Chemistry

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

The RDKit is an open-source toolkit for cheminformatics, 2D and 3D molecular operations, descriptor
generation for machine learning, etc.

The Chemistry Development Kit (CDK) is a collection of modular Java libraries for processing chemical
information (cheminformatics). The modules are free and open-source and are easy to integrate with other
open-source or in-house projects. Also cheminformatics nodes for KNIME.

Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization. Also capable of performing a molecular similarity search, it is 100% open source and provides enhanced stereochemistry support for end users, as well as a documented API for developers.

Open source Java-based chemistry library, also openchemlib-js JavaScript interface with the openchemlib java
library.

The ChemDoodle Web Components library is a pure Javascript chemical graphics and cheminformatics library
derived from the ChemDoodle® application and produced by iChemLabs. ChemDoodle Web Components
allow the developer to present publication quality 2D and 3D graphics and animations for chemical structures,
reactions and spectra.

Kekule.js is an open source JavaScript library for cheminformatics released under MIT licence. Currently, it is
molecule-centric, focusing on providing the ability to represent, draw, edit, compare and search molecule
structures on web browsers.

Cheminformatics toolkit built with TypeScript. Can be used to carry out some fairly sophisticated cheminformatics tasks on a contemporary web browser, such as rendering molecules for display, format conversions, calculations, interactive sketching, among other things. The library can be used within any JavaScript engine, including web browsers, NodeJS and Electron.

A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry).

A cheminformatics package for analysing drug-like small molecule data in R. Its latest version contains
functions for efficient processing of large numbers of small molecules, physicochemical/structural property
predictions, structural similarity searching, classification and clustering of compound libraries with a wide
spectrum of algorithms.

A graph-based molecule modelling and cheminformatics analysis toolkit fully implemented in Julia.

A C++ library for cheminformatics. This repo also contains a variety of useful command line tools, built with
LillyMol. LillyMol does only a subset of cheminformatics tasks, but tries to do those tasks efficiently and
correctly. LillyMol has some novel approaches to substructure searching, reaction enumeration and chemical
similarity.

Library for processing molecules and reactions in python way. Chython is fork of CGRtools for which there has
been no development for several years, but could be reinitiated.

CDPKit (short for Chemical Data Processing Toolkit) is an open-source cheminformatics toolkit implemented
in C++. CDPKit comprises a suite of software tools and a programming library called the Chemical Data
Processing Library (CDPL) which provides a high-quality and well-tested modular implementation of basic
functionality typically required by any higher-level software application in the field of cheminformatics. In
addition to the CDPL C++ API, an equivalent Python-interfacing layer is provided that allows to harness all of
CDPL’s functionality easily from Python code.