Open Source

Olympus is a Python framework for benchmarking noisy optimization and experiment planning, with mixed parameter domains, experimental benchmarks, analytical test functions and a shared planner interface.

Lab Automation · Process Optimization

BoFire is a Python framework for experimental design and Bayesian optimization, supporting mixed variables, constraints, molecular representations and iterative candidate selection.

Lab Automation · Process Optimization

Summit is a Python toolkit for chemical reaction optimisation, combining optimisation strategies, simulated reaction benchmarks and closed-loop workflows for evaluating experimental conditions.

Lab Automation · Process Optimization

BayBE is a Python toolbox for Bayesian experimental design that recommends parameter configurations from defined search spaces, objectives and measurements, including chemistry-aware and multi-target workflows.

Lab Automation · Process Optimization

DP-GEN is a Python concurrent-learning platform that coordinates molecular simulation, first-principles calculations and DeePMD-kit workflows to generate interatomic potential models.

Computational Chemistry · Materials Discovery

QML is an archived Python toolkit for quantum machine learning with Fortran-backed representation, kernel and solver modules. Further development has moved to qmllib.

Molecular Property Prediction · Quantum Chemistry

DScribe is a Python library that converts atomic structures into numerical descriptors for machine learning, visualization and similarity analysis, with batch processing and atomic-position derivatives.

Molecular Property Prediction · Materials Discovery

matminer is a Python library for materials-science data mining, bringing together community datasets, data retrieval methods and featurizers with citation support for research workflows.

Materials Discovery

Pymatgen is a Python materials-analysis library combining structure and file-format support with phase diagrams, electronic-structure analysis, thermodynamic calculations and database integrations.

Materials Discovery

Chemistry Development Kit (CDK) is a Java library for chemical representations, file conversion, structure searching, fingerprints, QSAR descriptors and molecular rendering within other programs.

Cheminformatics

Open Babel is a chemical data toolkit with ready-to-use programs and a Python interface for format conversion, molecular searching, and 2D or 3D coordinate generation.

Cheminformatics

Mordred is a Python molecular descriptor calculator with command-line and RDKit-based library workflows, producing descriptor tables for cheminformatics analysis and downstream model evaluation.

Molecular Property Prediction · Cheminformatics

SELFIES is a molecular string representation and Python library for translating SMILES, preparing token encodings, and generating molecular graphs under configurable semantic constraints.

Molecular Generation · Cheminformatics

Datamol is a Python molecular-processing library built on RDKit, with tools for structure conversion, standardization, fingerprints, conformers, visualization and local or remote file I/O.

Cheminformatics

Molfeat is a Python toolkit for small-molecule featurization, combining molecular fingerprints, descriptors and pretrained embeddings with parallel transformation, caching and extensible plugins.

Molecular Property Prediction · Cheminformatics

DeepPurpose is a PyTorch-based toolkit for training and applying compound and protein prediction models, with workflows for drug-target interactions, molecular properties, repurposing and virtual screening.

Drug Discovery

TorchDrug is a PyTorch-based toolkit for graph and molecular machine learning, with SMILES input, graph operations, property-prediction building blocks and multi-CPU/GPU execution.

Molecular Property Prediction · Drug Discovery

PubChemPy is a Python wrapper for the PubChem PUG REST API, supporting chemical searches, compound-property retrieval, standardization, file-format conversion and depiction.

Cheminformatics · Scientific Data

DeepChem is an open-source Python toolchain for scientific deep learning in drug discovery, materials science, quantum chemistry and biology, with backend-specific dependencies and guided tutorials.

Drug Discovery

RDKit is an open-source cheminformatics toolkit for 2D and 3D molecular operations, descriptor and fingerprint generation, and chemical searching through a PostgreSQL cartridge.

Cheminformatics