Tutorials
Generating Molecules with MolGAN ¶
In this tutorial, we will train a MolGAN network on the tox21 dataset which is a dataset of 12,060 training samples and 647 test samples of chemical compounds. The MolGAN network was first introduced in "MolGAN: An implicit generative model for small molecular graphs" by Cao and Kipf. It uses a GAN directly on graph data and a reinforcement learning objective to induce the network to generate molecules with certain chemical properties.
The architecture consits of 3 main sections: a generator, a discriminator, and a reward network.
The generator takes a sample (z) from a standard normal distribution to generate an a graph using a MLP (this limits the network to a fixed maximum size) to generate the graph at once. Sepcifically a dense adjacency tensor A (bond types) and an annotation matrix X (atom types) are produced. Since these are probabilities, a discrete, sparse x and a are generated through categorical sampling.
The discriminator and reward network have the same architectures and recieve graphs as inputs. A Relational-GCN and MLPs are used to produce the singular output.
Colab ¶
This tutorial and the rest in this sequence are designed to be done in Google colab. If you'd like to open this notebook in colab, you can use the following link.
Setup ¶
To run DeepChem within Colab, you'll need to run the following cell of installation commands.
In [1]:
!pip install --pre deepchem
import deepchem
deepchem.__version__
Requirement already satisfied: deepchem in /usr/local/lib/python3.10/dist-packages (2.8.1.dev20240603202041) Requirement already satisfied: joblib in /usr/local/lib/python3.10/dist-packages (from deepchem) (1.4.2) Requirement already satisfied: numpy>=1.21 in /usr/local/lib/python3.10/dist-packages (from deepchem) (1.25.2) Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from deepchem) (2.0.3) Requirement already satisfied: scikit-learn in /usr/local/lib/python3.10/dist-packages (from deepchem) (1.2.2) Requirement already satisfied: sympy in /usr/local/lib/python3.10/dist-packages (from deepchem) (1.12.1) Requirement already satisfied: scipy>=1.10.1 in /usr/local/lib/python3.10/dist-packages (from deepchem) (1.11.4) Requirement already satisfied: rdkit in /usr/local/lib/python3.10/dist-packages (from deepchem) (2023.9.6) Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.10/dist-packages (from pandas->deepchem) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->deepchem) (2023.4) Requirement already satisfied: tzdata>=2022.1 in /usr/local/lib/python3.10/dist-packages (from pandas->deepchem) (2024.1) Requirement already satisfied: Pillow in /usr/local/lib/python3.10/dist-packages (from rdkit->deepchem) (9.4.0) Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn->deepchem) (3.5.0) Requirement already satisfied: mpmath<1.4.0,>=1.1.0 in /usr/local/lib/python3.10/dist-packages (from sympy->deepchem) (1.3.0) Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.8.2->pandas->deepchem) (1.16.0)
WARNING:deepchem.feat.molecule_featurizers.rdkit_descriptors:No normalization for SPS. Feature removed! WARNING:deepchem.feat.molecule_featurizers.rdkit_descriptors:No normalization for AvgIpc. Feature removed! WARNING:tensorflow:From /usr/local/lib/python3.10/dist-packages/tensorflow/python/util/deprecation.py:588: calling function (from tensorflow.python.eager.polymorphic_function.polymorphic_function) with experimental_relax_shapes is deprecated and will be removed in a future version. Instructions for updating: experimental_relax_shapes is deprecated, use reduce_retracing instead WARNING:deepchem.models.torch_models:Skipped loading modules with pytorch-geometric dependency, missing a dependency. No module named 'torch_geometric' WARNING:deepchem.models:Skipped loading modules with pytorch-geometric dependency, missing a dependency. cannot import name 'DMPNN' from 'deepchem.models.torch_models' (/usr/local/lib/python3.10/dist-packages/deepchem/models/torch_models/__init__.py) WARNING:deepchem.models:Skipped loading modules with pytorch-lightning dependency, missing a dependency. No module named 'lightning' WARNING:deepchem.models:Skipped loading some Jax models, missing a dependency. No module named 'haiku'
Out[1]:
'2.8.1.dev'
Import the packages you'll need.
In [2]:
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import os
from collections import OrderedDict
import deepchem as dc
import deepchem.models
import torch
from deepchem.models.torch_models import BasicMolGANModel as MolGAN
from deepchem.models.optimizers import ExponentialDecay
from torch.nn.functional import one_hot
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
from deepchem.feat.molecule_featurizers.molgan_featurizer import GraphMatrix
Download, load, and extract the SMILES strings from the tox21 dataset. The original paper used the QM9 dataset, however we use the tox21 dataset here to save time.
In [3]:
# Download from MolNet
# Try tox21 or LIPO dataset
tasks, datasets, transformers = dc.molnet.load_tox21()
df = pd.DataFrame(data={'smiles': datasets[0].ids})
Specify the maximum number of atoms to enocde for the featurizer and the MolGAN network. The higher the number of atoms, the more data you'll have in the dataset. However, this also increases the model complexity as the input dimensions become higher.
In [4]:
num_atoms = 12
In [5]:
df
Out[5]:
| smiles | |
|---|---|
| 0 | CC(O)(P(=O)(O)O)P(=O)(O)O |
| 1 | CC(C)(C)OOC(C)(C)CCC(C)(C)OOC(C)(C)C |
| 2 | OC[C@H](O)[C@@H](O)[C@H](O)CO |
| 3 | CCCCCCCC(=O)[O-].CCCCCCCC(=O)[O-].[Zn+2] |
| 4 | CC(C)COC(=O)C(C)C |
| ... | ... |
| 6259 | CC1CCCCN1CCCOC(=O)c1ccc(OC2CCCCC2)cc1 |
| 6260 | Cc1cc(CCCOc2c(C)cc(-c3noc(C(F)(F)F)n3)cc2C)on1 |
| 6261 | O=C1OC(OC(=O)c2cccnc2Nc2cccc(C(F)(F)F)c2)c2ccc... |
| 6262 | CC(=O)C1(C)CC2=C(CCCC2(C)C)CC1C |
| 6263 | CC(C)CCC[C@@H](C)[C@H]1CC(=O)C2=C3CC[C@H]4C[C@... |
6264 rows × 1 columns
Uncomment the first line if you want to subsample from the full dataset.
