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iwatobipen/dgltest_IFG.ipynb

Created December 14, 2019 11:05
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added DGL example with functional features
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dgltest_IFG.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"RDKit WARNING: [19:30:17] Enabling RDKit 2019.09.2 jupyter extensions\n"
]
}
],
"source": [
"%matplotlib inline \n",
"import matplotlib.pyplot as plt\n",
"import os\n",
"import sys\n",
"from rdkit import Chem\n",
"from rdkit import RDPaths\n",
"\n",
"ifgs_path = os.path.join(RDPaths.RDContribDir, 'IFG')\n",
"sys.path.append(ifgs_path)\n",
"import dgl\n",
"import numpy as np\n",
"import random\n",
"import torch\n",
"import torch.nn as nn\n",
"import torch.nn.functional as F\n",
"from torch.utils.data import DataLoader\n",
"from torch.utils.data import Dataset\n",
"from dgl import model_zoo\n",
"\n",
"from dgl.data.chem.utils import mol_to_complete_graph, mol_to_bigraph\n",
"\n",
"from dgl.data.chem.utils import atom_type_one_hot\n",
"from dgl.data.chem.utils import atom_degree_one_hot\n",
"from dgl.data.chem.utils import atom_formal_charge\n",
"from dgl.data.chem.utils import atom_num_radical_electrons\n",
"from dgl.data.chem.utils import atom_hybridization_one_hot\n",
"from dgl.data.chem.utils import atom_total_num_H_one_hot\n",
"from dgl.data.chem.utils import one_hot_encoding\n",
"from dgl.data.chem import CanonicalAtomFeaturizer\n",
"from dgl.data.chem import CanonicalBondFeaturizer\n",
"from dgl.data.chem import ConcatFeaturizer\n",
"from dgl.data.chem import BaseAtomFeaturizer\n",
"from dgl.data.chem import BaseBondFeaturizer\n",
"\n",
"from dgl.data.chem import one_hot_encoding\n",
"from dgl.data.utils import split_dataset\n",
"\n",
"from functools import partial\n",
"from sklearn.metrics import roc_auc_score\n",
"\n",
"import ifgutil"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"torch.cuda.is_available()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"def chirality(atom):\n",
" try:\n",
" return one_hot_encoding(atom.GetProp('_CIPCode'), ['R', 'S']) + \\\n",
" [atom.HasProp('_ChiralityPossible')]\n",
" except:\n",
" return [False, False] + [atom.HasProp('_ChiralityPossible')]\n",
" \n",
"def collate_molgraphs(data):\n",
" \"\"\"Batching a list of datapoints for dataloader.\n",
" Parameters\n",
" ----------\n",
" data : list of 3-tuples or 4-tuples.\n",
" Each tuple is for a single datapoint, consisting of\n",
" a SMILES, a DGLGraph, all-task labels and optionally\n",
" a binary mask indicating the existence of labels.\n",
" Returns\n",
" -------\n",
" smiles : list\n",
" List of smiles\n",
" bg : BatchedDGLGraph\n",
" Batched DGLGraphs\n",
" labels : Tensor of dtype float32 and shape (B, T)\n",
" Batched datapoint labels. B is len(data) and\n",
" T is the number of total tasks.\n",
" masks : Tensor of dtype float32 and shape (B, T)\n",
" Batched datapoint binary mask, indicating the\n",
" existence of labels. If binary masks are not\n",
" provided, return a tensor with ones.\n",
" \"\"\"\n",
" assert len(data[0]) in [3, 4], \\\n",
" 'Expect the tuple to be of length 3 or 4, got {:d}'.format(len(data[0]))\n",
" if len(data[0]) == 3:\n",
" smiles, graphs, labels = map(list, zip(*data))\n",
" masks = None\n",
" else:\n",
" smiles, graphs, labels, masks = map(list, zip(*data))\n",
"\n",
" bg = dgl.batch(graphs)\n",
" bg.set_n_initializer(dgl.init.zero_initializer)\n",
" bg.set_e_initializer(dgl.init.zero_initializer)\n",
" labels = torch.stack(labels, dim=0)\n",
" \n",
" if masks is None:\n",
" masks = torch.ones(labels.shape)\n",
" else:\n",
" masks = torch.stack(masks, dim=0)\n",
" return smiles, bg, labels, masks\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"train=os.path.join(RDPaths.RDDocsDir, 'Book/data/solubility.train.sdf')\n",
"test=os.path.join(RDPaths.RDDocsDir, 'Book/data/solubility.test.sdf')"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"train_mols = Chem.SDMolSupplier(train)\n",
"train_mols = [ifgutil.map_fgs(mol) for mol in train_mols]\n",
"\n",
"train_smi =[Chem.MolToSmiles(m) for m in train_mols]\n",
"train_sol = torch.tensor([float(mol.GetProp('SOL')) for mol in train_mols]).reshape(-1,1)\n",
"\n",
"test_mols = Chem.SDMolSupplier(test)\n",
"test_mols = [ifgutil.map_fgs(mol) for mol in test_mols]\n",
"\n",
"test_smi = [Chem.MolToSmiles(m) for m in test_mols]\n",
"\n",
"\n",
"test_sol = torch.tensor([float(mol.GetProp('SOL')) for mol in test_mols]).reshape(-1,1)\n",
"\n",
"ifglist = ifgutil.make_ifg_list(train_mols)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['', 'c1cOCO1', 'O=C1ccC(=O)N1', 'CNC(=S)NC', 'C=C(C)C(=O)OC', 'CC(=O)NN(C)C', 'cOC(C)=O', 'CSP(=O)(SC)SC', 'c-n(c)nc', 'cOC(=O)NC', 'c=NC(C)=O', 'cBr', 'CC1=NccC(O)N1C', 'COC(C)O', 'cC(c)=CC', 'O=C1CC(=O)NC(=O)N1', 'COP(=S)(OC)SCSC', 'c-n(c)n(c)C', 'CC(=O)C=C(C)C', 'C=CC(C)=O', 'cnnc', 'cC(c)=C(Cl)Cl', 'COC(N)=O', 'cS(N)(=O)=O', 'cN1CCNC1=O', 'COP(=S)(OC)N1C(=O)ccC1=O', 'cSc', 'cS', 'COP(=S)(OC)SC(C)N1C(=O)ccC1=O', 'CC1=CC(=O)C=CC1', 'IC=CI', 'cS(=O)(=O)NC(C)=O', 'C=C(Cl)Cl', 'cF', 'C=CC#N', 'O=C1CC=NC=N1', 'cS(=O)(=O)NC(=N)N', 'CC1CO1', 'cNC(=O)Nc', 'C=C(C)Cl', 'ClC=C(Cl)Cl', 'COP(=S)(OC)SCSP(=S)(OC)OC', 'CC(Cl)=C(Cl)Cl', 'csc', 'CNC(C)=O', 'CC=C(C)C', 'CSC(C)=O', 'cNC(C)=O', 'C=CC=C', 'CC(=O)NC(N)=O', 'cN(c)N=O', 'cNO', 'CNN', 'cC(c)=O', 'cN1C(=O)ccNC1C', 'COCOC', 'cnc', 'CC1=CC(=O)ccC1=O', 'CS', 'CC(=O)C=C(C)OC(=O)N(C)C', 'N#CN=C(N)N', 'cnoc', 'CSN1C(=O)CCC1=O', 'CO', 'cS(C)=O', 'S=C1NCCN1', 'cNC(=O)N(C)C', 'CN1C(=O)ccNS1(=O)=O', 'O=C1NC(=O)C(=O)C(=O)N1', 'CCl', 'cS(c)(=O)=O', 'cC=CC=CC(=O)N(C)C', 'CC(=O)NC(C)=O', 'CBr', 'cNC=O', 'CNC(=O)ON=C(C)C', 'cC(=O)NC(c)=O', 'cNC(c)=O', 'cOS(C)(=O)=O', 'COC=O', 'C=C(C)C', 'cNC(=O)C1=C(O)ccS(=O)(=O)N1C', 'CC1=C(C)C(=O)C=CC1', 'CC1OC1C', 'C=COC', 'cNNc', 'ClC1=C(Cl)C(Cl)=C(Cl)C1', 'cN(C)C', 'CC=C(Cl)Cl', 'CN(C)N=O', 'cOC(C)OC', 'CSC(=S)N(C)C', 'NC(N)=O', 'CNC(=N)N', 'CN(C)C(=O)N(C)C', 'cC=O', 'O=C1CNC(=O)N1', 'O=C1CCC(=O)N1', 'c[N+](=O)[O-]', 'CSC', 'O=C1NC(=O)C(=O)N1', 'cOc', 'CC(O)N(C)C', 'cC=CC(=O)OC', 'COC(C)=O', 'cS(=O)(=O)NC(=O)NN(C)C', 'C=CC', 'cC(C)=O', 'COC(=O)C=CC1OC1C', 'CS(C)=O', 'cNC(=O)N(C)OC', 'cC(=C)C(=O)O', 'CC1(C)OCCO1', 'O=C1CC(=O)NCN1', 'c-n(c)oc', 'cN(C(C)=O)S(c)(=O)=O', 'C[Sn](C)(C)O', 'C#CC', 'cn(c)c', 'cC(=O)C(C)=C(C)O', 'cC1OCCO1', 'CN(N=O)C(N)=O', 'cCl', 'cSCSP(=S)(OC)OC', 'C[N+](=O)[O-]', 'CNC(N)=O', 'cN=Nc', 'cNc', 'CC(Cl)=C(C)Cl', 'cC=CC(=O)n(c)c', 'CC=CC', 'cnn(c)C', 'CC#N', 'cOP(=O)(Oc)Oc', 'NC(=O)NC1NC(=O)NC1=O', 'CC#CC', 'N=C(N)N[N+](=O)[O-]', 'CC(=O)C(C(N)=O)=C(C)O', 'cN(c)C', 'COC(C)(C)O', 'COC1COC(C)O1', 'cN=CN(C)C=Nc', 'COC(C)OC', 'O=C1ccS(=O)(=O)N1', 'CC(NC=O)N(C)C', 'CNC(=O)N(C)C', 'C=CC=O', 'c1cnsn1', 'CSC(=O)N(C)C', 'CC=C(C)C(C)=CC(C)=O', 'cNS(C)(=O)=O', 'COC', 'cC(=O)n(c)c', 'CC(C)=CC=O', 'cN1C(=O)CC(=O)N1c', 'cN(C)C(C)=O', 'CNC', 'O=S1(=O)ccN=CN1', 'CC(=O)O', 'CC(=O)N(C)C', 'cNC(=O)C(C)=C(C)OC', 'CC=CC(C)=CC(=O)OC', 'cOP(=S)(OC)OC', 'CNC(=O)N1CCNC1=O', 'cC(=O)O', 'cOC', 'c[nH]c', 'cO', 'cC=CC(=O)O', 'cn(c)C', 'CF', 'CN1CSC(=S)N(C)C1', 'CC(N)=O', 'cN(COC)C(C)=O', 'cC#N', 'cNC(=O)OC', 'CO[N+](=O)[O-]', 'cn[nH]c', 'CC=CC=O', 'cSC', 'COP(=S)(OC)SCN1C(=O)ccC1=O', 'cNC(=O)C1=C(C)OCCS1', 'cC=NO', 'cC(=O)NC', 'O=C1ccC(=O)O1', 'C=C(C)C(=O)O', 'cS(=O)(=O)NC(=O)NC', 'CC=C(Cl)C1=CC(=O)C=CC1', 'ClC=CCl', 'CC(=O)C=C(C)O', 'cC=Cc', 'CS(C)(=O)=O', 'cNS(c)(=O)=O', 'CC=O', 'O=S1(=O)ccNCN1', 'COP(=O)(OC)OC', 'cN=CN(C)C', 'cNC(=O)NC(c)=O', 'cC(=O)NN', 'CC=CC(C)=O', 'CC=C(C)C(C)=O', 'ClC(Cl)=CC(Cl)=C(Cl)Cl', 'cNC(=O)NN', 'cNC(N)=S', 'c[n+](c)[O-]', 'cN', 'cOC(=O)N(C)C', 'CN', 'cS(=O)(=O)NC', 'CC=CC=CC=CC=CC', 'O=C1CC(=O)NC(=S)N1', 'NC(=O)NO', 'c-n(c)c', 'cC=C', 'C=CC(=O)OC', 'CC(C)=O', 'CC1NccS(=O)(=O)N1', 'CC(=O)NO', 'O=C(O)C(=O)O', 'cOC(c)=O', 'CC1NccC(=O)N1', 'CC=CC=CC(=O)O', 'ClC(Cl)=C(Cl)Cl', 'c1c[nH]nn1', 'COP(=S)(OC)SC', 'coc', 'cNN', 'cC(C)=C(c)C', 'cC=CC', 'cC(c)=NC', 'cC1=NC(O)C(=O)Ncc1', 'CSS(C)=O', 'CI', 'cC(=O)OC', 'C=CC(=C)C', 'CN(C)C', 'CN1C(=O)CC(=O)NC1=O', 'c=O', 'cN=C=S', 'cNC(=O)NC', 'O=C1CN(Cl)C(=O)N1Cl', 'cC(N)=O', 'cNC', 'cI']\n"
]
}
],
"source": [
"print(ifglist)\n",
"fgdim = len(ifglist) + 1"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"atom_featurizer = BaseAtomFeaturizer(\n",
" {'hv': ConcatFeaturizer([\n",
" #partial(atom_type_one_hot, allowable_set=[\n",
" # 'B', 'C', 'N', 'O', 'F', 'Si', 'P', 'S', 'Cl', 'As', 'Se', 'Br', 'Te', 'I', 'At'],\n",
" # encode_unknown=True),\n",
" #partial(atom_degree_one_hot, allowable_set=list(range(6))),\n",
" #atom_formal_charge, atom_num_radical_electrons,\n",
" #partial(atom_hybridization_one_hot, encode_unknown=True),\n",
" #lambda atom: [0], # A placeholder for aromatic information,\n",
" #atom_total_num_H_one_hot, chirality, \n",
" partial(ifgutil.atom_ifg_one_hot, allowable_set=ifglist, encode_unknown=True)\n",
" ],\n",
" )})\n",
"bond_featurizer = BaseBondFeaturizer({\n",
" 'he': lambda bond: [0 for _ in range(10)]\n",
" })"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"train_graph =[mol_to_bigraph(mol,\n",
" atom_featurizer=atom_featurizer, \n",
" bond_featurizer=bond_featurizer) for mol in train_mols]\n",
"\n",
"test_graph =[mol_to_bigraph(mol,\n",
" atom_featurizer=atom_featurizer, \n",
