rail-berkeley/design-bench

design-bench's Issues

Failing to recognize the tokenizer

Hi,

I am trying to educate myself on how to use design-bench APIs. I tried to execute the "Reproducing Baseline Performance," and I keep getting the following error:

2024-01-05 18:53:35.795906: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1858] Adding visible gpu devices: 0, 1
Traceback (most recent call last):
File "/home/user_name/miniconda3/envs/design-baselines/bin/design-baselines", line 33, in
sys.exit(load_entry_point('design-baselines', 'console_scripts', 'design-baselines')())
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/user_name/Desktop/Projects/Superconductor-OKD/design-baselines/design_baselines/cli.py", line 804, in make_table
from design_bench.datasets.discrete.tf_bind_8_dataset import TFBind8Dataset
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/design_bench/init.py", line 766, in
feature_extractor=MorganFingerprintFeatures(dtype=np.int32),
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/design_bench/oracles/feature_extractors/morgan_fingerprint_features.py", line 74, in init
os.path.join(DATA_DIR, 'smiles_vocab.txt'))
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/deepchem/feat/smiles_tokenizer.py", line 87, in init
super().init(vocab_file, **kwargs)
File "/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/transformers/tokenization_bert.py", line 196, in init
"model use tokenizer = BertTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)".format(vocab_file)
ValueError: Can't find a vocabulary file at path '/home/user_name/miniconda3/envs/design-baselines/lib/python3.7/site-packages/design_bench_data/smiles_vocab.txt'. To load the vocabulary from a Google pretrained model use tokenizer = BertTokenizer.from_pretrained(PRETRAINED_MODEL_NAME)

Can someone help me with this?

Access to .npy datasets

Hi,
Thank you for releasing the package!
I wanted to check the procedure to access the offline datasets. It seems these are not part of the repo. I am not sure if I am missing something.

For example, I get the following error when using
task = design_bench.make('ChEMBL-ResNet-v0')
FileNotFoundError: [Errno 2] No such file or directory:
/chembl-GI50-CHEMBL1964047/chembl-y-2.npy'

Thank you!