',\n", " 'C=CCNC(=O)c1cc2sc(Br)cc2n1CC1CCCCO1',\n", " 'C=CCNC(=O)c1ccc(-c2ccc(=O)[nH]c2)s1',\n", " 'C=CCNC(=O)c1ccc(Sc2ccc(NS(=O)(=O)CC)cc2)nc1',\n", " 'C=CCNC(=O)c1ccc2c(c1)N(Cc1c(F)cccc1Cl)C(=O)CS2',\n", " 'C=CCNC(=O)c1coc(COc2ccc3ccc(OC)cc3c2)n1',\n", " 'C=CCNC(=O)c1nn(-c2ccccc2)cc1OC',\n", " 'C=CCNC(=O)c1nn(C)c(=O)c2ccccc12',\n", " 'C=CCNC(=O)c1sc2nc(C)cc(C)c2c1N',\n", " 'C=CCNC(=S)NN=c1nc(N2CCCC2)[nH]c(N2CCCC2)n1',\n", " 'C=CCNC(N)=S',\n", " 'C=CCNC(O)c1cc(O)n(-c2ccc(C)cc2)c1',\n", " 'C=CCNCc1ccc(OCC(=O)NC(C)(C)C)c(OC)c1',\n", " 'C=CCNCc1nc(-c2ccc(OC)c(OC)c2)no1',\n", " 'C=CCNS(=O)(=O)c1cc(Br)ccc1OC',\n", " 'C=CCNS(=O)(=O)c1ccc(NC(=O)Cc2ccccc2C)cc1',\n", " 'C=CCNS(=O)(=O)c1ccc(OC)c(-c2noc(C3CCCCC3)n2)c1',\n", " 'C=CCNS(=O)(=O)c1ccc2[nH]c(=O)[nH]c2c1',\n", " 'C=CCNS(=O)(=O)c1cccc(C(=O)N=c2[nH]c3ccccc3[nH]2)c1',\n", " 'C=CCNS(=O)(=O)c1nn(C)c2nc(C)c(Cl)c(C)c12',\n", " 'C=CCNc1oc(-c2ccco2)nc1S(=O)(=O)c1ccccc1',\n", " 'C=CCOC(=O)C1=C(C)N=C2CC(C)(C)CC(=O)C2C1c1cc(Cl)c(O)c(OC)c1',\n", " 'C=CCOC(=O)C1C(=O)CC(C)(O)C(C(=O)OCC=C)C1c1ccc(OCC)cc1',\n", " 'C=CCOC(=O)C1C(C)=NC(=O)NC1c1ccc(Cl)cc1',\n", " 'C=CCOC(=O)C1C(c2ccccc2)c2c([nH][nH]c2=O)CC1(C)O',\n", " 'C=CCOC(=O)c1nnn(-c2no[nH]c2=N)c1C',\n", " 'C=CCOC(Cn1ccnc1)c1ccc(Cl)cc1Cl',\n", " 'C=CCOC(O)=c1ccccc1=C(O)Nc1ccc(NC(C)O)cc1',\n", " 'C=CCOCCN(CCOCC=C)C1=NS(=O)(=O)c2ccccc21',\n", " 'C=CCON=C1c2ccccc2-c2nc(C#N)c(C#N)nc21',\n", " 'C=CCOc1c(Br)cc(C=c2c(=C)[nH]oc2=O)cc1OC',\n", " 'C=CCOc1c(CNc2ccc3[nH]c(=O)[nH]c3c2)cccc1OC',\n", " 'C=CCOc1c(OC)cccc1-c1cc(=O)[nH]c2c(-c3ccccc3)c(C(O)O)sc12',\n", " 'C=CCOc1ccc(-c2c(C(=O)c3ccccc3)c(O)c(O)n2-c2nnc(C)s2)cc1',\n", " 'C=CCOc1ccc(-c2cc(C(F)(F)F)c3c(n2)sc2c(=O)cc(O)[nH]c23)cc1',\n", " 'C=CCOc1ccc(C(=O)N2CCn3cc(C(F)(F)F)nc3C2)cc1',\n", " 'C=CCOc1ccc(C(=O)N=c2cccc[nH]2)cc1',\n", " 'C=CCOc1ccc(C(=O)NCC(c2ccco2)N2CCOCC2)cc1',\n", " 'C=CCOc1ccc(C(=O)NCC2(N3CCN(C)CC3)CCCCC2)cc1',\n", " 'C=CCOc1ccc(C=C2C(=O)NC(=O)NC2=O)cc1OCC',\n", " 'C=CCOc1ccc(C=C2SC(=N)N(c3nccs3)C2=O)cc1OCC',\n", " 'C=CCOc1ccc(CN(C)S(=O)(=O)c2ccc3c(c2)CCCN3C(C)=O)cc1',\n", " 'C=CCOc1ccc(CNc2ccc3[nH]c(=O)[nH]c3c2)cc1OC',\n", " 'C=CCOc1ccc(CNc2ccc3[nH]c(=O)[nH]c3c2)cc1OCC',\n", " 'C=CCOc1ccc(NC(=O)C2CCCN(S(=O)(=O)c3cccs3)C2)cc1',\n", " 'C=CCOc1ccc2c(C)cc(=O)oc2c1C(C)=O',\n", " 'C=CCOc1cccc(-c2cc(=O)[nH]c3c(-c4ccc(F)cc4)c(C(O)O)sc23)c1',\n", " 'C=CCOc1cccc(C2Oc3nc(SCc4ccccc4Cl)nnc3-c3ccccc3N2C(C)=O)c1',\n", " 'C=CCOc1cccc2c1cc(C(=O)NCc1ccccc1)n2CC',\n", " 'C=CCOc1ccccc1-c1cc(=O)[nH]c2c(-c3ccc(F)cc3)c(C(O)O)sc12',\n", " 'C=CCOc1ccccc1C1CC(=O)Nc2c(-c3ccc(Cl)cc3)csc21',\n", " 