" bond_featurizer=bond_featurizer) for mol in test_mols]"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"def run_a_train_epoch(n_epochs, epoch, model, data_loader,loss_criterion, optimizer):\n",
" model.train()\n",
" total_loss = 0\n",
" losses = []\n",
" \n",
" for batch_id, batch_data in enumerate(data_loader):\n",
" batch_data\n",
" smiles, bg, labels, masks = batch_data\n",
" if torch.cuda.is_available():\n",
" bg.to(torch.device('cuda'))\n",
" labels = labels.to('cuda')\n",
" masks = masks.to('cuda')\n",
" \n",
" prediction = model(bg, bg.ndata['hv'], bg.edata['he'])\n",
" loss = (loss_criterion(prediction, labels)*(masks != 0).float()).mean()\n",
" #loss = loss_criterion(prediction, labels)\n",
" #print(loss.shape)\n",
" optimizer.zero_grad()\n",
" loss.backward()\n",
" optimizer.step()\n",
" \n",
" losses.append(loss.data.item())\n",
" \n",
" #total_score = np.mean(train_meter.compute_metric('rmse'))\n",
" total_score = np.mean(losses)\n",
" print('epoch {:d}/{:d}, training {:.4f}'.format( epoch + 1, n_epochs, total_score))\n",
" return total_score"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"model = model_zoo.chem.AttentiveFP(#node_feat_size=39 + fgdim,\n",
" fgdim,\n",
" edge_feat_size=10,\n",
" num_layers=2,\n",
" num_timesteps=2,\n",
" graph_feat_size=200,\n",
" output_size=1,\n",
" dropout=0.2)\n",
"model = model.to('cuda')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"train_loader = DataLoader(dataset=list(zip(train_smi, train_graph, train_sol)), batch_size=128, collate_fn=collate_molgraphs)\n",
"test_loader = DataLoader(dataset=list(zip(test_smi, test_graph, test_sol)), batch_size=128, collate_fn=collate_molgraphs)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"epoch 1/100, training 6.0706\n",
"epoch 2/100, training 4.2468\n",
"epoch 3/100, training 2.7949\n",
"epoch 4/100, training 2.9024\n",
"epoch 5/100, training 3.0140\n",
"epoch 6/100, training 2.7901\n",
"epoch 7/100, training 1.9336\n",
"epoch 8/100, training 1.2830\n",
"epoch 9/100, training 1.3337\n",
"epoch 10/100, training 1.0717\n",
"epoch 11/100, training 1.1327\n",
"epoch 12/100, training 0.8222\n",
"epoch 13/100, training 1.2354\n",
"epoch 14/100, training 1.5881\n",
"epoch 15/100, training 0.8822\n",
"epoch 16/100, training 0.8301\n",
"epoch 17/100, training 0.9532\n",
"epoch 18/100, training 0.7896\n",
"epoch 19/100, training 0.5269\n",
"epoch 20/100, training 0.5431\n",
"epoch 21/100, training 0.5812\n",
"epoch 22/100, training 0.5527\n",
"epoch 23/100, training 0.5264\n",
"epoch 24/100, training 0.5756\n",
"epoch 25/100, training 0.4722\n",
"epoch 26/100, training 0.4201\n",
"epoch 27/100, training 0.4303\n",
"epoch 28/100, training 0.4114\n",
"epoch 29/100, training 0.3959\n",
"epoch 30/100, training 0.4454\n",
"epoch 31/100, training 0.4130\n",
"epoch 32/100, training 0.3977\n",
"epoch 33/100, training 0.4509\n",
"epoch 34/100, training 0.5423\n",
"epoch 35/100, training 0.4124\n",
"epoch 36/100, training 0.4027\n",
"epoch 37/100, training 0.3750\n",
"epoch 38/100, training 0.3306\n",
"epoch 39/100, training 0.3237\n",
"epoch 40/100, training 0.3613\n",
"epoch 41/100, training 0.3357\n",
"epoch 42/100, training 0.4632\n",
"epoch 43/100, training 0.4778\n",
"epoch 44/100, training 0.5378\n",
"epoch 45/100, training 0.5644\n",
"epoch 46/100, training 0.5662\n",
"epoch 47/100, training 0.4865\n",
"epoch 48/100, training 0.5088\n",
"epoch 49/100, training 0.7667\n",
"epoch 50/100, training 0.4411\n",
"epoch 51/100, training 0.4709\n",
"epoch 52/100, training 0.4541\n",
"epoch 53/100, training 0.3361\n",
"epoch 54/100, training 0.3615\n",
"epoch 55/100, training 0.3730\n",
"epoch 56/100, training 0.3709\n",
"epoch 57/100, training 0.4130\n",
"epoch 58/100, training 0.3628\n",
"epoch 59/100, training 0.3524\n",
"epoch 60/100, training 0.3191\n",
"epoch 61/100, training 0.3162\n",
"epoch 62/100, training 0.3178\n",
"epoch 63/100, training 0.3277\n",
"epoch 64/100, training 0.3161\n",
"epoch 65/100, training 0.3177\n",
"epoch 66/100, training 0.2966\n",
"epoch 67/100, training 0.2809\n",
"epoch 68/100, training 0.3048\n",
"epoch 69/100, training 0.3551\n",
"epoch 70/100, training 0.3869\n",
"epoch 71/100, training 0.4835\n",
"epoch 72/100, training 0.5968\n",
"epoch 73/100, training 0.4076\n",
"epoch 74/100, training 0.4718\n",
"epoch 75/100, training 0.4638\n",
"epoch 76/100, training 0.3073\n",
"epoch 77/100, training 0.2900\n",
"epoch 78/100, training 0.2851\n",
"epoch 79/100, training 0.2569\n",
"epoch 80/100, training 0.2796\n",
"epoch 81/100, training 0.2923\n",
"epoch 82/100, training 0.3972\n",
"epoch 83/100, training 0.3872\n",
"epoch 84/100, training 0.3795\n",
"epoch 85/100, training 0.4009\n",
"epoch 86/100, training 0.3622\n",
"epoch 87/100, training 0.2777\n",
"epoch 88/100, training 0.2645\n",
"epoch 89/100, training 0.2659\n",
"epoch 90/100, training 0.2613\n",
"epoch 91/100, training 0.2628\n",
"epoch 92/100, training 0.2569\n",
"epoch 93/100, training 0.2495\n",
"epoch 94/100, training 0.2563\n",
"epoch 95/100, training 0.2598\n",
"epoch 96/100, training 0.2329\n",
"epoch 97/100, training 0.2518\n",
"epoch 98/100, training 0.2490\n",
"epoch 99/100, training 0.2835\n",
"epoch 100/100, training 0.3677\n"
]
}
],
"source": [
"loss_fn = nn.MSELoss(reduction='none')\n",
"optimizer = torch.optim.Adam(model.parameters(), lr=10 ** (-2.5), weight_decay=10 ** (-5.0),)\n",
"n_epochs = 100\n",
"epochs = []\n",
"scores = []\n",
"for e in range(n_epochs):\n",
" score = run_a_train_epoch(n_epochs, e, model, train_loader, loss_fn, optimizer)\n",
" epochs.append(e)\n",
" scores.append(score)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[<matplotlib.lines.Line2D at 0x7f580402bcf8>]"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"image/png": 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\n",
"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"source": [
"plt.plot(epochs, scores)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"AttentiveFP(\n",
" (init_context): GetContext(\n",
" (project_node): Sequential(\n",
" (0): Linear(in_features=245, out_features=200, bias=True)\n",
" (1): LeakyReLU(negative_slope=0.01)\n",
" )\n",
" (project_edge1): Sequential(\n",
" (0): Linear(in_features=255, out_features=200, bias=True)\n",
" (1): LeakyReLU(negative_slope=0.01)\n",
" )\n",
" (project_edge2): Sequential(\n",
" (0): Dropout(p=0.2, inplace=False)\n",
" (1): Linear(in_features=400, out_features=1, bias=True)\n",
" (2): LeakyReLU(negative_slope=0.01)\n",
" )\n",
" (attentive_gru): AttentiveGRU1(\n",
" (edge_transform): Sequential(\n",
" (0): Dropout(p=0.2, inplace=False)\n",
" (1): Linear(in_features=200, out_features=200, bias=True)\n",
" )\n",
" (gru): GRUCell(200, 200)\n",
" )\n",
" )\n",
" (gnn_layers): ModuleList(\n",
" (0): GNNLayer(\n",
" (project_edge): Sequential(\n",
" (0): Dropout(p=0.2, inplace=False)\n",
" (1): Linear(in_features=400, out_features=1, bias=True)\n",
" (2): LeakyReLU(negative_slope=0.01)\n",
" )\n",
" (attentive_gru): AttentiveGRU2(\n",
" (project_node): Sequential(\n",
" (0): Dropout(p=0.2, inplace=False)\n",
" (1): Linear(in_features=200, out_features=200, bias=True)\n",
" )\n",
" (gru): GRUCell(200, 200)\n",
" )\n",
" )\n",
" )\n",
" (readouts): ModuleList(\n",
" (0): GlobalPool(\n",
" (compute_logits): Sequential(\n",
" (0): Linear(in_features=400, out_features=1, bias=True)\n",
" (1): LeakyReLU(negative_slope=0.01)\n",
" )\n",
" (project_nodes): Sequential(\n",
" (0): Dropout(p=0.2, inplace=False)\n",
" (1): Linear(in_features=200, out_features=200, bias=True)\n",
" )\n",
" (gru): GRUCell(200, 200)\n",
" )\n",
" (1): GlobalPool(\n",
" (compute_logits): Sequential(\n",
" (0): Linear(in_features=400, out_features=1, bias=True)\n",
" (1): LeakyReLU(negative_slope=0.01)\n",
" )\n",
" (project_nodes): Sequential(\n",
" (0): Dropout(p=0.2, inplace=False)\n",
" (1): Linear(in_features=200, out_features=200, bias=True)\n",
" )\n",
" (gru): GRUCell(200, 200)\n",
" )\n",
" )\n",
" (predict): Sequential(\n",
" (0): Dropout(p=0.2, inplace=False)\n",
" (1): Linear(in_features=200, out_features=1, bias=True)\n",
" )\n",
")"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"model.eval()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"all_pred = []\n",
"for test_data in test_loader:\n",
" smi_lst, bg, labels, masks = test_data\n",
" if torch.cuda.is_available():\n",
" bg.to(torch.device('cuda:0'))\n",
" labels = labels.to('cuda:0')\n",
" masks = masks.to('cuda:0')\n",
" pred = model(bg, bg.ndata['hv'], bg.edata['he'])\n",
" all_pred.append(pred.data.cpu().numpy())"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"res = np.vstack(all_pred)"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(257, 1)"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"res.shape"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(257, 1)"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"test_sol.numpy().shape"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Text(0, 0.5, 'exp')"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"image/png": 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\n",
"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"source": [
"plt.clf()\n",
"plt.scatter(res, test_sol)\n",
