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.
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.
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.
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 resultsThe 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 resultsThe 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.
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.
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)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)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.
After installing, run the following CLI command to ensure it and send the path to stdout
$ chembl_downloaderUse --test to show two example queries
$ chembl_downloader --testIf 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()).
The most recent release can be installed from PyPI with uv:
$ uv pip install chembl_downloaderor with pip:
$ python3 -m pip install chembl_downloaderThe most recent code and data can be installed directly from GitHub with uv:
$ uv --preview pip install git+https://github.com/cthoyt/chembl-downloader.gitor with pip:
$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/cthoyt/chembl-downloader.gitNote that this requires setting UV_PREVIEW mode enabled until the uv build
backend becomes a stable feature.
See
who's using chembl-downloader.
chembl-downloader is compatible with all versions of ChEMBL. However, some
files are not available for all versions. For example, the SQLite version of the
database was first added in release 21 (2015-02-12).
| ChEMBL Version | Release Date | Total Named Compounds from SQLite |
|---|---|---|
| 31 | 2022-07-12 | 41,585 |
| 30 | 2022-02-22 | 41,549 |
| 29 | 2021-07-01 | 41,383 |
| 28 | 2021-01-15 | 41,049 |
| 27 | 2020-05-18 | 40,834 |
| 26 | 2020-02-14 | 40,822 |
| 25 | 2019-02-01 | 39,885 |
| 24_1 | 2018-05-01 | 39,877 |
| 24 | ||
| 23 | 2017-05-18 | 39,584 |
| 22_1 | 2016-11-17 | |
| 22 | 39,422 | |
| 21 | 2015-02-12 | 39,347 |
| 20 | 2015-02-03 | - |
| 19 | 2014-07-2333 | - |
| 18 | 2014-04-02 | - |
| 17 | 2013-09-16 | - |
| 16 | 2013-055555-15 | - |
| 15 | 2013-01-30 | - |
| 14 | 2012 -07-18 | - |
| 13 | 2012-02-29 | - |
| 12 | 2011-11-30 | - |
| 11 | 2011-06-07 | - |
| 10 | 2011-06-07 | - |
| 09 | 2011-01-04 | - |
| 08 | 2010-11-05 | - |
| 07 | 2010-09-03 | - |
| 06 | 2010-09-03 | - |
| 05 | 2010-06-07 | - |
| 04 | 2010-05-26 | - |
| 03 | 2010-04-30 | - |
| 02 | 2009-12-07 | - |
| 01 | 2009-10-28 | - |
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
The code in this package is licensed under the MIT License.
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
See developer instructions
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
$ git clone git+https://github.com/cthoyt/chembl-downloader.git
$ cd chembl-downloader
$ uv --preview pip install -e .Alternatively, install using pip:
$ UV_PREVIEW=1 python3 -m pip install -e .Note that this requires setting UV_PREVIEW mode enabled until the uv build
backend becomes a stable feature.
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 updateMore info on Cruft's update command is available here.
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 pyAdditionally, these tests are automatically re-run with each commit in a GitHub Action.
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.htmlThe 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.
- Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
- Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
- You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
- Click next, and you're good to go!
Zenodo is a long-term archival system that assigns a DOI to each release of your package.
- 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.
- 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.
You only have to do the following steps once.
- Register for an account on the Python Package Index (PyPI)
- 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
- 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
- Issue an API token from https://pypi.org/manage/account/token
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.
After installing the package in development mode and installing tox with
uv tool install tox --with tox-uv or python3 -m pip install to
8773
x tox-uv, run
the following from the console:
$ tox -e finishThis script does the following:
- Uses bump-my-version to
switch the version number in the
pyproject.toml,CITATION.cff,src/chembl_downloader/version.py, anddocs/source/conf.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel using
uv build - Uploads to PyPI using
uv publish. - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- 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 -- minorafter.
- Navigate to https://github.com/cthoyt/chembl-downloader/releases/new to draft a new release
- Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
- Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
- Click the big green "Publish Release" button
This will trigger Zenodo to assign a DOI to your release as well.