'C=CCOc1ccccc1CN1CCN(Cc2ccsc2)C(CCO)C1',\n", " 'C=CCOc1ccccc1CNc1ccc2[nH]c(=O)[nH]c2c1',\n", " 'C=CCOc1ccccc1NC(=O)c1nc2nc(C)cc(C)n2n1',\n", " 'C=CCOc1ccccc1OCC(O)CNC(C)C',\n", " 'C=CCOc1nc(N2CCCC2)nc(N2CCCC2)n1',\n", " 'C=CCOc1nc2c(c(=O)n(C)c(=O)n2C)n1C',\n", " 'C=CCOn1c(=O)c(=O)n(OCc2ccccc2)c2ccccc21',\n", " 'C=CCSC',\n", " 'C=CCSCC(N)C(=O)O',\n", " 'C=CCSCC1Nc2cc(Cl)c(S(N)(=O)=O)cc2S(=O)(=O)N1',\n", " 'C=CCSCC=C',\n", " 'C=CCS[S+]([O-])CC=C',\n", " 'C=CCSc1n[nH]c(=NC(=O)Cc2csc(-c3ccccc3)n2)s1',\n", " 'C=CCSc1n[nH]c(=NC(=O)c2cc(=O)c3cc(CC)ccc3o2)s1',\n", " 'C=CCSc1n[nH]c(=NC(=O)c2ccc3c(c2)CC(C)N3S(C)(=O)=O)s1',\n", " 'C=CCSc1n[nH]c(=NC(=O)c2cccc(S(=O)(=O)N(C)c3ccccc3)c2)s1',\n", " 'C=CCSc1nc(-c2ccccc2)c2cc(Cl)ccc2n1',\n", " 'C=CCSc1nc(=O)c2c(C)c(C)sc2[nH]1',\n", " 'C=CCSc1nc(=O)c2c([nH]1)N=C(C)C(C(=O)OC)C2c1sccc1C',\n", " 'C=CCSc1nc2ccccc2[nH]1',\n", " 'C=CCSc1nc2ccccc2c(=O)n1CC(=C)C',\n", " 'C=CCSc1ncccc1C(=O)NCc1ccc(C)cc1',\n", " 'C=CCSc1nnc(-c2cccn(Cc3ccc(Cl)cc3Cl)c2=O)n1CC=C',\n", " 'C=CCSc1nnc(-c2cccnc2)o1',\n", " 'C=CCSc1nnc(CCCCCN2C(=O)c3cccc4cccc(c34)C2=O)o1',\n", " 'C=CCSc1nnc(Cc2c(C)[nH]c3ccccc23)o1',\n", " 'C=CCSc1nnc2c(n1)OC(c1c(C)nn(-c3ccccc3)c1Cl)N(C(C)=O)c1ccccc1-2',\n", " 'C=CCSc1nnc2c(n1)OC(c1cc(Br)c(OCc3ccccc3)c(OC)c1)N(C(=O)CC)c1ccccc1-2',\n", " 'C=CCSc1nnc2c(n1)OC(c1ccc(-c3cc(Cl)ccc3C)o1)Nc1ccccc1-2',\n", " 'C=CCSc1nnc2c(n1)OC(c1ccccc1OCc1ccccc1)Nc1ccccc1-2',\n", " 'C=CCSc1nnc2c(n1)OC(c1cn(C(C)=O)c3ccccc13)N(C(C)=O)c1ccccc1-2',\n", " 'C=CCSc1nnc2c(n1)[nH]c1c(C)cccc12',\n", " 'C=CCSc1nnc2c(n1)[nH]c1ccc(CC)cc12',\n", " 'C=CC[N+]1(C2CC3C4CCC5CC(O)C(N6CCOCC6)CC5(C)C4CCC3(C)C2OC(C)=O)CCCC1',\n", " 'C=CC[S+]([O-])CC(N)C(=O)O',\n", " 'C=CCc1c(C)nc2c(-c3ccccc3)cnn2c1N1CCCCC1',\n", " 'C=CCc1cc(OC)c(O)c(C(=O)NCCO)c1',\n", " 'C=CCc1cc(OC)c(OC)c(OC)c1',\n", " 'C=CCc1cc(OC)ccc1OCC(O)CN1CCN(c2ccc(OC)cc2)CC1',\n", " 'C=CCc1cc2c(oc(=O)c3ccccc32)c(C)c1O',\n", " 'C=CCc1ccc(O)c(-c2cc(CC=C)ccc2O)c1',\n", " 'C=CCc1ccc(O)c(-c2ccc(O)c(CC=C)c2)c1',\n", " 'C=CCc1ccc(O)c(OC)c1',\n", " 'C=CCc1ccc(OC(C)=O)c(OC)c1',\n", " 'C=CCc1ccc(OC)c(OC)c1',\n", " 'C=CCc1ccc(OC)cc1',\n", " 'C=CCc1ccc(OCC(=O)N2CCCCC2CNS(C)(=O)=O)c(OC)c1',\n", " 'C=CCc1ccc(OCC(O)CN2CCCCC2)c(OC)c1',\n", " 'C=CCc1ccc(OCc2ccc(C(=O)O)o2)c(OC)c1',\n", " 'C=CCc1ccc(OCc2ccc(C(=O)OC)o2)c(OC)c1',\n", " 'C=CCc1cccc(C=NNC(=O)CN2CCN(Cc3ccccc3)CC2)c1O',\n", " 'C=CCc1cccc2cc(C(=O)Nc3ccc(F)cc3)c(=O)oc12',\n", " 'C=CCc1ccccc1OCC(O)CN1CCN(C(=O)OCC)CC1',\n", " 'C=CCc1ccccc1OCC(O)CN1CCN(c2ccc(F)cc2)CC1',\n", " 'C=CCc1ccccc1OCC(O)CN1CCN(c2ccccc2F)CC1',\n", " 