In [6]:
#data = df[['smiles']].sample(4000, random_state=42)
data = df
Initialize the featurizer with the maxmimum number of atoms per molecule. atom_labels is a parameter to pass the atomic number of atoms you want to be able to parse. Similar to the num_atoms parameter above, more atom_labels means more data, though the model gets more complex/unstable.
In [7]:
# create featurizer
feat = dc.feat.MolGanFeaturizer(max_atom_count=num_atoms, atom_labels=[0, 5, 6, 7, 8, 9, 11, 12, 13, 14]) #15, 16, 17, 19, 20, 24, 29, 35, 53, 80])
Extract the smiles from the dataframe as a list of strings
In [8]:
smiles = data['smiles'].values
Filter out the molecules with too many atoms to reduce the number of unnecessary error messages in later steps.
In [9]:
filtered_smiles = [x for x in smiles if Chem.MolFromSmiles(x).GetNumAtoms() < num_atoms]
[13:29:08] WARNING: not removing hydrogen atom without neighbors
The next cell featurizes the filtered molecules, however, since we have limited the atomic numbers to
[5, 6, 7, 8, 9, 11, 12, 13, 14]
which is B, C, N, O, F, Na, Mg, Al and Si, the featurizer fails to featurize several molecules in the dataset. Feel free to experiment with more atomic numbers!
In [10]:
# featurize molecules
features = feat.featurize(filtered_smiles)
WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 0, CC(O)(P(=O)(O)O)P(=O)(O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 11, O=[N+]([O-])[O-].O=[N+]([O-])[O-].[Ca+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 20 [13:29:09] WARNING: not removing hydrogen atom without neighbors WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 12, F[B-](F)(F)F.[H+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 1 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 14, [I-].[K+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 19 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 17, C=CC(=O)OCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 25, ClCOCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 27, [Cu]I. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 29 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 32, BrCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 33, CCC(Cl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 39, NC(=S)NNC(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 40, NC(=S)C(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 41, C[Hg]Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 42, [Hg+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 80 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 44, O=[Cr](=O)([O-])O[Cr](=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 24 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 45, O=P(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 49, O=C(O)[C@@H](S)[C@H](S)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 54, CO[Si](CCCS)(OC)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 55, C[N+](C)=CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 57, O=[Zr](Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 61, CC(C)OS(C)(=O)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 66, CC(Cl)(Cl)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 67, O=C(CCl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 68, CC(=O)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 71, ClCCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 75, CCOP(=O)(CC)OCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 81, CSCCC=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 82, CC(C)(C)C(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 87, CNC(=O)NC(O)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 90, BrCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 91, O=S(=O)([O-])[O-].[Na+].[Na+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 98, [O-][Cl+3]([O-])([O-])[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 106, OCCSSCCO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 107, ClCCCCCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 108, [Ba+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 56 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 116, N#CSCSC#N. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 117, CCCCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 118, C[S+](C)CCC(N)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 120, CC[Sn](Br)(CC)CC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 122, CCOP(=O)(OCC)OCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 133, CCOP(=O)([O-])C(N)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 136, COC(=O)CCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 141, CCCCCCCCC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 142, COC(=O)C(Cl)C(=O)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 146, NCCOS(=O)(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 147, COP(=O)(OC)OC=C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 148, CC(Cl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 151, Cl[Pd]Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 152, ClC=CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 153, O=S(=O)([O-])CCCS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 154, [TlH2+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 81 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 155, CC(C)OP(C)(=O)OC(C)C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 156, COS(=O)(=O)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 158, O=P([O-])([O-])OC(CO)CO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 160, C=C(Cl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 161, OC(CCl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 162, Cl[Ba]Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 163, O=C(O)CP(=O)(O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 166, ClC(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 167, ClC(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 168, CC(C)(CCl)C(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 175, ClC(Cl)=C(Cl)C(Cl)=C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 180, ClC(Cl)(Cl)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 183, [Na]I. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 185, BrCCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 187, CCNC(=S)NCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 190, CC(C)(C)S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 193, Cl/C=C/Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 194, Cl/C=C\Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 195, OCC(Cl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 200, O=[Mo](=O)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 42 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 201, CCOP(=S)(S)OCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 203, O=[Cr]O[Cr]=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 24 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 204, [Cr+3]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 24 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 210, CCN(CC)C(=S)[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 211, C[Sn](C)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 212, CCCCC(CC)C(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 214, OCC(O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 217, O=S(=O)(O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 218, [Fe+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 26 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 223, N#C[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 224, CC(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 228, ClC(Cl)(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 230, CSCCCN=C=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 238, CCCC[Sn](Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 50 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 241, C=CCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 242, C=CCSSCCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 243, C=CCNC(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 245, Cl[Nd](Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 246, [Co+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 27 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 250, CC(C)C(Br)C(=O)NC(N)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 251, O=S(=O)([O-])CO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 253, CC(=O)C(Cl)C(=O)N(C)C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 259, O=C/C(Cl)=C(/Cl)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 260, O=C(O)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 263, C=CCSSCC=C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 267, Cl[Yb](Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 271, NS(=O)(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 272, [PbH2+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 82 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 276, OCC(S)CS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 279, CCCCNP(N)(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 281, N[C@@H](CS)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 282, CC(C)(O)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 284, NC(CS)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 290, ClCCN(CCCl)CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 291, O=C(Cl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 293, [Fe+3]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 26 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 294, CCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 295, ClC(Cl)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 305, CC(=O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 310, [Cu+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 29 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 311, ClCC(Cl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 316, Cl[In](Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 322, [As]#[In]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 33 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 323, COS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 332, O=S(=O)([O-])[O-].