"plt.xlabel('pred')\n",
"plt.ylabel('exp')"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"from sklearn.metrics import r2_score"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.8433981456967203\n"
]
}
],
"source": [
"print(r2_score(test_sol, res))"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [],
"source": [
"import copy\n",
"from rdkit.Chem import rdDepictor\n",
"from rdkit.Chem.Draw import rdMolDraw2D\n",
"from IPython.display import SVG\n",
"from IPython.display import display\n",
"import matplotlib\n",
"import matplotlib.cm as cm\n"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [],
"source": [
"def drawmol(idx, dataset, timestep):\n",
" smiles, graph, _ = dataset[idx]\n",
" print(smiles)\n",
" bg = dgl.batch([graph])\n",
" atom_feats, bond_feats = bg.ndata['hv'], bg.edata['he']\n",
" if torch.cuda.is_available():\n",
" print('use cuda')\n",
" bg.to(torch.device('cuda:0'))\n",
" atom_feats = atom_feats.to('cuda:0')\n",
" bond_feats = bond_feats.to('cuda:0')\n",
" \n",
" _, atom_weights = model(bg, atom_feats, bond_feats, get_node_weight=True)\n",
" assert timestep < len(atom_weights), 'Unexpected id for the readout round'\n",
" atom_weights = atom_weights[timestep]\n",
" min_value = torch.min(atom_weights)\n",
" max_value = torch.max(atom_weights)\n",
" atom_weights = (atom_weights - min_value) / (max_value - min_value)\n",
" \n",
" norm = matplotlib.colors.Normalize(vmin=0, vmax=1.28)\n",
" cmap = cm.get_cmap('Blues')\n",
" plt_colors = cm.ScalarMappable(norm=norm, cmap=cmap)\n",
" atom_colors = {i: plt_colors.to_rgba(atom_weights[i].data.item()) for i in range(bg.number_of_nodes())}\n",
"\n",
" mol = Chem.MolFromSmiles(smiles)\n",
" rdDepictor.Compute2DCoords(mol)\n",
" drawer = rdMolDraw2D.MolDraw2DSVG(280, 280)\n",
" drawer.SetFontSize(1)\n",
" op = drawer.drawOptions()\n",
" \n",
" mol = rdMolDraw2D.PrepareMolForDrawing(mol)\n",
" drawer.DrawMolecule(mol, highlightAtoms=range(bg.number_of_nodes()),\n",
" highlightBonds=[],\n",
" highlightAtomColors=atom_colors)\n",
" drawer.FinishDrawing()\n",
" svg = drawer.GetDrawingText()\n",
" svg = svg.replace('svg:', '')\n",
" if torch.cuda.is_available():\n",
" atom_weights = atom_weights.to('cpu')\n",
" return (Chem.MolFromSmiles(smiles), atom_weights.data.numpy(), svg)"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
"target = test_loader.dataset\n"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CCC(C)CC\n",
"use cuda\n"
]
},
{
"data": {
"image/svg+xml": [
"<svg baseProfile=\"full\" height=\"280px\" version=\"1.1\" viewBox=\"0 0 280 280\" width=\"280px\" xml:space=\"preserve\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
"<!-- END OF HEADER -->\n",
"<rect height=\"280\" style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"280\" x=\"0\" y=\"0\"> </rect>\n",
"<ellipse cx=\"248.062\" cy=\"77.6105\" rx=\"19.211\" ry=\"19.211\" style=\"fill:#F7FBFF;fill-rule:evenodd;stroke:#F7FBFF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"212.041\" cy=\"140\" rx=\"19.211\" ry=\"19.211\" style=\"fill:#F7FBFF;fill-rule:evenodd;stroke:#F7FBFF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"140\" cy=\"140\" rx=\"19.211\" ry=\"19.211\" style=\"fill:#F7FBFF;fill-rule:evenodd;stroke:#F7FBFF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"103.979\" cy=\"202.389\" rx=\"19.211\" ry=\"19.211\" style=\"fill:#F7FBFF;fill-rule:evenodd;stroke:#F7FBFF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"103.979\" cy=\"77.6105\" rx=\"19.211\" ry=\"19.211\" style=\"fill:#F7FBFF;fill-rule:evenodd;stroke:#F7FBFF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"31.9383\" cy=\"77.6105\" rx=\"19.211\" ry=\"19.211\" style=\"fill:#F7FBFF;fill-rule:evenodd;stroke:#F7FBFF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-0\" d=\"M 248.062,77.6105 L 212.041,140\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1\" d=\"M 212.041,140 L 140,140\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2\" d=\"M 140,140 L 103.979,202.389\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3\" d=\"M 140,140 L 103.979,77.6105\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 103.979,77.6105 L 31.9383,77.6105\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CC(C)CC(C)C\n",
"use cuda\n"
]
},
{
"data": {
"image/svg+xml": [
"<svg baseProfile=\"full\" height=\"280px\" version=\"1.1\" viewBox=\"0 0 280 280\" width=\"280px\" xml:space=\"preserve\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
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"use cuda\n"
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"use cuda\n"
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"use cuda\n"
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"use cuda\n"
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"use cuda\n"
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"CCc1ccccc1\n",
"use cuda\n"
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"Cc1cc(C)cc(C)c1\n",
"use cuda\n"
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"c1ccc2c(c1)CCC2\n",
"use cuda\n"
]
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"CC(C)Cc1ccccc1\n",
"use cuda\n"
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"CCCCCCc1ccccc1\n",
"use cuda\n"
]
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"text": [
"c1ccc(CCc2ccccc2)cc1\n",
"use cuda\n"
]
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"text": [
"CCc1cccc2ccccc12\n",
"use cuda\n"
]
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},
"metadata": {},
"output_type": "display_data"
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Cc1cc(C)c2ccccc2c1\n",
"use cuda\n"
]
},
{
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{
"name": "stdout",
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"text": [
"c1ccc2cc3ccccc3cc2c1\n",
"use cuda\n"
]
},
{
"data": {
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"<path class=\"bond-4\" d=\"M 141.329,106.6 L 168.261,122.149\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-6\" d=\"M 216.95,95.5727 L 255.425,117.786\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6\" d=\"M 218.279,106.6 L 245.211,122.149\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-10\" d=\"M 168.261,157.851 L 141.329,173.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 140,184.427 L 101.525,162.214\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 101.525,162.214 L 63.0497,184.427\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 91.3108,157.851 L 64.3782,173.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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},
"metadata": {},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Cc1c2ccccc2c(C)c2ccccc12\n",
"use cuda\n"
]
},
{
"data": {
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"<path class=\"bond-1\" d=\"M 140,184.427 L 178.475,162.214\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1\" d=\"M 141.329,173.4 L 168.261,157.851\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-16\" d=\"M 178.475,162.214 L 178.475,117.786\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-4\" d=\"M 255.425,162.214 L 255.425,117.786\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-8\" d=\"M 140,95.5727 L 140,51.1454\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-12\" d=\"M 33.46,124.45 L 33.46,155.55\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 24.5745,162.214 L 63.0497,184.427\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"</svg>"
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},
"metadata": {},
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{
"name": "stdout",
"output_type": "stream",
"text": [
"c1ccc2cc3cc4ccccc4cc3cc2c1\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-2\" d=\"M 52.3885,114.353 L 73.0692,126.293\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-16\" d=\"M 73.0692,153.707 L 52.3885,165.647\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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{
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"text": [
"c1ccc2c(c1)ccc1c3ccccc3ccc21\n",
"use cuda\n"
]
},
{
"data": {
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"<svg baseProfile=\"full\" height=\"280px\" version=\"1.1\" viewBox=\"0 0 280 280\" width=\"280px\" xml:space=\"preserve\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
"<!-- END OF HEADER -->\n",
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"<path class=\"bond-14\" d=\"M 191.011,115.901 L 175.486,96.1407\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-16\" d=\"M 146.929,100.233 L 137.579,123.559\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"c1ccc2c(c1)ccc1nccnc12\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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},
"metadata": {},
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},
{
"name": "stdout",
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"text": [