'C=CCc1ccccc1OCC(O)CNC(C)C',\n", " 'C=CCc1ccccc1OCCn1cnc2ccccc21',\n", " 'C=CCc1ccccc1OCc1nc2ccccc2[nH]1',\n", " 'C=CCn1c(-c2cc(OC)c(OC)c(OC)c2)nc2ccccc21',\n", " 'C=CCn1c(-c2ccc(Cl)cc2)cnc1SCc1c(C)noc1C',\n", " 'C=CCn1c(-c2ccc(Cl)cc2)cnc1SCc1cc(=O)n2ccc(C)cc2n1',\n", " 'C=CCn1c(-c2cccc([N+](=O)[O-])c2)n[nH]c1=S',\n", " 'C=CCn1c(-c2cccs2)nc2ccccc21',\n", " 'C=CCn1c(-c2no[nH]c2=N)nc2ccccc21',\n", " 'C=CCn1c(=N)c(C(=O)NCCCOC)cc2c(=O)n3cccc(C)c3nc21',\n", " 'C=CCn1c(=N)c(C(=O)OCC)cc2c(=O)n3cc(C)ccc3nc21',\n", " 'C=CCn1c(=N)c(C(=O)OCC)cc2c(=O)n3cccc(C)c3nc21',\n", " 'C=CCn1c(=N)n(CC(O)C(C)(C)C)c2ccccc21',\n", " 'C=CCn1c(=N)n(CC(O)COc2ccc(OC)cc2)c2ccccc21',\n", " 'C=CCn1c(=N)n(CC(O)c2ccc(Cl)c(Cl)c2)c2ccccc21',\n", " 'C=CCn1c(=NC(C)c2cc(Cl)ccc2O)[nH]c2ccccc21',\n", " 'C=CCn1c(=NCc2cc(C)ccc2O)[nH]c2ccccc21',\n", " 'C=CCn1c(=NCc2ccc(N(C)C)cc2)[nH]c2ccccc21',\n", " 'C=CCn1c(=NCc2ccc(OC)cc2)[nH]c2ccccc21',\n", " 'C=CCn1c(=O)[nH]c(O)c(C2=NN(C(=O)CC)C(c3cc(OC)ccc3OC)C2)c1=O',\n", " 'C=CCn1c(=O)[nH]c2nc3cc(NC(C)=O)c(C)cc3nc2c1=O',\n", " 'C=CCn1c(=O)c(=O)n(C(C)C)c2ccc(C(F)(F)F)cc21',\n", " 'C=CCn1c(=O)c(C(=O)NCCc2ccccc2)c(O)c2ccccc21',\n", " 'C=CCn1c(=O)c(C(=O)Nc2c(C)cccc2C)c(O)c2ccccc21',\n", " 'C=CCn1c(=O)c2c[nH]c(=Nc3ccc(N4CCN(C)CC4)cc3)nc2n1-c1cccc(C(C)(C)O)n1',\n", " 'C=CCn1c(=O)c2ccc(C(=O)NCc3ccccc3)cc2n(Cc2ccc(C)cc2)c1=O',\n", " 'C=CCn1c(=O)c2ccccc2n2c(SCC(=O)N3c4ccccc4Sc4ccccc43)nnc12',\n", " 'C=CCn1c(=O)n(C2CCCCC2)c(=O)c2cc(OC)c(OC)cc21',\n", " 'C=CCn1c(=O)n(C2OC(CO)C(O)C2O)c2nc(N)[nH]c(=O)c21',\n", " 'C=CCn1c(=O)oc2cc(NC(=O)Nc3ccc(C)c(Cl)c3)ccc21',\n", " 'C=CCn1c(=O)oc2cc(NC(=O)Nc3cccc(Cl)c3C)ccc21',\n", " 'C=CCn1c(=O)oc2ccc(C(=O)N3CCN(c4ccccn4)CC3)cc21',\n", " 'C=CCn1c(=S)[nH]c2c(c1=O)C1(CCCC1)Cc1ccccc1-2',\n", " 'C=CCn1c(C(=O)NC(C)CCc2ccccc2)cc2cc(S(=O)(=O)N(C)C)ccc21',\n", " 'C=CCn1c(C(=O)NCCC)cc2cc(S(=O)(=O)N(C)C)ccc21',\n", " 'C=CCn1c(C(=O)NCCCOC(C)C)cc2cc(S(=O)(=O)N(C)C)ccc21',\n", " 'C=CCn1c(C(=O)NCCCc2ccccc2)cc2cc(S(=O)(=O)N(C)C)ccc21',\n", " 'C=CCn1c(C(=O)NCCc2ccc(Cl)cc2)cc2cc(S(=O)(=O)N(C)C)ccc21',\n", " 'C=CCn1c(C(C)NC(=O)C(C)(C)C)nc2ccccc21',\n", " 'C=CCn1c(C(C)NC(=O)c2ccccc2)nc2ccccc21',\n", " 'C=CCn1c(C(C)NC(C)=O)nc2ccccc21',\n", " 'C=CCn1c(C)c(C(C)=O)c(N2CCN(c3ccccc3)CC2)nc1=S',\n", " 'C=CCn1c(C)c(C(C)=O)cc(NC(=O)c2ccccc2)c1=O',\n", " 'C=CCn1c(C)cc(C(=O)COC(=O)c2ccccc2O)c1C',\n", " 'C=CCn1c(C)cc(C(=O)COn2nnc3ccc(S(=O)(=O)N(C)C)cc32)c1C',\n", " 'C=CCn1c(C)nc2c(sc3nc4c(cc32)COC(C)(C)C4)c1=O',\n", " 'C=CCn1c(C)nnc1SCC(=O)N=c1[nH]ccs1',\n", " 'C=CCn1c(C)nnc1SCC(=O)NC1CCCCC1',\n", " 