ChEMBL Downloader

Reproducibly download, open, parse, and query ChEMBL.

Don't worry about downloading/extracting ChEMBL or versioning - just use chembl_downloader to write code that knows how to download it and use it automatically.

💪 Getting Started

Download an extract the SQLite dump using the following:

import chembl_downloader

path = chembl_downloader.download_extract_sqlite(version='28')

After it's been downloaded and extracted once, it's smart and does not need to download again. It gets stored using pystow automatically in the ~/.data/chembl directory.

Full technical documentation can be found on ReadTheDocs. Tutorials can be found in Jupyter notebooks in the notebooks/ directory of the repository.

Download the Latest Version

You can modify the previous code slightly by omitting the version keyword argument to automatically find the latest version of ChEMBL:

import chembl_downloader

path = chembl_downloader.download_extract_sqlite()

The version keyword argument is available for all functions in this package (e.g., including connect(), cursor(), and query()), but will be omitted below for brevity.

Automatically Connect to SQLite

Inside the archive is a single SQLite database file. Normally, people manually untar this folder then do something with the resulting file. Don't do this, it's not reproducible! Instead, the file can be downloaded and a connection can be opened automatically with:

import chembl_downloader

with chembl_downloader.connect() as conn:
    with conn.cursor() as cursor:
        cursor.execute(...)  # run your query string
        rows = cursor.fetchall()  # get your results

The cursor() function provides a convenient wrapper around this operation:

import chembl_downloader

with chembl_downloader.cursor() as cursor:
    cursor.execute(...)  # run your query string
    rows = cursor.fetchall()  # get your results

Run a Query and Get a Pandas DataFrame

The most powerful function is query() which builds on the previous connect() function in combination with pandas.read_sql to make a query and load the results into a pandas DataFrame for any downstream use.

import chembl_downloader

sql = """
SELECT
    MOLECULE_DICTIONARY.chembl_id,
    MOLECULE_DICTIONARY.pref_name
FROM MOLECULE_DICTIONARY
JOIN COMPOUND_STRUCTURES ON MOLECULE_DICTIONARY.molregno == COMPOUND_STRUCTURES.molregno
WHERE molecule_dictionary.pref_name IS NOT NULL
LIMIT 5
"""

df = chembl_downloader.query(sql)
df.to_csv(..., sep='\t', index=False)

Suggestion 1: use pystow to make a reproducible file path that's portable to other people's machines (e.g., it doesn't have your username in the path).

Suggestion 2: RDKit is now pip-installable with pip install rdkit-pypi, which means most users don't have to muck around with complicated conda environments and configurations. One of the powerful but understated tools in RDKit is the rdkit.Chem.PandasTools module.

SDF Usage

Access an RDKit supplier over entries in the SDF dump

This example is a bit more fit-for-purpose than the last two. The supplier() function makes sure that the latest SDF dump is downloaded and loads it from the gzip file into a rdkit.Chem.ForwardSDMolSupplier using a context manager to make sure the file doesn't get closed until after parsing is done. Like the previous examples, it can also explicitly take a version.

from rdkit import Chem

import chembl_downloader

with chembl_downloader.supplier() as suppl:
    data = []
    for i, mol in enumerate(suppl):
        if mol is None or mol.GetNumAtoms() > 50:
            continue
        fp = Chem.PatternFingerprint(mol, fpSize=1024, tautomerFingerprints=True)
        smi = Chem.MolToSmiles(mol)
        data.append((smi, fp))

This example was adapted from Greg Landrum's RDKit blog post on generalized substructure search.

Iterate over SMILES

This example uses the supplier() method and RDKit to get SMILES strings from molecules in ChEMBL's SDF file. If you want direct access to the RDKit molecule objects, use supplier().

import chembl_downloader

for smiles in chembl_downloader.iterate_smiles():
    print(smiles)

Get an RDKit substructure library

Building on the supplier() function, the get_substructure_library() makes the preparation of a substructure library automated and reproducible. Additionally, it caches the results of the build, which takes on the order of tens of minutes, only has to be done once and future loading from a pickle object takes on the order of seconds.

The implementation was inspired by Greg Landrum's RDKit blog post, Some new features in the SubstructLibrary. The following example shows how it can be used to accomplish some of the first tasks presented in the post:

from rdkit import Chem

import chembl_downloader

library = chembl_downloader.get_substructure_library()
query = Chem.MolFromSmarts('[O,N]=C-c:1:c:c:n:c:c:1')
matches = library.GetMatches(query)

Morgan Fingerprints Usage

Get the Morgan Fingerprint file

ChEMBL makes a file containing pre-computed 2048 bit radius 2 morgan fingerprints for each molecule available. It can be downloaded using:

import chembl_downloader

path = chembl_downloader.download_fps()

The version and other keyword arguments are also valid for this function.