[Li+].[Li+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 3 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 333, CCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 334, CS(=O)(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 339, S=C([S-])NCCNC(=S)[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 341, C[N+]([O-])(CCCl)CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 350, CCC(C)S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 355, O=C(O)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 356, FC(F)(Cl)C(F)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 357, BrC(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 360, COP(=O)(NC(C)=O)SC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 362, ClP(Cl)(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 370, OCC(CBr)(CBr)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 371, O=C(O)C(Cl)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 372, O=C(O)C(Cl)(Cl)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 374, OCCCCCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 384, CSSC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 387, CC(Cl)(Cl)[N+](=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 390, O=[N+]([O-])C(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 395, CNC(=S)NN. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 397, O=S(=O)(O)C(F)(F)F. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 400, CCSCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 401, CCCC[Sn](Cl)(Cl)CCCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 50 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 403, [C-]#N.[Cu+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 29 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 404, CC(C)(C)C(=O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 405, CC(S)C(=O)NCC(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 406, [Cd+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 48 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 409, CC(CC(=O)Cl)CC(C)(C)C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 411, CCCCCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 413, C[N+](C)(C)CC(O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 417, CNC(=S)[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 418, [SnH2+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 50 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 420, COC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 422, C=CC(Cl)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 423, O=[Se]([O-])[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 34 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 424, CCOC(=S)[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 429, Cl[Au](Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 436, N#CCCC(Br)(C#N)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 440, C=CC(=O)[O-].C=CC(=O)[O-].[Zn+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 30 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 441, CCCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 442, OCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 444, CCCCCCI. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 445, CCOC(=O)CS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 448, CC(C)S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 449, COP(OC)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 450, C[Se]CC[C@H](N)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 34 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 454, CN(C)C(=S)SC(=S)N(C)C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 455, OC[P+](CO)(CO)CO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 457, CCOS(C)(=O)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 458, COP(=O)(O)OP(=O)(O)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 463, OCC(Br)=C(Br)CO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 464, BrC/C=C/CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 465, N#CC(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 467, O=S(=O)([O-])CCO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 471, COP(=O)(O)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 473, Cl[Dy](Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 474, CCCSSCCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 477, N#CC(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 478, NC(=O)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 479, CC(=O)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 481, CCCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 487, OC(O)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 491, ClC(Cl)=C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 492, ClC(Cl)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 493, ClCC(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 495, OCCSCSCCO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 497, CC(=O)[O-].[K+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 19 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 498, O=C(Cl)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 501, CCSC(=O)N(CC)CC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 504, ClCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 506, CC(Br)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 507, S=C([S-])NCCNC(=S)[S-].[Mn+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 511, COS(=O)(=O)C(F)(F)F. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 515, O=C(O)C(Br)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 516, O=C([O-])CS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 518, O=S(=O)([O-])SSS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 520, BrCC(Br)(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 521, BrC(Br)C(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 523, CS(C)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 532, CNC(=S)N(C)C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 534, CSC(C)(C)/C=N\O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 535, N#CCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 536, ClCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 537, O=C([O-])C(=O)[O-].[Ca+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 20 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 539, Br[Ca]Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 543, CN(C)C(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 544, C#CC(O)(/C=C\Cl)CC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 545, BrCCCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 546, O=P([O-])(O)C(Cl)(Cl)P(=O)([O-])O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 548, CCOP(OCC)OCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 551, CCCCCCC(C)(C)S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 559, CC(CCl)OC(C)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 560, OCC(CO)(CBr)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 561, ClCCOCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 563, OCCSCCO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 564, P#[In]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 565, O=C(O)CC(Cl)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 566, N#CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 567, [Mn+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 25 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 568, CCC(C)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 571, FC(F)OC(Cl)C(F)(F)F. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 576, CC(O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 578, O=C([O-])[O-].