"Nc1cc2c3ccccc3ccc2c2ccccc12\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-0\" d=\"M 89.9422,193.295 L 94.5047,183.635\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-0\" d=\"M 94.5047,183.635 L 99.0672,173.975\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1\" d=\"M 99.0672,173.975 L 134.885,171.019\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1\" d=\"M 103.849,166.368 L 128.921,164.299\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 99.0672,173.975 L 78.5983,144.434\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-13\" d=\"M 93.9474,111.936 L 73.4785,82.395\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-15\" d=\"M 37.6604,85.3509 L 22.3112,117.848\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 41.8575,93.2953 L 31.1131,116.043\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 22.3112,117.848 L 42.7801,147.39\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 42.7801,147.39 L 78.5983,144.434\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 47.5617,139.783 L 72.6344,137.714\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:23px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"58.9527\" y=\"219.651\"><tspan>NH</tspan><tspan style=\"baseline-shift:sub;font-size:17.25px;\">2</tspan><tspan/></text>\n",
"</svg>"
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},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Cc1ccc2cc3c(ccc4ccccc43)c3c2c1CC3\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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"use cuda\n"
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"use cuda\n"
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"use cuda\n"
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"CC(C)I\n",
"use cuda\n"
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"use cuda\n"
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"use cuda\n"
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"use cuda\n"
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"text": [
"CCCCCCCBr\n",
"use cuda\n"
]
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"text": [
"BrC=CBr\n",
"use cuda\n"
]
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"text": [
"ClC1=C(Cl)C2(Cl)C3C(Cl)C=CC3C1(Cl)C2(Cl)Cl\n",
"use cuda\n"
]
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"text": [
"ClC(Cl)=C(Cl)C(Cl)=C(Cl)Cl\n",
"use cuda\n"
]
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"text": [
"Brc1ccccc1\n",
"use cuda\n"
]
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"text": [
"Clc1ccccc1Br\n",
"use cuda\n"
]
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"Brc1cccc(Br)c1\n",
"use cuda\n"
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"Brc1ccc(Br)c(Br)c1\n",
"use cuda\n"
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"Clc1cc(Cl)c(Cl)c(Cl)c1Cl\n",
"use cuda\n"
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"Fc1cccc(F)c1\n",
"use cuda\n"
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"text": [
"Clc1ccc(-c2ccccc2)cc1\n",
"use cuda\n"
]
},
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"<path class=\"bond-11\" d=\"M 154.702,115.857 L 180.076,115.857\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"text": [
"Clc1ccc(-c2ccccc2Cl)cc1\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-10\" d=\"M 80.9965,165.966 L 86.3012,175.927\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 150.334,95.7092 L 186.58,96.9509\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<text style=\"font-size:24px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"226.173\" y=\"142.292\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:24px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"79.0394\" y=\"200.105\"><tspan>Cl</tspan></text>\n",
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Clc1ccc(Cl)c(-c2ccccc2Cl)c1\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-11\" d=\"M 233.172,137.603 L 203.328,132.17\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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{
"name": "stdout",
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"text": [
"Clc1ccc(-c2ccccc2Cl)cc1Cl\n",
"use cuda\n"
]
},
{
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"text": [
"Clc1cc(-c2ccccc2)c(Cl)c(Cl)c1Cl\n",
"use cuda\n"
]
},
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"text": [
"Clc1ccc(Cl)c(-c2c(Cl)cccc2Cl)c1\n",
"use cuda\n"
]
},
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{
"name": "stdout",
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"text": [
"Clc1ccc(Cl)c(-c2ccc(Cl)c(Cl)c2Cl)c1\n",
"use cuda\n"
]
},
{
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{
"name": "stdout",
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"text": [
"Clc1c(Cl)c(Cl)c(-c2ccccc2)c(Cl)c1Cl\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-5\" d=\"M 149.265,171.392 L 131.14,140\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-12\" d=\"M 131.14,140 L 149.265,108.608\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 94.8913,140 L 76.7669,108.608\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 85.8942,138.916 L 73.2071,116.941\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-8\" d=\"M 76.7669,108.608 L 40.518,108.608\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 40.518,108.608 L 22.3936,140\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 44.0779,116.941 L 31.3908,138.916\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10\" d=\"M 22.3936,140 L 40.518,171.392\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 40.518,171.392 L 76.7669,171.392\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 45.9554,164.143 L 71.3296,164.143\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 149.265,108.608 L 143.69,98.9529\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 143.69,98.9529 L 138.116,89.2981\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 149.265,108.608 L 185.513,108.608\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 154.702,115.857 L 180.076,115.857\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 185.513,108.608 L 191.088,98.9529\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 191.088,98.9529 L 196.662,89.2981\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:24px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"226.194\" y=\"152.083\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:24px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"189.945\" y=\"214.868\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:24px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"117.447\" y=\"214.868\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:24px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"117.447\" y=\"89.2981\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:24px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"189.945\" y=\"89.2981\"><tspan>Cl</tspan></text>\n",
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"metadata": {},
"output_type": "display_data"
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Clc1ccc(Cl)c(-c2cc(Cl)c(Cl)c(Cl)c2Cl)c1\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-10\" d=\"M 185.739,173.347 L 205.892,144.678\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-12\" d=\"M 205.892,144.678 L 191.14,112.89\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 191.14,112.89 L 197.111,104.396\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 197.111,104.396 L 203.082,95.9021\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 191.14,112.89 L 156.235,109.771\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 185.281,119.403 L 160.847,117.22\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 156.235,109.771 L 151.57,99.7181\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 151.57,99.7181 L 146.904,89.6648\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:23px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"12.7273\" y=\"201.223\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:23px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"93.3407\" y=\"86.5461\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:23px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"187.252\" y=\"216.817\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:23px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"227.559\" y=\"159.478\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:23px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"198.056\" y=\"95.9021\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:23px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"128.246\" y=\"89.6648\"><tspan>Cl</tspan></text>\n",
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"metadata": {},
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Clc1ccc(-c2ccc(Cl)c(Cl)c2Cl)c(Cl)c1Cl\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-15\" d=\"M 178.072,126.684 L 198.94,130.664\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 204.55,125.555 L 210.099,119.126\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"232.879\" y=\"170.02\"><tspan>Cl</tspan></text>\n",
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"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"44.1549\" y=\"187.537\"><tspan>Cl</tspan></text>\n",
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"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"212.916\" y=\"112.697\"><tspan>Cl</tspan></text>\n",
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},
