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Use local cache of ZINC dataset, since original URL is not available anymore #58

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merged 2 commits into from
Oct 23, 2019
Merged

Use local cache of ZINC dataset, since original URL is not available anymore #58

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0e9a315
use local cache of ZINC dataset, since original URL is not available …
daniil-polykovskiy-insilico Oct 23, 2019
bb549cb
fix flake8
daniil-polykovskiy-insilico Oct 23, 2019
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use local cache of ZINC dataset, since original URL is not available … 
…anymore
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@daniil-polykovskiy-insilico
daniil-polykovskiy-insilico committed Oct 23, 2019
commit 0e9a3156905cfd6deb45313ba23aefea6f79475b
3 changes: 3 additions & 0 deletions data/11_p0.smi.gz
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17 changes: 8 additions & 9 deletions scripts/prepare_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,9 @@ def get_parser():
'--seed', type=int, default=0, help='Random state'
)
parser.add_argument(
'--url', type=str,
default='http://zinc.docking.org/db/bysubset/11/11_p0.smi.gz',
help='url to .smi.gz file with smiles'
'--zinc', type=str,
default='../data/11_p0.smi.gz',
help='path to .smi.gz file with ZINC smiles'
)
parser.add_argument(
'--n_jobs', type=int, default=1,
Expand All @@ -41,7 +41,7 @@ def get_parser():
)
parser.add_argument(
'--isomeric', action='store_true', default=False,
help='Save non-isomeric SMILES'
help='Save isomeric SMILES (non-isomeric by default)'
)
return parser

Expand All @@ -56,10 +56,9 @@ def process_molecule(mol_row, isomeric):
return _id, smiles


def download_dataset(url):
logger.info('Downloading from {}'.format(url))
req = requests.get(url)
with gzip.open(BytesIO(req.content)) as smi:
def unzip_dataset(path):
logger.info("Unzipping dataset")
with gzip.open(path) as smi:
lines = smi.readlines()
return lines

Expand Down Expand Up @@ -104,7 +103,7 @@ def split_dataset(dataset, seed):


def main(config):
lines = download_dataset(config.url)
lines = unzip_dataset(config.zinc)
dataset = filter_lines(lines, config.n_jobs, config.isomeric)
dataset = split_dataset(dataset, config.seed)
if not config.keep_ids:
Expand Down