mlchem

mlchem is a Python cheminformatics library designed for the scientific community. It provides a comprehensive set of tools for data handling, molecule manipulation, drawing, machine learning, and plotting. The library has been tested for python 3.12, 3.13 and 3.14 (experimental).

Documentation

Available at seacunilever.github.io/mlchem.

Features

• Data Handling: Efficiently manage and process chemical data, including loading, cleaning, and transforming datasets.
• Molecule Manipulation: Tools for manipulating molecular structures, such as adding or removing atoms, modifying bonds, and generating molecular conformations.
• Pattern Recognition: An extensive list of functions to search for specific structural patterns.
• Molecule Drawing: Visualise molecules with customisable drawing options, creating high-quality images for presentations and publications.
• Machine Learning: Implement machine learning models for cheminformatics, including training, evaluating, and deploying models to predict chemical properties and activities.
• Feature Analysis and Interpretation: Interpret model features and provide insightful plots.

Architecture

Modules

chem.visualise/

• space.py: Computes and visualises datasets in a lower-dimensional space.
• simmaps.py: Generates "rdkit-like" similarity maps based on atomic importance weights.
• drawing.py: Handles the drawing of molecular structures with many customisable options.

chem.calculator/

• tools.py: Provides numerous tools for chemical calculations.
• descriptors.py: Calculates various descriptors for molecules, including RDKit and Mordred descriptors, atomic descriptors, chemotypes, fingerprints, and some quantum chemistry properties.

chem.manipulation.py

The mlchem.chem.manipulation module offers a variety of tools for creating, converting, manipulating molecular structures, generate new molecules and recognise molecular patterns.

ml.feature_selection/

• filters.py: Provides functionalities for filtering features.
• wrappers.py: Offers simplified interfaces for feature selection.

ml.modelling/

• model_interpretation.py: Provides tools for interpreting machine learning models.
• model_evaluation.py: Contains tools for evaluating machine learning models.

ml.preprocessing/

• dimensional_reduction.py: Provides functionalities for compressing dataframes using various dimensionality reduction techniques.
• feature_transformation.py: Expands features to polynomial features.
• scaling.py: Provides functionalities for scaling dataframes using different scaling techniques.
• undersampling.py: Contains techniques for handling imbalanced datasets.

Installation

To install mlchem, open your command prompt and use either:

pip install git+https://github.com/seacunilever/mlchem.git

or, from PyPI:

pip install mlchem-ul

Then import in Python as:

import mlchem

Development installation, to modify the code or contribute with some changes:

# Clone the repository
git clone https://github.com/seacunilever/mlchem
cd mlchem

# (Optional: create a virtual environment)
python -m venv _venv

# Activate on macOS/Linux:
source _venv/bin/activate

# Activate on Windows (PowerShell):
.\_venv\Scripts\Activate.ps1

# Activate on Windows (cmd.exe):
_venv\Scripts\activate.bat

# Make an editable install of mlchem from the source tree
pip install -e .

# and install requirements
pip install -r requirements.txt

Logging

mlchem emits diagnostic logs during pipeline execution (feature selection, model evaluation, data preprocessing) to help users track progress and debug issues. Logs are emitted at the INFO level by default and appear on the console.

Logs appear automatically when running mlchem functions:

from mlchem.ml.feature_selection.wrappers import SequentialForwardSelection
from mlchem.metrics import get_geometric_S

sfs = SequentialForwardSelection(estimator=..., metric=get_geometric_S, ...)
sfs.fit(X_train, y_train, X_test, y_test)
# Logs appear on console: e.g., "10:35:55 - mlchem.ml.feature_selection.wrappers - INFO - SFS start: ..."

Controlling Log Level

Change the logging level to filter output (e.g., show only warnings, suppress info messages):

sfs = SequentialForwardSelection(..., log_level='WARNING')
sfs.fit(...)  # Only WARNING+ logs appear

Valid log levels: DEBUG, INFO, WARNING, ERROR, CRITICAL

Post-Pipeline Inspection and File Logging

Capture logs to memory or file for later inspection without modifying function calls:

from mlchem.helper import start_logging

# Capture to console + memory
logs = start_logging(log_level='INFO', to_console=True)
sfs.fit(X_train, y_train, X_test, y_test)
print(logs.get_logs())  # View captured logs

# Capture to file + console
logs = start_logging(log_level='INFO', to_file='pipeline.log')
sfs.fit(...)
# Logs written to pipeline.log + displayed on console

# Capture to file only (silent)
logs = start_logging(to_console=False, to_file='pipeline.log')
sfs.fit(...)  # Silent; logs only in file

Use this for non-interactive scripts and production environments.