"metadata": {},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Clc1cc(Cl)c(Cl)c(-c2c(Cl)c(Cl)cc(Cl)c2Cl)c1Cl\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-11\" d=\"M 228.453,178.301 L 235.254,190.081\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 235.254,190.081 L 242.055,201.86\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 228.453,178.301 L 250.566,140\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 224.11,168.133 L 239.589,141.323\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 250.566,140 L 228.453,101.699\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 228.453,101.699 L 235.254,89.9192\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 235.254,89.9192 L 242.055,78.1397\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 228.453,101.699 L 184.226,101.699\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 221.819,110.544 L 190.86,110.544\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 184.226,101.699 L 177.426,89.9192\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 177.426,89.9192 L 170.625,78.1397\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 95.7735,178.301 L 102.574,190.081\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 102.574,190.081 L 109.375,201.86\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"12.7273\" y=\"231.345\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"12.7273\" y=\"78.1397\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"101.18\" y=\"78.1397\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"145.407\" y=\"231.345\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"233.86\" y=\"231.345\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"233.86\" y=\"78.1397\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"145.407\" y=\"78.1397\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"101.18\" y=\"231.345\"><tspan>Cl</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Clc1ccc(C(c2ccc(Cl)cc2)C(Cl)Cl)cc1\n",
"use cuda\n"
]
},
{
"data": {
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"<path class=\"bond-7\" d=\"M 166.121,177.703 L 192.243,192.784\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-8\" d=\"M 193.145,185.298 L 211.429,174.741\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 218.364,177.703 L 225.728,181.954\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 225.728,181.954 L 233.091,186.206\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10\" d=\"M 218.364,177.703 L 218.364,147.541\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-13\" d=\"M 140,102.297 L 147.364,98.0457\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 147.364,98.0457 L 154.727,93.7943\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 140,102.297 L 132.636,98.0457\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 132.636,98.0457 L 125.273,93.7943\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 113.879,177.703 L 87.7575,192.784\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 106.944,174.741 L 88.6594,185.298\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"24.1211\" y=\"202.838\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"233.091\" y=\"202.838\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"154.727\" y=\"97.2702\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"102.485\" y=\"97.2702\"><tspan>Cl</tspan></text>\n",
"</svg>"
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},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Brc1ccc2ccccc2c1\n",
"use cuda\n"
]
},
{
"data": {
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"CC(O)C(C)(C)C\n",
"use cuda\n"
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"CCCCCCCCCCO\n",
"use cuda\n"
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"Cc1ccc(CO)cc1\n",
"use cuda\n"
]
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"use cuda\n"
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"Cc1cccc(O)c1\n",
"use cuda\n"
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"Cc1ccc(C(C)C)c(O)c1\n",
"use cuda\n"
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"Oc1ccc2ccccc2c1\n",
"use cuda\n"
]
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"CCCC=O\n",
"use cuda\n"
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"CCCCCCCCC=O\n",
"use cuda\n"
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"O=C1CCCCC1\n",
"use cuda\n"
]
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"CCCCCCCC(C)=O\n",
"use cuda\n"
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"<path class=\"bond-8\" d=\"M 233.755,136.479 L 234.445,125.119\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8\" d=\"M 226.244,147.424 L 226.933,136.065\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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},
"metadata": {},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"O=C1C=CC(=O)C=C1\n",
"use cuda\n"
]
},
{
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"text": [
"O=C(c1ccccc1)c1ccccc1\n",
"use cuda\n"
]
},
{
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"text": [
"O=C(O)CCC(=O)O\n",
"use cuda\n"
]
},
{
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"text": [
"CCCCCCCCCC(=O)O\n",
"use cuda\n"
]
},
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{
"name": "stdout",
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"text": [
"Cc1cccc(C(=O)O)c1\n",
"use cuda\n"
]
},
{
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"text": [
"O=C(O)C=Cc1ccccc1\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-9\" d=\"M 246.453,167.423 L 209.694,176.247\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<text style=\"font-size:25px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"35.4187\" y=\"124.226\"><tspan>HO</tspan></text>\n",
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"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"O=C(O)Cc1cccc2ccccc12\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-2\" d=\"M 84.6181,119.013 L 121.121,109.402\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-4\" d=\"M 153.492,143.657 L 146.542,169.15\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-10\" d=\"M 247.859,108.667 L 229.256,89.9023\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-12\" d=\"M 194.128,90.1779 L 184.2,126.597\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 199.922,97.6263 L 192.973,123.119\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"O=C(O)C(c1ccccc1)c1ccccc1\n",
"use cuda\n"
]
},
{
"data": {
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"<path class=\"bond-10\" d=\"M 92.6394,122.229 L 92.6394,91.13\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-12\" d=\"M 61.7212,73.2793 L 34.7885,88.8289\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 24.5745,84.4659 L 24.5745,128.893\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 24.5745,128.893 L 63.0497,151.107\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 34.7885,124.53 L 61.7212,140.08\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<text style=\"font-size:29px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"74.8578\" y=\"232.557\"><tspan>HO</tspan></text>\n",
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"text": [
"CCCCCCCCCCCCCC(=O)O\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-14\" d=\"M 231.706,146.241 L 234.599,148.016\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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{
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"text": [
"CCOC=O\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<path class=\"bond-3\" d=\"M 183.153,120.319 L 199.37,129.682\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3\" d=\"M 199.37,129.682 L 215.587,139.044\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"text": [
"CCOC(=O)CC\n",
"use cuda\n"
]
},
{
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"CCCC(=O)OCC\n",
"use cuda\n"
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"CCCOC(=O)CCC\n",
"use cuda\n"
]
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"CCCCCC(=O)OCC\n",
"use cuda\n"
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{
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"text": [
"CCCCCCCCC(=O)OCC\n",
"use cuda\n"
]
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{
"name": "stdout",
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"text": [
"COC(=O)c1ccccc1\n",
"use cuda\n"
]
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{
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"text": [
"CCCCOC(=O)c1ccccc1C(=O)OCCCC\n",
"use cuda\n"
]
},
{
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"CCOCC\n",
"use cuda\n"
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"COC(C)(C)C\n",
"use cuda\n"
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"CCCOC(C)C\n",
"use cuda\n"
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"COc1ccccc1\n",
"use cuda\n"
]
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"c1ccc(C2CO2)cc1\n",
"use cuda\n"
]
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"CCCCOCCO\n",
"use cuda\n"
]
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"text": [
"CC12CCC(=O)C=C1CCC1C2C(O)CC2(C)C1CCC2(O)C(=O)CO\n",
"use cuda\n"
]
},