[Sr+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 38 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 583, CNC(=S)NC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 586, ClCCOCCOCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 588, CC(C)(C)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 593, N#CC(Br)(Br)C(N)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 597, CCCC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 598, CCCCCCCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 599, CC(Cl)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 600, O=C(O)CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 601, O=[Cd]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 48 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 604, S=C=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 608, ClC(Cl)(Cl)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 611, O=S(=O)([O-])CCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 613, OCC(O)CS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 614, [Be+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 4 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 615, CC(C)(C)C(=O)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 617, O=S(=O)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 618, O=S(=O)([O-])[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 621, O=C([O-])CC(S[Au])C(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 629, CN(C)CCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 637, O=P(O)(O)CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 638, N#CC(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 639, NC(=O)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 640, CC(Cl)C(C)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 644, CC=C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 648, CC(=O)N[C@@H](CS)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 650, [Zn+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 30 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 651, O=C(O)C(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 653, O=C([O-])P(=O)([O-])[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 654, C=CS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 660, CCCCCCCCCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 666, O=S(=O)([O-])O.[Na+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 668, ClSC(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 671, N[Pt](N)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 678, CCCCSCCCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 681, COS(C)(=O)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 686, O=C(O)CS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 688, NCCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 692, CN(C)P(=O)(N(C)C)N(C)C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 694, CC(C)OC(=S)[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 695, CNC(=O)ON=C(C)SC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 698, CCOC(=O)CC(=O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 699, BrC(Br)C(Br)(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 700, CCOC(=O)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 702, O=[Se](O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 34 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 703, NC(N)=[Se]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 34 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 704, CCOS(=O)(=O)OCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 707, C=C(C)CS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 708, CCCCOC(=O)CCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 712, CNCCS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 713, FC(F)(F)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 715, CCSCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 716, ClCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 718, OCC(Br)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 721, C[Si](C)(C)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 722, O=[N+]([O-])C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 724, O=C([O-])CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 728, CCCCCSCCCCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 729, CC(S)C(C)S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 732, O=[Se]=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 34 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 733, ClC/C=C\CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 735, COC(=O)CS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 737, ClCC(Br)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 738, BrCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 740, IC(I)=C(I)I. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 741, O=P([O-])([O-])OP(=O)([O-])[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 742, CCCCCCCCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 743, N#CCCSCCC#N. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 745, CC(Cl)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 748, CC(C)(Cl)[N+](=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 749, CCC(Cl)[N+](=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 751, N#CSCC(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 755, CCN(CC)CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 757, C=CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 758, C=CCN=C=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 761, O=S([O-])CO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 762, CCSC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 764, CCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 765, OCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 767, C=CCOCC(O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 770, C/C(Cl)=C/CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 771, BrCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 773, O=S(=O)([O-])OOS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 774, O=[N+]([O-])[O-].[K+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 19 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 778, CS(=O)(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 780, Cl[Zn]Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 781, ClC/C=C/CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 782, CC(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 783, ClCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 786, NC(=S)NC(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 788, CC(Cl)(Cl)C(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 790, C[Sn](Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 791, C=CCS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 792, O=P([O-])(O)OP(=O)([O-])O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 799, CN(CCCl)CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 800, C=C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 801, N=C(N)S(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 803, COP(=O)(OC)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 810, Cl[Ni]Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 812, CCOP(=S)(Cl)OCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 813, COP(=S)(Cl)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 814, Cl[Sb](Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 823, O=[Bi]Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 824, [Br-].[Na+]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 839, N[C@@H](CSCCCO)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 843, O=C(C(Cl)(Cl)Cl)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 849, II. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 853, O=C([O-])C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 857, O=C(CCl)NCO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 858, SCCCCCCCCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 861, O=C(Cl)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 863, COC(=O)C(Br)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 864, ClC=C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 865, ClCC(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 866, CC(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 867, FC(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 873, ClCC=CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 877, CCOC(=O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 879, O=S(=O)([O-])CC(S)CS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 880, O=[N+]([O-])C(Br)(CO)CO. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 881, OCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 888, SCCSCCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 889, CCCCNC(C)(C)[PH](=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 892, CCCCCCCCSCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 893, O=S(O)CO[Na]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 901, COP(C)(=O)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 906, [Ca+2].[Cl-].[Cl-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 911, CCCCCCCCCI. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 918, CC(C)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 919, [SbH6+3]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 51 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 920, ClC(Cl)C(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 924, O=P(O)(O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 927, NC(CSCC(=O)O)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 935, [Ni+2]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 28 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 940, O=[N+]([O-])O[Cd]O[N+](=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 48 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 941, CCOC(=O)C(Cl)C(C)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 943, N[C@@H](COP(=O)(O)O)C(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 947, NNC(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 948, CCCCS(=O)(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 949, NC(N)=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 952, CCOC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 953, NS(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 954, COCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 955, C[N+](C)(C)CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 956, CCOP(=S)(OCC)SCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 958, CC[Ge](Cl)(CC)CC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 960, CCOP(=O)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 967, O=C(O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 968, CCC(C)SSC(C)CC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 970, O=CC(Br)(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 971, O=C(O)C(Br)(Br)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 978, C=C(C)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 979, CCCCCCCCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 981, CCCCC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 982, CCC(C)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 983, N#CCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 984, O=C(O)CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 985, O=S(=O)(O)F. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 986, O=C(Cl)/C=C/C(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 987, O=C(O)CCSCCC(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 989, FC(F)(F)C(Cl)Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 991, O=C(O)CCS. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 997, CO[PH](=O)OC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1003, CC(C)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1008, O=C(CCl)C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1009, N#C[Au-]C#N. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 79 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1010, ClC(Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1013, CCCSC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1017, ClC=CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1018, NCCS(=O)(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1020, CCOP(O)OCC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1022, FC(Cl)(Cl)C(F)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1024, CN(C)C(=S)[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1027, ClCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1028, CCCCCCCCCBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1029, Cl[Sn](Cl)(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1030, CC(O)(P(=O)([O-])O)P(=O)([O-])O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1041, CN=C=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1043, ClCCOCOCCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1044, CC(C)=CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1046, C[As](C)(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 33 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1049, COP(N)(=O)SC. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1053, O=S(=O)([O-])CC(O)CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1054, CC(C)CP(=S)([S-])CC(C)C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1060, O=C([O-])C(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1061, NNC(=S)NN. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1065, O=CCCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1067, CCCCCCCC(=O)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1070, NC(=O)CI. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1071, IC(I)I. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1073, FC(F)OC(F)(F)C(F)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1074, O=S(=O)(Cl)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1077, Nc1ccccc1S(=O)(=O)O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1087, ClCc1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1090, Nc1cc(Cl)cc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1093, ClCc1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1094, COc1cccc(Br)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1099, Cc1cc(O)cc(C)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1100, S=C=NCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1101, ClCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1107, O=C=Nc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1109, O=Cc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1111, O=Cc1cccc(Br)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1117, O=C(CBr)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1120, Cc1cc(C)c(N)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1122, NC(=S)Nc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1127, O=C(Cl)c1cc(Cl)cc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1128, COC(=O)c1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1129, O=[N+]([O-])c1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1135, [S-]c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1137, O=[N+]([O-])c1cccc(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1138, O=[N+]([O-])c1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1139, O=[N+]([O-])c1ccc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1140, Oc1ccc(Cl)c(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1141, Oc1cc(Cl)cc(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1142, Oc1c(Cl)ccc(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1143, ClC(Cl)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1146, O=C(Cl)OCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1151, BrCCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1153, Cc1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1159, Cc1ccccc1CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1164, Nc1ccc(Cl)cc1[N+](=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1167, Oc1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1170, Cc1c(N)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1171, Cc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1172, Nc1ccc(Br)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1177, NC(=S)c1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1178, Cc1ccccc1Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1184, BrCCOc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1185, Brc1ccc(Br)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1191, CCc1ccc(Br)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1196, Cc1ccccc1S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1199, O=S(=O)([O-])c1ccc(O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1205, Nc1cc(Cl)c(N)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1206, Oc1cc(Cl)c(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1210, O=[N+]([O-])c1ccccc1CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1211, O=[N+]([O-])c1ccc(CCl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1212, O=[N+]([O-])c1cccc(CCl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1213, Nc1ccc(S(=O)(=O)[O-])cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1221, CC(=O)O[Hg]c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 80 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1222, NC(=O)c1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1223, Fc1cccc(Cl)c1CCl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1231, O=C(CCl)Nc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1232, COc1ccc(OC)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1233, Cc1cc(O)c(Cl)cc1C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1237, O=C(Cl)c1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1241, Cc1ccc(S(=O)(=O)O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1246, ICCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1247, O=[N+]([O-])c1cccc(I)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1248, Nc1c(Cl)cc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1249, Nc1cc(Cl)ccc1O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1250, O=Cc1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1251, N#Cc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1252, COC(=O)c1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1255, N#CSCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1260, O=P(O)(O)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1263, Clc1ccc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1274, O=[N+]([O-])c1ccc(CBr)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1275, Cc1ccc(Br)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1277, COc1ccc(Br)c(C)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1278, Oc1c(Cl)c(Cl)cc(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1287, C=Cc1cccc(CCl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1288, Cc1cc(O)c(Cl)c(C)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1290, Cc1ccc(S(N)(=O)=O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1291, CCC(=O)c1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1293, CC(C)(C)c1ccc(S)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1294, O=C(CS)Nc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1306, Nc1cc(Cl)ccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1307, Nc1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1308, O=[PH](O)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1313, O=C(CBr)c1ccc(O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1314, FC(F)(F)c1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1315, O=C(O)c1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1316, O=C(O)c1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1317, O=C(O)c1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1318, FC(F)(F)c1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1322, Cc1ccccc1S(=O)(=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1324, O=Cc1cc(O)ccc1Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1326, Clc1ccc(C(Cl)(Cl)Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1328, Cc1cc(Cl)c(C)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1329, Clc1ccc(Cl)c(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1330, [O-]c1cc(Cl)c(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1332, COc1cc(Cl)ccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1333, CSc1ccc(C=O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1338, Cc1ccc(Cl)c(O)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1344, Cc1cc(O)ccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1345, Oc1c(Cl)cc(Cl)c(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1347, COc1ccc(Cl)cc1C. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1348, Cc1cc(Cl)ccc1N. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1351, Cc1ccc(Cl)cc1N. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1352, Cc1ccc(N)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1353, Nc1ccc(N)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1354, Nc1ccc(Cl)cc1N. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1355, Nc1ccc(Cl)c(N)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1356, O=[N+]([O-])c1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1359, O=S(=O)(O)c1ccccc1O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1361, N#Cc1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1363, ClC(Cl)(Cl)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1367, Sc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1368, Nc1cc(Cl)c(O)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1369, O=C(O)c1ccc([Hg]Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1370, Oc1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1374, SCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1379, Oc1cc(Cl)c(Cl)c(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1380, Nc1cc(C(=O)O)ccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1381, N#CCc1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1383, Cc1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1384, Oc1cc(O)c(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1391, Oc1ccccc1[Hg]Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 80 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1394, O=S(=O)(O)c1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1395, O=C(O)c1cc(Cl)cc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1396, O=C(O)c1ccc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1398, Clc1c(Cl)cc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1402, Oc1ccc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1403, Oc1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1405, Oc1cc(Cl)cc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1406, Oc1cccc(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1407, Clc1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1408, Oc1cc(Cl)ccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1411, CC(C)(CCl)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1419, Nc1ccc([As](=O)([O-])O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 33 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1421, O=Cc1ccc(F)c(Br)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1422, O=C(O)c1ccccc1S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1423, O=P(O)(O)Oc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1429, Oc1cc(Cl)c(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1436, Nc1ccc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1437, Nc1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1438, FC(F)(F)c1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1440, Nc1ccc([As](=O)(O)O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 33 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1443, OCCSc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1446, O=S(=O)(O)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1450, Sc1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1451, ClCc1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1453, Fc1cc(Br)ccc1CBr. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1455, Oc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1457, Cc1c(Cl)cccc1[N+](=O)[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1460, Cc1cc(Cl)ccc1O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1462, Clc1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1463, Clc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1464, Oc1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1465, Brc1ccc(Br)c(Br)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1471, N#Cc1cc(Br)c(O)c(Br)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1472, N#Cc1cc(I)c(O)c(I)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 53 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1477, O=S(=O)(O)c1ccc(O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1480, Clc1cc(Cl)cc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1481, Clc1cccc(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1483, Clc1cc(Cl)c(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1484, Nc1ccc(S(N)(=O)=O)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1487, Nc1cccc(S(=O)(=O)O)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1493, Brc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1498, Oc1c(Br)cc(Br)cc1Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1499, Oc1ccc([Hg]Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1500, Oc1c(Cl)cc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1501, O=C(Cl)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1508, Clc1cc(Cl)c(Cl)c(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1509, Cc1cccc(Br)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1510, BrCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1513, O=[N+]([O-])c1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1517, Cl[Hg]c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1521, Cc1ccccc1S(N)(=O)=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1523, Cc1ccc(Cl)c(N)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1525, O=C(Cl)c1ccccc1F. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1530, Fc1ccc(Br)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1533, OCc1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1536, S=C=NCCc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1539, S=C=Nc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1541, Cc1ccc(S)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1542, CCCCc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1562, ClP(Cl)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1571, O=Cc1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1572, Nc1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1580, CCC(=O)c1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1581, O=[N+]([O-])c1ccc(F)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1585, OB(O)O[Hg]c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 80 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1588, BrCc1ccc(Br)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1589, O=C(O)c1cc(Cl)ccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1590, O=C(O)c1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1591, O=C(O)c1cccc(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1592, O=C(O)c1ccc(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1593, O=Cc1c(Cl)cccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1594, O=Cc1ccc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1595, O=C(Cl)c1ccc(F)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1598, Cc1ccc([N+](=O)[O-])cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1599, Cc1cccc(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1600, NS(=O)(=O)c1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1603, O=C=Nc1ccc(Cl)c(Cl)c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1605, NC(=O)Nc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1607, O=C(CCl)c1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1608, Nc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1609, CSc1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1610, Cc1ccccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1611, CS(=O)(=O)c1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1612, Clc1ccccc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1614, Oc1nc(Cl)c(Cl)cc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1616, O=C(O)c1cccc(Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1619, Clc1ccccn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1620, ClCc1ccccn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1621, ClCc1cccnc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1626, Clc1nc(Cl)c(Cl)c(Cl)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1629, Clc1cccc(C(Cl)(Cl)Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1637, CCc1cc(C(N)=S)ccn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1643, Clc1ccc(C(Cl)(Cl)Cl)cn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1648, Cc1nc(C)c(Cl)c(O)c1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1649, O=C(O)c1nc(Cl)ccc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1659, Clc1cc(Cl)c(Cl)nc1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1665, Clc1cccc2ccccc12. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1668, Clc1ccc2ccccc2c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1674, O=S(=O)(O)NC1CCCCC1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1683, SC1CCCCC1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1694, O=S(=O)([O-])NC1CCCCC1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1706, CCn1cc[n+](C)c1.N#C[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1729, [O-][n+]1ccccc1[S-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1740, [O-][n+]1ccc(Cl)cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1748, Nc1nc(N)nc(Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1750, Clc1nc(Cl)nc(Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1751, CCNc1nc(N)nc(Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1754, CC(C)SCc1ccco1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1758, Cc1c(S)cco1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1759, CSSc1c(C)occ1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1764, CC(=O)SCc1ccco1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1777, C[C@@H]1O[C@@H]1P(=O)([O-])[O-]. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 15 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1781, BrCC1CO1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1784, ClCC1CO1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1787, Cc1nc2ccccc2s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1788, Nc1nc2c(Cl)cccc2s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1789, Sc1nc2ccccc2s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1790, [S-]c1nc2ccccc2s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1791, c1ccc2scnc2c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1792, Nc1nc2ccccc2s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1793, Brc1nc2ccccc2s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1794, Cc1cccc2c1nc(N)s2. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1795, Nc1nc(Cl)cc(Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1796, Clc1cc(Cl)nc(Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1797, Clc1ccnc(Cl)n1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1808, Cc1c(CCCl)scn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1809, Cc1cscn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1810, CC(C)Cc1nccs1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1811, Nc1nc(CC(=O)O)cs1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1812, Nc1nccs1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1813, CC(=O)c1nccs1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1814, Nc1ncc([N+](=O)[O-])s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1815, Cc1c(CCO)scn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1816, CCCc1ncc(C(=O)O)s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1817, CC(=O)c1c(C)nc(C)s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1849, Cc1nc2ccc(Cl)cc2[nH]1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1870, O=C1CCCCC1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1892, CSc1cnccn1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1896, ClCCN1CCCC1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1902, CC1(C)C(=O)N(Cl)C(=O)N1Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1903, CC1(C)C(=O)N(Br)C(=O)N1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1905, CC1(C)C(=O)N(Br)C(=O)N1Br. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1906, CC1(C)C(=O)N(Cl)C(=O)N1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1920, SC1CCCC1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1924, O=C1OC(O)C(C(Cl)Cl)=C1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1925, Clc1c(Cl)c(Cl)c(Cl)s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1926, c1cscc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1927, Cc1ccc(C=O)s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1928, Cc1c(Br)ccs1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1933, O=c1[nH]c(=O)n(Cl)c(=O)n1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1937, O=[N+]([O-])C1(Br)COCOC1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 35 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1952, Clc1ccc2[nH]nnc2c1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1954, Oc1ccc(Cl)c2c1CCC2. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1962, O=c1[nH]c2cc(Cl)ccc2o1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1963, O=c1[nH]c2ccc(Cl)cc2o1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1974, [Fe+2].c1c[cH-]cc1.c1c[cH-]cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 26 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1975, [Ni+2].c1c[cH-]cc1.c1c[cH-]cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 28 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1976, [Cr+2].c1c[cH-]cc1.c1c[cH-]cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 24 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1977, [Co+2].c1c[cH-]cc1.c1c[cH-]cc1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 27 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1982, Cn1sccc1=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1983, Cn1sc(Cl)cc1=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1984, Cc1c[nH]c(=S)[nH]c1=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1985, Cc1cc(=O)[nH]c(=S)[nH]1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1986, O=c1cc[nH]c(=S)[nH]1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1987, CCCc1cc(=O)[nH]c(=S)[nH]1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 1998, O=C1CCC(=O)N1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2008, Cl[C@H]1OCCO[C@@H]1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2011, Sc1nnc(S)s1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2024, O=c1[nH]sc2ccccc12. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2025, O=c1[nH]sc2cc(Cl)ccc12. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2033, Cn1cc[nH]c1=S. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2040, O=C1Cc2cc(Cl)ccc2N1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2058, ClC1=C(Cl)C(Cl)(Cl)C(Cl)=C1Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2061, C1CSCCS1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2062, CC1(O)CSC(C)(O)CS1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2063, O=S1(=O)CCCC1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2064, O=S1(=O)CC(Cl)(Cl)C(Cl)(Cl)C1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2065, CC(=O)NC1CCSC1=O. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2069, S=C1NC=NC2N=CNC12. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2070, S=c1[nH]c2ccccc2[nH]1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 16 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2072, O=c1cc(O)c(Cl)c[nH]1. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Failed to featurize datapoint 2079, ClC1=C(Cl)C1(Cl)Cl. Appending empty array WARNING:deepchem.feat.base_classes:Exception message: 17 WARNING:deepchem.feat.base_classes:Exception message: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2081,) + inhomogeneous part.
Remove more invalid molecules.
In [11]:
indices = [ i for i, data in enumerate(features) if type(data) is GraphMatrix ]
print(indices)
features = [features[i] for i in indices]
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 43, 46, 47, 48, 50, 51, 52, 53, 56, 58, 59, 60, 62, 63, 64, 65, 69, 70, 72, 73, 74, 76, 77, 78, 79, 80, 83, 84, 85, 86, 88, 89, 92, 93, 94, 95, 96, 97, 99, 100, 101, 102, 103, 104, 105, 109, 110, 111, 112, 113, 114, 115, 119, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 134, 135, 137, 138, 139, 140, 143, 144, 145, 149, 150, 157, 159, 164, 165, 169, 170, 171, 172, 173, 174, 176, 177, 179, 181, 182, 184, 186, 188, 189, 191, 192, 196, 197, 198, 199, 202, 205, 206, 207, 208, 209, 213, 215, 216, 219, 220, 221, 222, 225, 226, 227, 229, 231, 232, 233, 234, 235, 236, 237, 239, 240, 244, 247, 248, 249, 252, 254, 255, 256, 257, 258, 261, 262, 264, 265, 266, 268, 269, 270, 273, 274, 275, 277, 278, 280, 283, 285, 286, 287, 288, 289, 292, 296, 297, 298, 299, 300, 301, 302, 303, 304, 306, 307, 308, 309, 312, 313, 314, 315, 317, 318, 319, 320, 321, 324, 325, 326, 327, 328, 329, 330, 331, 335, 336, 337, 338, 340, 342, 343, 344, 345, 346, 347, 348, 349, 351, 352, 353, 354, 358, 359, 361, 363, 364, 365, 366, 367, 368, 369, 373, 375, 376, 377, 378, 379, 380, 381, 382, 383, 385, 386, 388, 389, 391, 392, 393, 394, 396, 398, 399, 402, 407, 408, 410, 412, 414, 415, 416, 419, 421, 425, 426, 427, 428, 430, 431, 432, 433, 434, 437, 438, 439, 443, 446, 447, 451, 452, 453, 456, 459, 460, 461, 462, 466, 468, 469, 470, 472, 475, 476, 480, 482, 483, 484, 485, 486, 488, 489, 490, 494, 499, 500, 502, 503, 505, 508, 509, 510, 512, 513, 514, 517, 519, 522, 524, 525, 526, 527, 528, 529, 530, 531, 533, 538, 540, 541, 542, 547, 549, 550, 552, 553, 554, 555, 556, 557, 558, 562, 569, 570, 572, 573, 574, 575, 577, 579, 580, 581, 582, 584, 585, 587, 589, 590, 591, 592, 594, 595, 596, 602, 603, 605, 606, 607, 609, 610, 612, 616, 619, 620, 622, 623, 624, 625, 626, 627, 628, 630, 631, 632, 633, 634, 635, 636, 641, 642, 643, 645, 646, 647, 649, 652, 655, 656, 657, 658, 659, 661, 662, 663, 664, 665, 667, 669, 670, 672, 673, 674, 675, 676, 677, 679, 680, 682, 683, 684, 687, 689, 690, 691, 693, 696, 697, 701, 705, 706, 709, 710, 711, 714, 717, 