Load fingerprints with chemfp

The following wraps the download_fps function with chemfp's fingerprint loader:

import chembl_downloader

arena = chembl_downloader.chemfp_load_fps()

The version and other keyword arguments are also valid for this function. More information on working with the arena object can be found here.

Command Line Interface

After installing, run the following CLI command to ensure it and send the path to stdout:

$ chembl_downloader download

Use the test subcommand to show two example queries:

$ chembl_downloader test

Configuration

If you want to store the data elsewhere using pystow (e.g., in pyobo I also keep a copy of this file), you can use the prefix argument.

import chembl_downloader

# It gets downloaded/extracted to
# ~/.data/pyobo/raw/chembl/29/chembl_29/chembl_29_sqlite/chembl_29.db
path = chembl_downloader.download_extract_sqlite(prefix=['pyobo', 'raw', 'chembl'])

See the pystow documentation on configuring the storage location further.

The prefix keyword argument is available for all functions in this package (e.g., including connect(), cursor(), and query()).

🚀 Installation

The most recent release can be installed from PyPI with uv:

$ uv pip install chembl_downloader

or with pip:

$ python3 -m pip install chembl_downloader

The most recent code and data can be installed directly from GitHub with uv:

$ uv pip install git+https://github.com/cthoyt/chembl-downloader.git

or with pip:

$ python3 -m pip install git+https://github.com/cthoyt/chembl-downloader.git

Users

See who's using chembl-downloader.

Statistics and Compatibility

chembl-downloader is compatible with all versions of ChEMBL (with a few caveats in the SQLite dumps of the first few versions, see discussion here). The following table can be generated with chembl_downloader history && chembl_downloader history-draw. These data can be found as a TSV in docs/_data/summary.tsv.

Version	Date	Compounds	Named Compounds	Assays	Activities	Documents	Targets	Cells	Tissues	Drug Warnings	Drug Indications	Drug Mechanisms
35	2024-12-01	2,496,335	42,231	1,740,546	21,123,501	92,121	16,003	2,129	782	1,676	55,442	7,330
34	2024-03-28	2,431,025	42,387	1,644,390	20,772,701	89,892	15,598	2,023	782	1,676	55,442	7,330
33	2023-05-31	2,399,743	41,923	1,610,596	20,334,684	88,630	15,398	2,021	782	1,636	51,582	7,098
32	2023-01-26	2,354,965	41,923	1,536,903	20,038,828	86,361	15,139	2,015	759	1,636	51,582	7,098
31	2022-07-12	2,331,700	41,585	1,498,681	19,780,369	85,431	15,072	2,000	757	1,293	48,816	6,656
30	2022-02-22	2,157,379	41,549	1,458,215	19,286,751	84,092	14,855	1,991	752	1,293	48,816	6,656
29	2021-07-01	2,105,464	41,383	1,383,553	18,635,916	81,544	14,554	1,978	743	1,262	45,902	6,202
28	2021-01-15	2,086,898	41,049	1,358,549	17,276,334	80,480	14,347	1,950	739	1,256	42,988	5,347
27	2020-05-18	1,961,462	40,834	1,221,361	16,066,124	76,086	13,382	1,831	707	0	37,259	5,134
26	2020-02-14	1,950,765	40,822	1,221,311	15,996,368	76,076	13,377	1,830	707	0	37,259	5,070
25	2019-02-01	1,879,206	39,885	1,125,387	15,504,603	72,271	12,482	1,670	655	0	29,457	4,992
24.1	2018-05-01	1,828,820	39,877	1,060,283	15,207,914	69,861	12,091	1,667	655	0	29,163	4,992
24	2018-05-01	1,828,820	39,877	1,060,283	15,207,914	69,861	12,091	1,667	655	0	29,163	4,992
23	2017-05-18	1,735,442	39,584	1,302,147	14,675,320	67,722	11,538	1,624	125	0	13,504	4,305
22.1	2016-11-17	1,686,695	39,422	1,246,683	14,371,197	65,213	11,224	1,619	111	0	12,573	3,834
22	2016-09-28	1,686,695	39,422	1,246,132	14,371,219	65,213	11,224	1,619	111	0	12,573	3,834
21	2015-02-12	1,592,191	39,347	1,212,831	13,968,617	62,502	11,019	1,612	0	0	5,951	3,799
20	2015-02-03	1,463,270	39,016	1,148,942	13,520,737	59,610	10,774	1,647	0	0	0	2,266
19	2014-07-23	1,411,786	38,910	1,106,285	12,843,338	57,156	10,579	1,653	0	0	0	2,239
18	2014-04-02	1,359,508	35,817	1,042,374	12,419,715	53,298	9,414	1,655	0	0	0	2,233
17	2013-09-16	1,324,941	32,692	734,201	12,077,491	51,277	9,356	1,746	0	0	0	2,213
16	2013-05-15	1,295,510	23,532	712,836	11,420,351	50,095	9,844	1,432	0	0	0	0
15	2013-01-30	1,254,575	23,528	679,259	10,509,572	48,735	9,570	1,432	0	0	0	0
14	2012-07-18	1,213,242	16,573	644,734	10,129,256	46,133	9,003	0	0	0	0	0
13	2012-02-29	1,143,682	16,397	617,681	6,933,068	44,682	8,845	0	0	0	0	0
12	2011-11-30	1,077,189	16,658	596,122	5,654,847	43,418	8,703	0	0	0	0	0
11	2011-06-07	1,060,258	16,264	582,982	5,479,146	42,516	8,603	0	0	0	0	0
10	2011-06-07	1,000,468	16,159	534,391	4,668,202	40,624	8,372	0	0	0	0	0
9	2011-01-04	658,075	3,746	499,867	3,030,317	39,094	8,091	0	0	0	0	0
8	2010-11-05	636,269	0	488,898	2,973,034	38,462	8,088	0	0	0	0	0
7	2010-09-03	602,500	0	485,095	2,948,069	38,204	8,078	0	0	0	0	0
6	2010-09-03	600,625	0	481,752	2,925,588	38,029	8,054	0	0	0	0	0
5	2010-06-07	578,715	0	459,823	2,787,240	36,624	7,493	0	0	0	0	0
4	2010-05-26	565,245	0	446,645	2,705,136	35,821	7,330	0	0	0	0	0
3	2010-04-30	547,133	0	432,022	2,490,742	34,982	7,330	0	0	0	0	0
2	2009-12-07	517,261	0	416,284	2,404,622	33,956	7,192	0	0	0	0	0
1	2009-10-28	440,055	0	329,250	1,936,969	26,299	5,694	0	0	0	0	0