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"<path class=\"bond-0\" d=\"M 175.898,159.405 L 186.082,139.412\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-3\" d=\"M 220.711,157.051 L 230.895,137.058\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 231.013,139.298 L 238.724,138.893\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-4\" d=\"M 230.777,134.817 L 238.488,134.412\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 238.488,134.412 L 246.199,134.007\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-12\" d=\"M 157.173,166.25 L 160.855,171.919\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 153.491,160.582 L 131.084,161.759\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 131.084,161.759 L 118.861,142.942\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 118.861,142.942 L 109.028,163.111\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 118.861,142.942 L 129.045,122.949\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-28\" d=\"M 118.861,142.942 L 96.6995,139.435\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-18\" d=\"M 113.178,107.085 L 93.1868,117.274\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-19\" d=\"M 93.1868,117.274 L 96.6995,139.435\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-20\" d=\"M 96.6995,139.435 L 95.4114,146.744\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-20\" d=\"M 95.4114,146.744 L 94.1233,154.053\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-21\" d=\"M 96.6995,139.435 L 74.2927,140.612\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 72.2934,139.594 L 69.1062,145.851\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 69.1062,145.851 L 65.919,152.108\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 76.292,141.63 L 73.1048,147.888\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 73.1048,147.888 L 69.9177,154.145\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-23\" d=\"M 74.2927,140.612 L 62.07,121.796\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-24\" d=\"M 62.07,121.796 L 57.6006,122.03\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-24\" d=\"M 57.6006,122.03 L 53.1312,122.265\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"246.317\" y=\"143.36\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"152.245\" y=\"186.877\"><tspan>OH</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"79.3373\" y=\"169.011\"><tspan>OH</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"57.1232\" y=\"168.085\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"26.1953\" y=\"130.452\"><tspan>HO</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CC(=O)OCC(=O)C1(O)CCC2C3CCC4=CC(=O)C=CC4(C)C3C(O)CC21C\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<path class=\"bond-4\" d=\"M 73.4877,136.774 L 86.4152,153.653\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 84.4517,152.838 L 81.8462,159.112\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 81.8462,159.112 L 79.2407,165.386\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 88.3787,154.468 L 85.7732,160.742\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 85.7732,160.742 L 83.1677,167.017\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6\" d=\"M 86.4152,153.653 L 107.497,150.897\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 107.497,150.897 L 105.104,144.48\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 105.104,144.48 L 102.711,138.063\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8\" d=\"M 107.497,150.897 L 108.034,172.151\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-28\" d=\"M 107.497,150.897 L 127.545,143.818\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 108.034,172.151 L 128.414,178.208\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10\" d=\"M 128.414,178.208 L 140.472,160.697\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 140.472,160.697 L 161.554,157.941\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-29\" d=\"M 140.472,160.697 L 127.545,143.818\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 161.554,157.941 L 174.482,174.821\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-30\" d=\"M 161.554,157.941 L 169.708,138.306\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-14\" d=\"M 195.563,172.065 L 203.717,152.43\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 203.717,152.43 L 224.799,149.674\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 206.328,147.8 L 221.085,145.871\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-31\" d=\"M 203.717,152.43 L 190.79,135.55\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 224.799,149.674 L 232.953,130.038\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 233.229,132.147 L 240.46,131.201\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 240.46,131.201 L 247.691,130.256\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 232.677,127.93 L 239.909,126.985\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 239.909,126.985 L 247.14,126.04\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 232.953,130.038 L 220.025,113.159\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-19\" d=\"M 220.025,113.159 L 198.944,115.915\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-19\" d=\"M 217.414,117.789 L 202.657,119.718\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-20\" d=\"M 198.944,115.915 L 190.79,135.55\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-21\" d=\"M 190.79,135.55 L 177.862,118.671\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 190.79,135.55 L 169.708,138.306\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-23\" d=\"M 169.708,138.306 L 156.781,121.427\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-24\" d=\"M 156.781,121.427 L 159.386,115.153\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-24\" d=\"M 159.386,115.153 L 161.992,108.879\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-25\" d=\"M 156.781,121.427 L 135.699,124.183\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-26\" d=\"M 135.699,124.183 L 127.545,143.818\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-27\" d=\"M 127.545,143.818 L 114.914,126.716\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"41.0135\" y=\"110.102\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"45.787\" y=\"146.617\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"71.6421\" y=\"180.375\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"87.3069\" y=\"138.063\"><tspan>OH</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"247.416\" y=\"134.369\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"152.173\" y=\"108.879\"><tspan>OH</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CC12CCC(=O)C=C1CCC1C2CCC2(C)C(C(=O)CO)CCC12\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<path class=\"bond-15\" d=\"M 118.046,143.211 L 96.3318,137.018\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-26\" d=\"M 118.046,143.211 L 130.647,124.474\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 96.3318,137.018 L 78.5574,150.944\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-20\" d=\"M 96.3318,137.018 L 95.5125,114.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 76.3217,151.262 L 77.3743,158.676\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 77.3743,158.676 L 78.4269,166.091\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 80.793,150.627 L 81.8456,158.042\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 81.8456,158.042 L 82.8982,165.456\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 78.5574,150.944 L 57.6093,142.514\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-19\" d=\"M 57.6093,142.514 L 53.5253,145.714\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-19\" d=\"M 53.5253,145.714 L 49.4413,148.914\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-21\" d=\"M 95.5125,114.452 L 116.721,106.699\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 116.721,106.699 L 130.647,124.474\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"246.183\" y=\"160.002\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"74.7011\" y=\"180.828\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"26.2811\" y=\"163.968\"><tspan>HO</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CC12CCC(=O)C=C1CCC1C3CCC(O)(C(=O)CO)C3(C)CC(O)C12F\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<ellipse cx=\"186.102\" cy=\"139.382\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#E5EFF9;fill-rule:evenodd;stroke:#E5EFF9;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<ellipse cx=\"64.1997\" cy=\"160.891\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#95C5DF;fill-rule:evenodd;stroke:#95C5DF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"62.0605\" cy=\"122.091\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#88BEDC;fill-rule:evenodd;stroke:#88BEDC;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<ellipse cx=\"109.12\" cy=\"163.279\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#6BAED6;fill-rule:evenodd;stroke:#6BAED6;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"131.169\" cy=\"161.87\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#B7D5EA;fill-rule:evenodd;stroke:#B7D5EA;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"153.57\" cy=\"160.635\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#95C5DF;fill-rule:evenodd;stroke:#95C5DF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"165.84\" cy=\"179.417\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#E4EEF8;fill-rule:evenodd;stroke:#E4EEF8;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"163.701\" cy=\"140.618\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#3282BE;fill-rule:evenodd;stroke:#3282BE;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<ellipse