Compatibility checks (Python 3.12, 3.13, 3.14)

This repository includes a local matrix runner and CI workflow scaffold to keep cross-version support visible on every push.

For most local development, running python -m pytest -vv tests from repo root is enough. The commands in this section are mainly for maintainers, release checks, or contributors who want local parity with CI across multiple Python versions.

Prerequisite for all commands below: activate your project virtual environment first.

Warning policy note:

• A narrowly scoped pytest warning filter is used for an upstream SHAP PendingDeprecationWarning (shap.plots.colors._colors) tied to matplotlib colormap API changes.
• Keep this filter temporary and remove it once SHAP resolves the upstream issue.
• To periodically audit all warnings explicitly, run:

python -m pytest -vv tests -W default

Coverage baseline (canonical: Python 3.12):

python -m pytest -vv tests --cov=mlchem --cov-config=.coveragerc --cov-branch --cov-report=term --cov-report=xml:coverage.xml
python - <<'PY'
import xml.etree.ElementTree as ET
root = ET.parse('coverage.xml').getroot()
line_pct = round(float(root.get('line-rate', 0.0)) * 100)
branch_pct = round(float(root.get('branch-rate', 0.0)) * 100)
print(f'line={line_pct}, branch={branch_pct}')
PY
python -m anybadge --label "line cov" --value <LINE_PERCENT> --file assets/coverage.svg --overwrite 50=red 60=orange 70=yellow 80=yellowgreen 90=green
python -m anybadge --label "branch cov" --value <BRANCH_PERCENT> --file assets/coverage-branch.svg --overwrite 50=red 60=orange 70=yellow 80=yellowgreen 90=green

Note: both badges (assets/coverage.svg for line coverage and assets/coverage-branch.svg for branch coverage) are refreshed automatically by GitHub CI on push (py312 job), so local regeneration is optional and mainly useful for previewing changes before pushing.

Current policy:

• Python 3.12 and 3.13 are required to pass.
• Python 3.14 is currently experimental (reported, not blocking).

Local matrix (default envs under ~/Envs)

The matrix helper expects existing Python environments (for example py312, py313, py314). If you do not use this layout, use the tox entrypoint below instead.

Run all environments in fast mode (default: no dependency reinstall):

From repository root:

python scripts/run_local_matrix.py

From scripts/ directory:

python run_local_matrix.py

On Windows, if output appears buffered/silent, use unbuffered mode:

py -u scripts/run_local_matrix.py

By default, the runner streams live progress (active env/step and pytest output).

Run all environments with full dependency reinstall + tests:

python scripts/run_local_matrix.py --full-install -- -vv tests

Strict mode (make Python 3.14 failures blocking):

python scripts/run_local_matrix.py --strict-314 -- -vv tests

Quiet mode (disable live streaming and print only summary):

python scripts/run_local_matrix.py --no-live-output -- -vv tests

tox entrypoint

You can also run the same idea via tox:

python -m pip install tox

python -m tox -e py312,py313,py314

The py314 tox environment is marked non-blocking during early adoption.

Usage

Here's some basic examples of how to use mlchem:

calculate rdkit descriptors for two molecules

from mlchem.chem.manipulation import create_molecule
from mlchem.chem.calculator import descriptors
mol1 = create_molecule('c1ccccc1CCCO')
mol2 = create_molecule('CCCCCN')
desc_df = descriptors.get_rdkitDesc([mol1, mol2],include_3D=True)

calculate fingerprints

from mlchem.chem.calculator import descriptors

smiles_list = ['CCO', 'CCN', 'CCC']

# Morgan bit-vectors (default configuration is radius=2 and nBits=2048)
fp_df = descriptors.get_fingerprint_df(smiles_list, fp_type='m', radius=2, nBits=2048)

# Include bit info for interpretability on a single molecule
fp, bit_info = descriptors.get_fingerprint('CCO', fp_type='m', radius=2, nBits=2048, include_bit_info=True)

calculate chemotypes faster on larger datasets

from mlchem.chem.calculator import descriptors

smiles_list = ['CCO', 'CCN', 'COCC', 'c1ccccc1O']

# n_jobs=1 keeps serial execution (default)
# n_jobs>1 enables multi-threaded molecule processing
# n_jobs=-1 uses all available CPU cores
chemotypes = descriptors.get_chemotypes(smiles_list, n_jobs=4)

Performance note: since v1.1.0, chemotype execution reuses per-molecule rule results and avoids repeated molecule preparation. This is especially important for large rule dictionaries and medium-to-large training sets.

control ML verbosity in notebooks and development runs

import logging
from sklearn.linear_model import LogisticRegression
from mlchem.ml.feature_selection.wrappers import (
  SequentialForwardSelection,
  CombinatorialSelection,
)