'C=CCn1c(CC(=O)Nc2ccc(F)cc2)c(O)n(-c2ccc(Cl)cc2)c1=O',\n", " 'C=CCn1c(CCC(=O)O)ccc1-c1ccc(OC)cc1',\n", " 'C=CCn1c(CCCNC(=O)CCC)nc2ccccc21',\n", " 'C=CCn1c(CCN2CCCCC2)nnc1SCc1cc(=O)n2cccc(C)c2n1',\n", " 'C=CCn1c(CCc2ccccc2)nnc1SCC(=O)OC',\n", " 'C=CCn1c(CCc2ccccc2)nnc1SCC(N)=O',\n", " 'C=CCn1c(CCc2ccccc2)nnc1SCc1cc(=O)n2ccsc2n1',\n", " 'C=CCn1c(COc2ccc(C)cc2)nnc1SCc1cc(=O)n2ccsc2n1',\n", " 'C=CCn1c(COc2ccc(OC)cc2)nc2ccccc21',\n", " 'C=CCn1c(COc2cccc3ccc(C)nc23)nnc1SCC(=O)OC',\n", " 'C=CCn1c(COc2cccc3cccnc23)nnc1SCC(=O)O',\n", " 'C=CCn1c(CSc2nc3ccccc3s2)nnc1SCC(=O)NCCO',\n", " 'C=CCn1c(Cc2cccc3ccccc23)n[nH]c1=S',\n", " 'C=CCn1c(Cc2cccs2)nnc1SCC(=O)NC1CC1',\n", " 'C=CCn1c(N)c(-c2nc3ccccc3n2C)sc1=S',\n", " 'C=CCn1c(N)cc(=O)nc1SCC(=O)N1CCN(c2ccc(F)cc2)CC1',\n", " 'C=CCn1c(N)cc(=O)nc1SCC(=O)NC(C)c1ccccc1',\n", " 'C=CCn1c(O)c(CC(=O)Nc2ccccc2)n(Cc2ccccn2)c1=S',\n", " 'C=CCn1c(Oc2cccc(C)c2)nc2c1c(=O)n(C)c(=O)n2C',\n", " 'C=CCn1c(SC(C)C(=O)Nc2ccccc2C#N)nc2ccccc21',\n", " 'C=CCn1c(SCC(=O)N2CC(=O)Nc3ccccc32)nc2scc(-c3ccccc3)c2c1=O',\n", " 'C=CCn1c(SCC(=O)N2CCC(C)CC2)nc2sc3c(c2c1=O)CCCC3',\n", " 'C=CCn1c(SCC(=O)N2CCN(CCO)CC2)nc2sc3c(c2c1=O)CCC3',\n", " 'C=CCn1c(SCC(=O)N2CCN(c3ccc(F)cc3)CC2)nnc1-c1ccco1',\n", " 'C=CCn1c(SCC(=O)N2CCN(c3ccc(F)cc3)CC2)nnc1-c1cccs1',\n", " 'C=CCn1c(SCC(=O)N2CCNC2=O)nnc1-c1ccc(OC)cc1',\n", " 'C=CCn1c(SCC(=O)NC2CCCC2)nnc1-c1ccncc1',\n", " 'C=CCn1c(SCC(=O)NC2CCCCC2)nnc1-c1ccc(OC)cc1',\n", " 'C=CCn1c(SCC(=O)NCc2ccc3c(c2)OCO3)nc2sc3c(c2c1=O)CCCC3',\n", " 'C=CCn1c(SCC(=O)NCc2ccc3c(c2)OCO3)nc2scc(-c3ccccc3)c2c1=O',\n", " 'C=CCn1c(SCC(=O)Nc2ccc(-c3ccccc3)cc2)nc2sc3c(c2c1=O)CCCC3',\n", " 'C=CCn1c(SCC(=O)Nc2ccc(-c3nc4ccc(C)cc4s3)cc2)nnc1-c1ccccc1',\n", " 'C=CCn1c(SCC(=O)Nc2ccc(C(=O)OCC)cc2)nnc1-c1cccs1',\n", " 'C=CCn1c(SCC(=O)Nc2ccc(C)cc2C)nnc1-c1ccc2ccccc2n1',\n", " 'C=CCn1c(SCC(=O)Nc2ccc(Cl)cc2)nnc1-c1cccs1',\n", " 'C=CCn1c(SCC(=O)Nc2sc3c(c2C#N)CCCCCC3)nnc1-c1ccncc1',\n", " 'C=CCn1c(SCC(=O)O)nnc1-c1ccc([N+](=O)[O-])cc1',\n", " 'C=CCn1c(SCC(=O)O)nnc1-c1cccc(C)c1',\n", " 'C=CCn1c(SCC(=O)c2ccc(Br)cc2)nc2sc(CC)cc2c1=O',\n", " 'C=CCn1c(SCC(=O)c2ccc(CNC(C)=O)s2)nnc1-c1ccc(Cl)cc1',\n", " 'C=CCn1c(SCC(=O)c2ccc([N+](=O)[O-])cc2)nc2ccccc2c1=O',\n", " 'C=CCn1c(SCC(=O)c2cccs2)nc2sc3c(c2c1=O)CCCC3',\n", " 'C=CCn1c(SCC(=O)c2cccs2)nnc1-c1cccc(OC)c1',\n", " 'C=CCn1c(SCc2cc(=O)n3ccsc3n2)nnc1-c1ccccn1',\n", " 'C=CCn1c(SCc2cc(=O)n3ccsc3n2)nnc1-c1ccncc1',\n", " 'C=CCn1c(SCc2cc(=O)n3ccsc3n2)nnc1C1CCCN(S(C)(=O)=O)C1',\n", " 'C=CCn1c(SCc2ccc(C(=O)NCCO)cc2)nc2sc(C)c(C)c2c1=O',\n", " 