cx=\"169.54\" cy=\"152.509\" rx=\"5.9826\" ry=\"5.9826\" style=\"fill:#F7FBFF;fill-rule:evenodd;stroke:#F7FBFF;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-0\" d=\"M 181.605,151.843 L 186.102,139.382\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1\" d=\"M 186.102,139.382 L 198.371,158.165\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-26\" d=\"M 186.102,139.382 L 196.232,119.365\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-28\" d=\"M 186.102,139.382 L 163.701,140.618\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2\" d=\"M 198.371,158.165 L 220.772,156.929\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3\" d=\"M 220.772,156.929 L 230.903,136.912\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 231.027,139.152 L 238.735,138.727\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 238.735,138.727 L 246.443,138.302\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 230.779,134.672 L 238.488,134.247\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 238.488,134.247 L 246.196,133.822\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 230.903,136.912 L 218.633,118.13\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6\" d=\"M 218.633,118.13 L 196.232,119.365\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6\" d=\"M 215.52,122.796 L 199.839,123.66\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 196.232,119.365 L 183.962,100.583\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8\" d=\"M 183.962,100.583 L 161.562,101.818\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 161.562,101.818 L 151.431,121.835\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10\" d=\"M 151.431,121.835 L 129.03,123.071\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-27\" d=\"M 151.431,121.835 L 163.701,140.618\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 129.03,123.071 L 113.123,107.25\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-29\" d=\"M 129.03,123.071 L 118.899,143.088\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 113.123,107.25 L 93.1614,117.489\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 93.1614,117.489 L 96.7312,139.638\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 96.7312,139.638 L 95.462,146.951\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 95.462,146.951 L 94.1929,154.264\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 96.7312,139.638 L 74.3305,140.873\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-19\" d=\"M 96.7312,139.638 L 118.899,143.088\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 72.3288,139.86 L 69.1558,146.13\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 69.1558,146.13 L 65.9828,152.399\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 76.3322,141.887 L 73.1592,148.156\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 73.1592,148.156 L 69.9862,154.425\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 74.3305,140.873 L 62.0605,122.091\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 62.0605,122.091 L 57.5933,122.338\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 57.5933,122.338 L 53.126,122.584\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-20\" d=\"M 118.899,143.088 L 109.12,163.279\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-21\" d=\"M 118.899,143.088 L 131.169,161.87\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 131.169,161.87 L 153.57,160.635\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-23\" d=\"M 153.57,160.635 L 157.262,166.287\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-23\" d=\"M 157.262,166.287 L 160.955,171.939\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-24\" d=\"M 153.57,160.635 L 163.701,140.618\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-25\" d=\"M 163.701,140.618 L 164.784,142.824\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-25\" d=\"M 164.784,142.824 L 165.868,145.03\" style=\"fill:none;fill-rule:evenodd;stroke:#33CCCC;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"246.319\" y=\"143.155\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"79.4287\" y=\"169.221\"><tspan>OH</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"57.2152\" y=\"168.369\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"26.1935\" y=\"130.805\"><tspan>HO</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"152.374\" y=\"186.895\"><tspan>OH</tspan></text>\n",
"<text style=\"font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#33CCCC\" x=\"164.055\" y=\"159.987\"><tspan>F</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"O=C(O)c1ccccc1O\n",
"use cuda\n"
]
},
{
"data": {
"image/svg+xml": [
"<svg baseProfile=\"full\" height=\"280px\" version=\"1.1\" viewBox=\"0 0 280 280\" width=\"280px\" xml:space=\"preserve\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
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"text": [
"CCOC(=O)c1ccc(O)cc1\n",
"use cuda\n"
]
},
{
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"text": [
"Oc1ccccc1Cl\n",
"use cuda\n"
]
},
{
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"Oc1c(Cl)cc(Cl)cc1Cl\n",
"use cuda\n"
]
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"O=C(O)c1ccc(Cl)cc1\n",
"use cuda\n"
]
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"text": [
"ClC1=C(Cl)C2(Cl)C3C4CC(C5OC45)C3C1(Cl)C2(Cl)Cl\n",
"use cuda\n"
]
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"<path class=\"bond-1\" d=\"M 71.2374,120.324 L 71.2374,159.676\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-2\" d=\"M 71.2374,159.676 L 63.8806,166.537\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2\" d=\"M 63.8806,166.537 L 56.5237,173.398\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3\" d=\"M 71.2374,159.676 L 108.663,171.836\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-4\" d=\"M 104.714,183.991 L 100.765,196.145\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 108.663,171.836 L 146.089,159.676\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-20\" d=\"M 146.089,159.676 L 146.089,120.324\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 183.516,171.836 L 160.385,140\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-21\" d=\"M 183.516,171.836 L 220.942,159.676\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8\" d=\"M 160.385,140 L 183.516,108.164\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 183.516,108.164 L 220.942,120.324\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 183.516,108.164 L 146.089,120.324\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10\" d=\"M 220.942,120.324 L 231.856,126.625\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10\" d=\"M 231.856,126.625 L 242.77,132.927\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-22\" d=\"M 220.942,120.324 L 220.942,159.676\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 242.77,147.073 L 231.856,153.375\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 231.856,153.375 L 220.942,159.676\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 146.089,120.324 L 108.663,108.164\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 108.663,108.164 L 104.714,96.0092\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 104.714,96.0092 L 100.765,83.8548\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 108.663,108.164 L 85.5329,140\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 85.5329,140 L 74.5958,135.803\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 74.5958,135.803 L 63.6587,131.605\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 85.5329,140 L 74.5958,144.197\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 74.5958,144.197 L 63.6587,148.395\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:26px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"27.5926\" y=\"106.602\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:26px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"27.5926\" y=\"199.632\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:26px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"81.6377\" y=\"222.38\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:26px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"242.77\" y=\"153.117\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:26px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"81.6377\" y=\"83.8548\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:26px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"33.9281\" y=\"139.018\"><tspan>Cl</tspan></text>\n",
"<text style=\"font-size:26px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"33.9281\" y=\"167.217\"><tspan>Cl</tspan></text>\n",
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"text": [
"CCCCCCN\n",
"use cuda\n"
]
