#!/usr/bin/python
#-*-coding:utf-8-*-
# Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
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# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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# http://www.apache.org/licenses/LICENSE-2.0
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"""
Processing of ZINC dataset.
The ZINC database is a curated collection of commercially available chemical compounds prepared especially for virtual screening. ZINC15 is designed to bring together biology and chemoinformatics with a tool that is easy to use for nonexperts, while remaining fully programmable for chemoinformaticians and computational biologists.
"""
import os
from os.path import join, exists
import pandas as pd
import numpy as np
from pahelix.datasets.inmemory_dataset import InMemoryDataset
__all__ = ['load_zinc_dataset']
[docs]def load_zinc_dataset(data_path):
"""Load ZINC dataset,process the input information.
Description:
The data file contains a csv table, in which columns below are used:
smiles: SMILES representation of the molecular structure.
zinc_id: the id of the compound
Args:
data_path(str): the path to the cached npz path.
Returns:
an InMemoryDataset instance.
Example:
.. code-block:: python
dataset = load_zinc_dataset('./zinc')
print(len(dataset))
References:
[1]Teague Sterling and John J. Irwin. Zinc 15 – ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11):2324–2337, 2015. doi: 10.1021/acs.jcim.5b00559. PMID: 26479676.
"""
smiles_list = _load_zinc_dataset(data_path)
data_list = []
for i in range(len(smiles_list)):
data = {}
data['smiles'] = smiles_list[i]
data_list.append(data)
dataset = InMemoryDataset(data_list)
return dataset
def _load_zinc_dataset(data_path):
"""
Args:
data_path(str): the path to the cached npz path.
Returns:
smile_list: the smile list of the input.
"""
raw_path = join(data_path, 'raw')
csv_file = os.listdir(raw_path)[0]
input_df = pd.read_csv(
join(raw_path, csv_file), sep=',', compression='gzip', dtype='str')
smiles_list = list(input_df['smiles'])
return smiles_list