'C=CCn1c(SCc2cccc(OC)c2)nnc1-c1ccncc1',\n", " 'C=CCn1c(SCc2ccccc2Cl)nc2c1c(=O)[nH]c(=O)n2C',\n", " 'C=CCn1c(Sc2nc(C)cs2)nc2c1c(=O)[nH]c(=O)n2C',\n", " 'C=CCn1c(Sc2ncc(Br)cc2[N+](=O)[O-])n[nH]c1=O',\n", " 'C=CCn1c2ccccc2c2nnc(SC(CC)C(=O)N=c3[nH]c(C)c(C(=O)OCC)s3)nc21',\n", " 'C=CCn1c2ccccc2c2nnc(SCC(=O)N=c3cc(C)o[nH]3)nc21',\n", " 'C=CCn1c2ccccc2n2c(C(=O)OC)c(C)nc12',\n", " 'C=CCn1ccc2c(OCC(=O)NC(C)C)cccc2c1=O',\n", " 'C=CCn1ccc2c(OCC(=O)Nc3ccc(C(N)=O)cc3)cccc2c1=O',\n", " 'C=CCn1ccc2c(OCC(=O)Nc3ccccc3C)cccc2c1=O',\n", " 'C=CCn1cnc2c(=NCc3ccccc3)[nH]cnc21',\n", " 'C=CCn1nnc(=NCc2ccc(-c3ccccc3)cc2)[nH]1',\n", " 'C=CN1CCCC1=O',\n", " 'C=CS(=O)(=O)NC1CCN(C(=O)CNc2cc(I)c(Cl)cc2OC)CC1',\n", " 'C=C[C@@]1(C)CC(=O)[C@]2(O)[C@@]3(C)[C@@H](O)CCC(C)(C)[C@@H]3[C@H](O)[C@H](OC(=O)CCCN3CCN(C)CC3)[C@@]2(C)O1',\n", " 'C=C[C@@]12CN(C)[C@H]3[C@H]1[C@@]1(C(=O)Nc4ccccc41)C1CC2[C@@H]3CO1',\n", " 'C=C[C@H]1CN2CC[C@H]1C[C@@H]2[C@@H](O)c1ccnc2ccc(OC)cc12',\n", " 'C=Cc1c(C)c2[nH]c1=Cc1[nH]c(c(C=CC(=O)O)c1C)C=c1[nH]c(c(C)c1C=CC(=O)O)=Cc1[nH]c(c(CC)c1C)C=2',\n", " 'C=Cc1c(O)[nH]c(=Cc2[nH]c(=Cc3[nH]c(C=c4[nH]c(O)c(C)c4=CC)c(C)c3CCC(=O)O)c(=CCC(=O)O)c2C)c1=C',\n", " 'C=Cc1cc(O)cc2nc(-c3ccc(O)c(F)c3)oc12',\n", " 'C=Cc1ccc(CN2C(=O)N(Cc3ccc(OC)cc3)S(=O)(=O)c3ccccc32)cc1',\n", " 'C=Cc1ccc(Cn2c(=O)c3cnc(-c4cccnc4)nc3n(C)c2=O)cc1',\n", " 'C=Cc1ccc(Cn2c(=O)n(CC3CCC(C(=O)NC(C)C)CC3)c(=O)c3sccc32)cc1',\n", " 'C=Cc1ccc(Cn2c(C(=O)O)c(CNC3CCCC3)c3ccc(C)cc32)cc1',\n", " 'C=Cc1ccc(Cn2ccn3nc(-c4ccc(C)c(C)c4)cc3c2=O)cc1',\n", " 'C=Cc1ccc(Cn2nc(-c3nc(C(C)(C)C)no3)ccc2=O)cc1',\n", " 'C=Cn1cnc2c1c(=O)n(C)c(=O)n2C',\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccc(S(=O)(=O)Cc4c(Cl)cccc4Cl)cc23)c(C)c1C(=O)N1CCCC1CN1CCCC1',\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccc(S(=O)(=O)N(C)c4cccc(Cl)c4)cc23)c(C)c1C(=O)N1CCN(C)CC1',\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccccc23)c(C)c1C(=O)OCC',\n", " 'C=c1[nH]c(=Cc2c(O)[nH]c3ccccc23)c(C)c1CCC(=O)O',\n", " 'C=c1[nH]c(=Cc2cc(F)c(O)c(F)c2)c(=O)n1C',\n", " 'C=c1[nH]n(-c2ccc(C(=O)O)cc2)c(=O)c1=Cc1ccc(-c2cc(C)c(C)cc2[N+](=O)[O-])o1',\n", " 'C=c1[nH]n(-c2ccc(C)c(C)c2)c(=O)c1=Cc1ccc2c(c1)n(C)c(=O)n2C',\n", " ...]" ] }, "execution_count": 32, "metadata": {}, "output_type": "execute_result" } ], "source": [ "standardized_smiles" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "66530\n" ] } ], "source": [ "print(len(chemberta2_features_dict))" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "字典已成功保存到 /home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/ChemBERTa2_emb384.pickle\n" ] } ], "source": [ "# 保存字典为pickle文件\n", "pickle_path = '/home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/ChemBERTa2_emb384.pickle'\n", "with open(pickle_path, 'wb') as pickle_file:\n", " pickle.dump(chemberta2_features_dict, pickle_file)\n", "\n", "print(f\"字典已成功保存到 {pickle_path}\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate MolT5 embedding for all smiles" ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "torch.Size([1, 768])\n" ] } ], "source": [ "from transformers import T5ForConditionalGeneration, AutoTokenizer\n", "model = T5ForConditionalGeneration.from_pretrained(\"laituan245/molt5-base\")\n", "tokenizer = AutoTokenizer.from_pretrained(\"laituan245/molt5-base\")\n", "inputs = tokenizer(\"CCO\", return_tensors=\"pt\")\n", "embeddings = model.encoder(**inputs).last_hidden_state.mean(dim=1) # 平均池化\n", "print(embeddings.shape)" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "100%|██████████| 1040/1040 [00:44<00:00, 23.35it/s]\n" ] } ], "source": [ "import pickle\n", "from transformers import T5ForConditionalGeneration, AutoTokenizer\n", "import torch\n", "import numpy as np\n", "from rdkit import Chem\n", "from tqdm import tqdm\n", "\n", "def smiles_to_molt5(smiles_list, model_name=\"laituan245/molt5-base\", batch_size=32, pooling=\"mean\"):\n", " \"\"\"\n", " 使用 MolT5 生成 SMILES 的嵌入向量（基于 encoder 的隐藏状态）\n", " \n", " 参数:\n", " smiles_list (list): SMILES 字符串列表\n", " model_name (str): Hugging Face 模型 ID，默认为 MolT5-base\n", " batch_size (int): 批处理大小，根据 GPU 内存调整\n", " pooling (str): 池化方法，可选 \"mean\"（平均池化）或 \"cls\"（取 CLS token）\n", " \n", " 返回:\n", " dict: 键为 SMILES，值为嵌入向量（numpy 数组）\n", " \"\"\"\n", " # 加载 MolT5 的 tokenizer 和模型\n", " model = T5ForConditionalGeneration.from_pretrained(model_name)\n", " tokenizer = AutoTokenizer.from_pretrained(model_name)\n", " model.eval()\n", " \n", " # 设备设置\n", " device = torch.device(\"cuda\" if torch.cuda.is_available() else \"cpu\")\n", " model.to(device)\n", " \n", " molt5_dict = {}\n", " \n", " # 分批处理\n", " for i in tqdm(range(0, len(smiles_list), batch_size)):\n", " batch_smiles = smiles_list[i:i+batch_size]\n", " valid_indices = []\n", " batch_inputs = []\n", " \n", " # 过滤无效 SMILES\n", " for idx, smiles in enumerate(batch_smiles):\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol is not None:\n", " valid_indices.append(idx)\n", " batch_inputs.append(smiles)\n", " else:\n", " print(f\"Invalid SMILES: {smiles}\")\n", " molt5_dict[smiles] = np.zeros(model.config.d_model, dtype=np.float32) # 填充零向量\n", " \n", " if not