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"<path class=\"bond-2\" d=\"M 87.0975,149.302 L 119.321,130.698\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3\" d=\"M 119.321,130.698 L 151.545,149.302\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 151.545,149.302 L 183.769,130.698\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 183.769,130.698 L 188.066,133.178\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 188.066,133.178 L 192.362,135.659\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"text": [
"CCCCCCCCN\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-0\" d=\"M 20.645,147.423 L 46.3585,132.577\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1\" d=\"M 46.3585,132.577 L 72.0721,147.423\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2\" d=\"M 72.0721,147.423 L 97.7857,132.577\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3\" d=\"M 97.7857,132.577 L 123.499,147.423\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4\" d=\"M 123.499,147.423 L 149.213,132.577\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5\" d=\"M 149.213,132.577 L 174.926,147.423\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6\" d=\"M 174.926,147.423 L 200.64,132.577\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 200.64,132.577 L 204.068,134.557\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 204.068,134.557 L 207.497,136.536\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:19px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"205.894\" y=\"158.31\"><tspan>NH</tspan><tspan style=\"baseline-shift:sub;font-size:14.25px;\">2</tspan><tspan/></text>\n",
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"text": [
"CNc1ccccc1\n",
"use cuda\n"
]
},
{
"data": {
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"<svg baseProfile=\"full\" height=\"280px\" version=\"1.1\" viewBox=\"0 0 280 280\" width=\"280px\" xml:space=\"preserve\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
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"<path class=\"bond-0\" d=\"M 43.0686,136.962 L 57.0067,152.063\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1\" d=\"M 96.8544,161.199 L 113.856,157.365\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"CN(C)c1ccccc1\n",
"use cuda\n"
]
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"Nc1cccc2ccccc12\n",
"use cuda\n"
]
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"Cc1ccc(C)nc1\n",
"use cuda\n"
]
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"c1ccc2cnccc2c1\n",
"use cuda\n"
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"O=C(O)c1cccnc1\n",
"use cuda\n"
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"Cc1cc(N)nc(C)n1\n",
"use cuda\n"
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"<path class=\"bond-7\" d=\"M 97.3731,97.5894 L 115.11,97.5894\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"text": [
"c1cc[nH]c1\n",
"use cuda\n"
]
},
{
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"text": [
"Sc1nc2ccccc2s1\n",
"use cuda\n"
]
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"text": [
"Oc1ccc2ncccc2c1\n",
"use cuda\n"
]
},
{
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"<path class=\"bond-7\" d=\"M 249.334,107.561 L 209.604,92.2242\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7\" d=\"M 240.307,113.206 L 212.496,102.471\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8\" d=\"M 209.604,92.2242 L 176.457,118.962\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 176.457,118.962 L 136.728,103.626\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 167.431,124.608 L 139.62,113.872\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:28px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"38.2896\" y=\"129.223\"><tspan>HO</tspan></text>\n",
"<text style=\"font-size:28px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"210.465\" y=\"190.57\"><tspan>N</tspan></text>\n",
"</svg>"
],
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"<IPython.core.display.SVG object>"
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},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CCC1(CC)C(=O)NC(=O)N(C)C1=O\n",
"use cuda\n"
]
},
{
"data": {
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"<path class=\"bond-5\" d=\"M 89.5285,85.3497 L 77.4085,76.1855\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-11\" d=\"M 169.769,156.746 L 154.013,163.404\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11\" d=\"M 154.013,163.404 L 138.257,170.062\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 133.31,169.446 L 131.267,185.87\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 131.267,185.87 L 129.223,202.293\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 143.203,170.677 L 141.159,187.101\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 141.159,187.101 L 139.115,203.525\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:33px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"49.3797\" y=\"77.091\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:33px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"121.766\" y=\"87.7525\"><tspan>NH</tspan></text>\n",
"<text style=\"font-size:33px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"220.72\" y=\"98.414\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:33px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"169.769\" y=\"167.276\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:33px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"116.584\" y=\"236.138\"><tspan>O</tspan></text>\n",
"</svg>"
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"<IPython.core.display.SVG object>"
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},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CN1C2CCC1CC(OC(=O)C(CO)c1ccccc1)C2\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<path class=\"bond-8\" d=\"M 144.197,149.845 L 136.357,144.259\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8\" d=\"M 136.357,144.259 L 128.516,138.673\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-9\" d=\"M 132.607,128.652 L 133.594,118.333\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 125.414,138.376 L 126.401,128.058\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9\" d=\"M 126.401,128.058 L 127.389,117.739\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-11\" d=\"M 100.162,151.614 L 97.1922,182.64\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13\" d=\"M 100.162,151.614 L 74.7775,133.529\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 97.1922,182.64 L 92.3692,184.842\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12\" d=\"M 92.3692,184.842 L 87.5462,187.043\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 74.7775,133.529 L 77.7472,102.503\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14\" d=\"M 69.0177,128.282 L 71.0966,106.563\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-21\" d=\"M 74.7775,133.529 L 46.4232,146.471\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15\" d=\"M 77.7472,102.503 L 52.3627,84.4184\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 52.3627,84.4184 L 24.0085,97.3596\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16\" d=\"M 50.6978,92.0304 L 30.8498,101.089\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17\" d=\"M 24.0085,97.3596 L 21.0387,128.386\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 21.0387,128.386 L 46.4232,146.471\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18\" d=\"M 28.4634,126.021 L 46.2325,138.681\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"199.853\" y=\"144.018\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"144.197\" y=\"167.147\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"121.783\" y=\"118.036\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:20px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"50.1298\" y=\"205.971\"><tspan>HO</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"NS(=O)(=O)c1cc(C(=O)O)c(NCc2ccco2)cc1Cl\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<path class=\"bond-19\" d=\"M 115.881,174.321 L 112.682,181.983\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-19\" d=\"M 112.682,181.983 L 109.483,189.644\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"30.6394\" y=\"169.826\"><tspan>H</tspan><tspan style=\"baseline-shift:sub;font-size:12.75px;\">2</tspan><tspan>N</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#CCCC00\" x=\"67.395\" y=\"165.639\"><tspan>S</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"62.9202\" y=\"139.857\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"69.5606\" y=\"191.42\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"122.068\" y=\"90.356\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"156.106\" y=\"107.703\"><tspan>OH</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"162.439\" y=\"152.358\"><tspan>NH</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"228.754\" y=\"188.611\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:17px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"96.046\" y=\"206.974\"><tspan>Cl</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CCC1(CCC(C)C)C(=O)NC(=O)NC1=O\n",
"use cuda\n"
]
},
{
"data": {
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"<!-- END OF HEADER -->\n",
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