chembl_ml_tools

Tools to obtain data from the ChEMBL database to be used as input for Machine Learning models.

This package provides:

• Function chembl_activity_target, to extract all assay results for a given organism.

• Class ChemblMoleculeSampler, to obtain a random sample of molecules existing in the ChEMBL database, excluding a list of known molecules. Useful to generate negative cases for a model.

Requirements

These tools require access to a postgres database server containing the ChEMBL database. You may install ChEMBL in your own computer by following these instructions: How to install ChEMBL

This package is a general ChEMBL access prepared to work within the Antimicrobial ML tasks package. If you want to use it for other applications please make the necessary modifications.

Installation

To install the package in a conda environment, please run:

pip install git+https://github.com/ersilia-os/chembl_ml_tools.git

Testing

You can use the folowing code to check that the package is working. This test assumes that there is a DB user called chembl_user with permissions to read the database.

Before running, make sure that the postgres service with the ChEMBL database is up.

import pandas as pd
from chemblmltools import chembl_activity_target

df1 = chembl_activity_target(
        db_user='chembl_user',
        db_password='aaa',
        organism_contains='enterobacter',
        max_heavy_atoms=100)

print(df1.head(5))