batch_inputs:\n", " continue\n", " \n", " # Tokenize 并生成嵌入\n", " inputs = tokenizer(\n", " batch_inputs,\n", " return_tensors=\"pt\",\n", " padding=True,\n", " truncation=True,\n", " max_length=512\n", " ).to(device)\n", " \n", " with torch.no_grad():\n", " # 获取 encoder 的隐藏状态（形状: [batch_size, seq_len, hidden_dim]）\n", " encoder_outputs = model.encoder(**inputs)\n", " hidden_states = encoder_outputs.last_hidden_state\n", " \n", " # 池化策略\n", " if pooling == \"mean\":\n", " embeddings = hidden_states.mean(dim=1) # 平均池化\n", " elif pooling == \"cls\":\n", " embeddings = hidden_states[:, 0, :] # CLS token\n", " else:\n", " raise ValueError(\"pooling 必须是 'mean' 或 'cls'\")\n", " \n", " # 存储结果\n", " for j, idx in enumerate(valid_indices):\n", " molt5_dict[batch_smiles[idx]] = embeddings[j].cpu().numpy()\n", " \n", " return molt5_dict\n", "\n", "# 使用示例\n", "smiles_list = standardized_smiles # 假设 idx2smi 是 SMILES 字典\n", "molt5_embeddings = smiles_to_molt5(smiles_list, batch_size=64, pooling=\"mean\")" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "66530\n" ] } ], "source": [ "print(len(molt5_embeddings))" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "字典已成功保存到 /home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/molt5_emb768.pickle\n" ] } ], "source": [ "# 保存字典为pickle文件\n", "pickle_path = '/home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/molt5_emb768.pickle'\n", "with open(pickle_path, 'wb') as pickle_file:\n", " pickle.dump(molt5_embeddings, pickle_file)\n", "\n", "print(f\"字典已成功保存到 {pickle_path}\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate Chemprop embedding for all smiles" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# git clone https://github.com/chemprop/chemprop.git\n", "# https://chemprop.readthedocs.io/en/main/installation.html\n", "\n", "chemprop fingerprint --test-path ./image_all_unique_smiles.csv --model-path /home/bob/boom/VCBench/Molecule_encoder/chemprop/tests/data/example_model_v2_regression_mol.ckpt --output /home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/fps.csv --ffn-block-index -2" ] }, { "cell_type": "code", "execution_count": 40, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "66530" ] }, "execution_count": 40, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import csv\n", "import numpy as np\n", "\n", "# CSV文件路径\n", "csv1_path = 'image_all_unique_smiles.csv'\n", "csv2_path = '/home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/fps_0.csv'\n", "\n", "# 初始化一个空字典来存储SMILES和对应的表征\n", "smiles_to_representation = {}\n", "\n", "# 