719, 720, 723, 725, 726, 727, 730, 731, 734, 736, 739, 744, 746, 747, 750, 752, 753, 754, 756, 759, 760, 763, 766, 768, 769, 772, 775, 776, 777, 779, 784, 785, 787, 789, 793, 794, 795, 796, 797, 798, 802, 804, 805, 806, 807, 808, 809, 811, 815, 816, 817, 818, 819, 820, 821, 822, 825, 826, 827, 828, 829, 830, 831, 832, 833, 834, 835, 836, 837, 838, 840, 841, 842, 844, 845, 846, 847, 848, 850, 851, 852, 854, 855, 856, 859, 860, 862, 868, 869, 870, 871, 872, 874, 875, 876, 878, 882, 883, 884, 885, 886, 887, 890, 891, 894, 895, 896, 897, 898, 899, 900, 902, 903, 904, 905, 907, 908, 909, 910, 912, 913, 914, 915, 916, 917, 921, 922, 923, 925, 926, 928, 929, 930, 931, 932, 933, 934, 936, 937, 938, 939, 942, 944, 945, 946, 950, 951, 957, 959, 961, 962, 963, 964, 965, 966, 969, 972, 973, 974, 975, 976, 977, 980, 988, 990, 992, 993, 994, 995, 996, 998, 999, 1000, 1001, 1002, 1004, 1005, 1006, 1007, 1011, 1012, 1014, 1015, 1016, 1019, 1021, 1023, 1025, 1026, 1031, 1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1042, 1045, 1047, 1048, 1050, 1051, 1052, 1055, 1056, 1057, 1058, 1059, 1062, 1063, 1064, 1066, 1068, 1069, 1072, 1075, 1076, 1078, 1079, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1088, 1089, 1091, 1092, 1095, 1096, 1097, 1098, 1102, 1103, 1104, 1105, 1106, 1108, 1110, 1112, 1113, 1114, 1115, 1116, 1118, 1119, 1121, 1123, 1124, 1125, 1126, 1130, 1131, 1132, 1133, 1134, 1136, 1144, 1145, 1147, 1148, 1149, 1150, 1152, 1154, 1155, 1156, 1157, 1158, 1160, 1161, 1162, 1163, 1165, 1166, 1168, 1169, 1173, 1174, 1175, 1176, 1179, 1180, 1181, 1182, 1183, 1186, 1187, 1188, 1189, 1190, 1192, 1193, 1194, 1195, 1197, 1198, 1200, 1201, 1202, 1203, 1204, 1207, 1208, 1209, 1214, 1215, 1216, 1217, 1218, 1219, 1220, 1224, 1225, 1226, 1227, 1228, 1229, 1230, 1234, 1235, 1236, 1238, 1239, 1240, 1242, 1243, 1244, 1245, 1253, 1254, 1256, 1257, 1258, 1259, 1261, 1262, 1264, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1276, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1289, 1292, 1295, 1296, 1297, 1298, 1299, 1300, 1301, 1302, 1303, 1304, 1305, 1309, 1310, 1311, 1312, 1319, 1320, 1321, 1323, 1325, 1327, 1331, 1334, 1335, 1336, 1337, 1339, 1340, 1341, 1342, 1343, 1346, 1349, 1350, 1357, 1358, 1360, 1362, 1364, 1365, 1366, 1371, 1372, 1373, 1375, 1376, 1377, 1378, 1382, 1385, 1386, 1387, 1388, 1389, 1390, 1392, 1393, 1397, 1399, 1400, 1401, 1404, 1409, 1410, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1420, 1424, 1425, 1426, 1427, 1428, 1430, 1431, 1432, 1433, 1434, 1435, 1439, 1441, 1442, 1444, 1445, 1447, 1448, 1449, 1452, 1454, 1456, 1458, 1459, 1461, 1466, 1467, 1468, 1469, 1470, 1473, 1474, 1475, 1476, 1478, 1479, 1482, 1485, 1486, 1488, 1489, 1490, 1491, 1492, 1494, 1495, 1496, 1497, 1502, 1503, 1504, 1505, 1506, 1507, 1511, 1512, 1514, 1515, 1516, 1518, 1519, 1520, 1522, 1524, 1526, 1527, 1528, 1529, 1531, 1532, 1534, 1535, 1537, 1538, 1540, 1543, 1544, 1545, 1546, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1555, 1556, 1557, 1558, 1559, 1560, 1561, 1563, 1564, 1565, 1566, 1567, 1568, 1569, 1570, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 1582, 1583, 1584, 1586, 1587, 1596, 1597, 1601, 1602, 1604, 1606, 1613, 1615, 1617, 1618, 1622, 1623, 1624, 1625, 1627, 1628, 1630, 1631, 1632, 1633, 1634, 1635, 1636, 1638, 1639, 1640, 1641, 1642, 1644, 1645, 1646, 1647, 1650, 1651, 1652, 1653, 1654, 1655, 1656, 1657, 1658, 1660, 1661, 1662, 1663, 1664, 1666, 1667, 1669, 1670, 1671, 1672, 1673, 1675, 1676, 1677, 1678, 1679, 1680, 1681, 1682, 1684, 1685, 1686, 1687, 1688, 1689, 1690, 1691, 1692, 1693, 1695, 1696, 1697, 1698, 1699, 1700, 1701, 1702, 1703, 1704, 1705, 1707, 1708, 1709, 1710, 1711, 1712, 1713, 1714, 1715, 1716, 1717, 1718, 1719, 1720, 1721, 1722, 1723, 1724, 1725, 1726, 1727, 1728, 1730, 1731, 1732, 1733, 1734, 1735, 1736, 1737, 1738, 1739, 1741, 1742, 1743, 1744, 1745, 1746, 1747, 1749, 1752, 1753, 1755, 1756, 1757, 1760, 1761, 1762, 1763, 1765, 1766, 1767, 1768, 1769, 1770, 1771, 1772, 1773, 1774, 1775, 1776, 1778, 1779, 1780, 1782, 1783, 1785, 1786, 1798, 1799, 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1807, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1827, 1828, 1829, 1830, 1831, 1832, 1833, 1834, 1835, 1836, 1837, 1838, 1839, 1840, 1841, 1842, 1843, 1844, 1845, 1846, 1847, 1848, 1850, 1851, 1852, 1853, 1854, 1855, 1856, 1857, 1858, 1859, 1860, 1861, 1862, 1863, 1864, 1865, 1866, 1867, 1868, 1869, 1871, 1872, 1873, 1874, 1875, 1876, 1877, 1878, 1879, 1880, 1881, 1882, 1883, 1884, 1885, 1886, 1887, 1888, 1889, 1890, 1891, 1893, 1894, 1895, 1897, 1898, 1899, 1900, 1901, 1904, 1907, 1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918, 1919, 1921, 1922, 1923, 1929, 1930, 1931, 1932, 1934, 1935, 1936, 1938, 1939, 1940, 1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951, 1953, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1964, 1965, 1966, 1967, 1968, 1969, 1970, 1971, 1972, 1973, 1978, 1979, 1980, 1981, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2009, 2010, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2026, 2027, 2028, 2029, 2030, 2031, 2032, 2034, 2035, 2036, 2037, 2038, 2039, 2041, 2042, 2043, 2044, 2045, 2046, 2047, 2048, 2049, 2050, 2051, 2052, 2053, 2054, 2055, 2056, 2057, 2059, 2060, 2066, 2067, 2068, 2071, 2073, 2074, 2075, 2076, 2077, 2078, 2080]
Instantiate the MolGAN model and set the learning rate and maximum number of atoms as the size of the vertices. Then, we create the dataset in the format of the input to MolGAN.
In [12]:
# create model
gan = MolGAN(learning_rate=ExponentialDecay(0.001, 0.9, 5000), vertices=num_atoms)
dataset = dc.data.NumpyDataset([x.adjacency_matrix for x in features],[x.node_features for x in features])
Define the iterbatches function because the gan_fit function requires an iterable for the batches.
In [13]:
def iterbatches(epochs):
for i in range(epochs):
for batch in dataset.iterbatches(batch_size=gan.batch_size, pad_batches=True):
flattened_adjacency = torch.from_numpy(batch[0]).view(-1).to(dtype=torch.int64) # flatten the input because torch.nn.functional.one_hot only works with 1D inputs
invalid_mask = (flattened_adjacency < 0) | (flattened_adjacency >= gan.edges) # edge type cannot be negative or >= gan.edges, these entries are invalid
clamped_adjacency = torch.clamp(flattened_adjacency, 0, gan.edges-1) # clamp the input so it can be fed to the one_hot function
adjacency_tensor = one_hot(clamped_adjacency, num_classes=gan.edges) # actual one_hot
adjacency_tensor[invalid_mask] = torch.zeros(gan.edges, dtype=torch.long) # make the invalid entries, a vector of zeros
adjacency_tensor = adjacency_tensor.view(*batch[0].shape, -1) # reshape to original shape and change dtype for stability.
flattened_node = torch.from_numpy(batch[1]).view(-1).to(dtype=torch.int64)
invalid_mask = (flattened_node < 0) | (flattened_node >= gan.nodes)
clamped_node = torch.clamp(flattened_node, 0, gan.nodes-1)
node_tensor = one_hot(clamped_node, num_classes=gan.nodes)
node_tensor[invalid_mask] = torch.zeros(gan.nodes, dtype=torch.long)
node_tensor = node_tensor.view(*batch[1].shape, -1)
yield {gan.data_inputs[0]: adjacency_tensor, gan.data_inputs[1]:node_tensor}
Train the model with the fit_gan function and generate molecules with the predict_gan_generator function.
In [14]:
gan.fit_gan(iterbatches(25), generator_steps=0.2, checkpoint_interval=5000)
generated_data = gan.predict_gan_generator(1000)
/usr/local/lib/python3.10/dist-packages/torch/autograd/graph.py:744: UserWarning: Attempting to run cuBLAS, but there was no current CUDA context! Attempting to set the primary context... (Triggered internally at ../aten/src/ATen/cuda/CublasHandlePool.cpp:135.) return Variable._execution_engine.run_backward( # Calls into the C++ engine to run the backward pass
Ending global_step 349: generator average loss -3.55075, discriminator average loss -5.23049 TIMING: model fitting took 8.770 s Generating 1000 samples
Convert the generated graphs to RDKit molecules.
In [15]:
nmols = feat.defeaturize(generated_data)
print("{} molecules generated".format(len(nmols)))
[13:29:24] Explicit valence for atom # 2 O, 30, is greater than permitted [13:29:24] Explicit valence for atom # 0 C, 26, is greater than permitted [13:29:24] non-ring atom 0 marked aromatic
1000 molecules generated
[13:29:24] Explicit valence for atom # 1 B, 7, is greater than permitted [13:29:24] non-ring atom 2 marked aromatic [13:29:24] Explicit valence for atom # 1 C, 11, is greater than permitted
Remove invalid molecules from list.
In [16]:
nmols = list(filter(lambda x: x is not None, nmols))
Print out the number of valid molecules, but training can be unstable so some the number can vary significantly.
In [17]:
# currently training is unstable so 0 is a common outcome
print ("{} valid molecules".format(len(nmols)))
411 valid molecules
Remove duplicate generated molecules.
In [18]:
nmols_smiles = [Chem.MolToSmiles(m) for m in nmols]
nmols_smiles_unique = list(OrderedDict.fromkeys(nmols_smiles))
nmols_viz = [Chem.MolFromSmiles(x) for x in nmols_smiles_unique]
print ("{} unique valid molecules".format(len(nmols_viz)))
48 unique valid molecules
Print out up to 100 unique valid molecules.
In [19]:
img = Draw.MolsToGridImage(nmols_viz[0:100], molsPerRow=5, subImgSize=(250, 250), maxMols=100, legends=None, returnPNG=False)
In [20]:
img
Out[20]:
This is an example of what the molecules should look like.