Or, as a chart:

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

📖 Citation

Improving reproducibility of cheminformatics workflows with chembl-downloader Hoyt, C.T. (2025) arXiv, 2507.17783

@article{hoyt2025chembl,
   title={Improving reproducibility of cheminformatics workflows with chembl-downloader},
   author={Hoyt, Charles Tapley},
   year={2025},
   doi={10.21105/joss.08844},
   journal={Journal of Open Source Software},
   url={https://joss.theoj.org/papers/10.21105/joss.08844},
   month=sep,
   number={113},
   pages={8844},
   volume={10},
}

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

$ git clone git+https://github.com/cthoyt/chembl-downloader.git
$ cd chembl-downloader
$ uv pip install -e .

Alternatively, install using pip:

$ python3 -m pip install -e .

Updating Package Boilerplate

This project uses cruft to keep boilerplate (i.e., configuration, contribution guidelines, documentation configuration) up-to-date with the upstream cookiecutter package. Install cruft with either uv tool install cruft or python3 -m pip install cruft then run:

$ cruft update

More info on Cruft's update command is available here.

🥼 Testing

After cloning the repository and installing tox with uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, the unit tests in the tests/ folder can be run reproducibly with:

$ tox -e py

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ git clone git+https://github.com/cthoyt/chembl-downloader.git
$ cd chembl-downloader
$ tox -e docs
$ open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the pyproject.toml. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

The documentation can be deployed to ReadTheDocs using this guide. The .readthedocs.yml YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with tox -e docs-test) but also that ReadTheDocs can build it too.

Configuring ReadTheDocs

1. Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
4. Click next, and you're good to go!

📦 Making a Release

Configuring Zenodo

Zenodo is a long-term archival system that assigns a DOI to each release of your package.

1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once.
2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this

After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/cthoyt/chembl-downloader to see the DOI for the release and link to the Zenodo record for it.

Registering with the Python Package Index (PyPI)

You only have to do the following steps once.

1. Register for an account on the Python Package Index (PyPI)
2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button
3. 2-Factor authentication is required for PyPI since the end of 2023 (see this blog post from PyPI). This means you have to first issue account recovery codes, then set up 2-factor authentication
4. Issue an API token from https://pypi.org/manage/account/token

Configuring your machine's connection to PyPI

You have to do the following steps once per machine.

$ uv tool install keyring
$ keyring set https://upload.pypi.org/legacy/ __token__
$ keyring set https://test.pypi.org/legacy/ __token__

Note that this deprecates previous workflows using .pypirc.

Uploading to PyPI

After installing the package in development mode and installing tox with uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, run the following from the console:

$ tox -e finish

This script does the following:

1. Uses bump-my-version to switch the version number in the pyproject.toml, CITATION.cff, src/chembl_downloader/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using uv build
3. Uploads to PyPI using uv publish.
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion -- minor after.

Releasing on GitHub

1. Navigate to https://github.com/cthoyt/chembl-downloader/releases/new to draft a new release
2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
4. Click the big green "Publish Release" button

This will trigger Zenodo to assign a DOI to your release as well.