读取第一个CSV文件（SMILES信息）\n", "smiles_list = []\n", "with open(csv1_path, mode='r', newline='', encoding='utf-8') as csvfile:\n", " reader = csv.DictReader(csvfile)\n", " for row in reader:\n", " smiles = row['SMILES'] # 假设CSV文件中列名为'SMILES'\n", " smiles_list.append(smiles)\n", "\n", "# 读取第二个CSV文件（表征信息），跳过第一行\n", "representation_list = []\n", "with open(csv2_path, mode='r', newline='', encoding='utf-8') as csvfile:\n", " reader = csv.reader(csvfile)\n", " next(reader) # 跳过第一行\n", " for row in reader:\n", " # 将字符串转换为浮点数\n", " representation = [np.float32(x) for x in row] # 假设表征信息是整行数据\n", " representation_list.append(representation)\n", "\n", "# 将列表转换为numpy数组\n", "representation_array = np.array(representation_list)\n", "\n", "# 将SMILES和对应的表征合并到字典中\n", "for smiles, representation in zip(smiles_list, representation_array):\n", " smiles_to_representation[smiles] = representation\n", "\n", "len(smiles_to_representation)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "import pickle\n", "# 保存字典为pickle文件\n", "pickle_path = '/home/bob/boom/VCBench/Molecule_encoder/embeddings/Image/Chemprop_emb300.pickle'\n", "with open(pickle_path, 'wb') as pickle_file:\n", " pickle.dump(smiles_to_representation, pickle_file)\n", "\n", "print(f\"字典已成功保存到 {pickle_path}\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate MolCLR embedding for all smiles\n", "\n", "## see MolCLR/Get_emd.ipynb\n", "\n", "### We use GIN model, which has a better performance in their paper" ] }, { "cell_type": "markdown", "metadata": {}, "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Generate Mole-BERT embedding for all smiles\n", "\n", "## see Mole-BERT/Get_emd.ipynb\n", "\n", "### We use GNN_graphpred model, which has a better performance in their paper" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# 3D UniMol" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# pip install unimol_tools" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "2025-08-27 22:42:16 | unimol_tools/models/unimolv2.py | 161 | INFO | Uni-Mol Tools | Loading pretrained weights from /home/bob/anaconda3/envs/boom/lib/python3.11/site-packages/unimol_tools/weights/modelzoo/310M/checkpoint.pt\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "开始生成66530个SMILES的嵌入表示...\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "处理SMILES: 0%| | 0/66530 [00:00" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "print(len(unimol_feat))\n", "\n", "unimol_feat.keys" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { 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