# Enable library logs in your notebook session
logging.basicConfig(level=logging.INFO)

sfs = SequentialForwardSelection(
  estimator=LogisticRegression(),
  estimator_string='lr',
  metric=lambda y_true, y_pred: (y_true == y_pred).mean(),
  log_level='INFO',
)

# Runtime toggle (use DEBUG for very verbose traces)
sfs.set_log_level('DEBUG')
sfs.set_log_level('WARNING')

cs = CombinatorialSelection(
  estimator=LogisticRegression(),
  metric=lambda y_true, y_pred: (y_true == y_pred).mean(),
  log_level='INFO',
)

optional diagnostics for undersampling and y-scrambling

from mlchem.ml.preprocessing.undersampling import undersample
from mlchem.ml.modelling.model_evaluation import y_scrambling

train_balanced, test_updated = undersample(
  train_set=train_df,
  test_set=test_df,
  class_column='class',
  desired_proportion_majority=0.5,
  log_level='INFO',
)

y_scrambling(
  estimator=model,
  train_set=X_train,
  y_train=y_train,
  test_set=X_test,
  y_test=y_test,
  metric_function=metric_fn,
  n_iter=50,
  plot=False,
  log_level='INFO',
)

pattern recognition

de novo molecule generation and cleaning

show pre-defined colour palette

More examples in the examples folder.

Building the documentation

The documentation is built with Sphinx using the autodoc and myst-parser extensions. Source files live under docs/source/, build output lands in docs/build/html/, and a small post-build script (docs/_publish.py) mirrors that build into docs/ so GitHub Pages always serves the latest version.

Single-source content: docs/source/welcome.md {include}s this README, so you only edit README.md — never duplicate content into the welcome page.

What is tracked, what is not

Only the inputs and the published output are tracked in git:

• Tracked (do edit / commit)
  • docs/source/ — Sphinx inputs (conf.py, *.rst, welcome.md, _static/custom.css).
  • docs/Makefile, docs/make.bat, docs/_publish.py — build entry points.
  • docs/.nojekyll — tells GitHub Pages to keep _static/ and _sources/.
  • docs/*.html, docs/_static/, docs/_sources/, docs/_images/, docs/objects.inv, docs/searchindex.js — the published mirror that GitHub Pages serves; updated automatically by make html via _publish.py.
• Not tracked (regenerated on every build, ignored via .gitignore)
  • docs/build/ — Sphinx scratch output, including build/html/.doctrees/ and build/html/.buildinfo incremental-build caches.
  • docs/*warnings*.{log,txt} — ad-hoc diagnostic logs.

Prerequisites

The documentation toolchain is part of requirements.txt. If you only want the doc deps:

pip install sphinx myst-parser

Build & publish

Run the commands from the docs/ directory (NOT from docs/source/ — source is the value of SOURCEDIR inside the Makefile / make.bat, not the working directory):

# from the repository root
cd docs

# wipe previous build artefacts (clears docs/build/)
make clean

# build HTML and automatically mirror docs/build/html/ -> docs/
make html

make html runs Sphinx and then invokes _publish.py, which:

1. removes every stale published asset at the root of docs/ (everything except source/, build/, Makefile, make.bat, _publish.py, .nojekyll, .gitignore);
2. copies the freshly built site from docs/build/html/ into docs/;
3. ensures the .nojekyll marker is present so GitHub Pages keeps _static/ and _sources/.

Then commit the regenerated files at the root of docs/ — that is what gets published. docs/build/ stays local.

If you ever build with a raw sphinx-build invocation, run the mirror step manually:

make publish

On Windows the same targets are dispatched through make.bat, so the commands work in both cmd and PowerShell as long as sphinx-build and python are on the PATH.

Common pitfalls: running make html from docs/source/ (no Makefile there → "no rule" / "missing Makefile" error), or typing make build (the Sphinx target is html; build is the output directory, not a target).

Contributing

We welcome contributions to mlchem. Users are free to propose new functionalities, flag new bugs, fix old bugs and issue pull requests. Please consult the contribution guide on how to properly propose and submit changes.

Third-Party Dependencies

This project uses the SELFIES Python package for molecular string representations.
SELFIES is licensed under the Apache License 2.0. In accordance with its license, the relevant license is included in this repository.

This project uses and adapts code from the RDKit cheminformatics toolkit, which is licensed under the BSD 3-Clause License.

License

This project is licensed under the BSD-3 License.

Note: This project includes components licensed under the Apache License 2.0 (e.g., the SELFIES package), as well as source code taken and adapted from RDKit library.

Acknowledgements

Special thanks to the Safety, Environmental & Regulatory Science (SERS) Department at Unilever.