A powerful cheminformatics and molecule rendering toolbelt for JavaScript
Explore the docs ยป
Report Bug
ยท
Request Feature
ยท
Star Repository
| Resources | URL | Contributor(s) |
|---|---|---|
| JavaScript Examples | rdkitjs.com | @greglandrum , @MichelML |
| React.js Examples | react.rdkitjs.com | @MichelML |
| Vue.js Examples | vue.rdkitjs.com | @adam-of-barrot, @MichelML |
| Angular.js Examples | angular.rdkitjs.com | @Phil-DS |
| Next.js Examples | source code | @bugzpodder |
| Node.js Examples | source code | @adam-of-barrot |
| API Docs | docs.rdkitjs.com | @adam-of-barrot, @MichelML |
| WASM Module | source code | @ptosco |
 |
|---|
| Molecule Rendering Examples |
Table of contents
- Introduction
- Install
- Usage
- Usage in TypeScript
- Contributing
- Release process
- Website deployment
- Maintainers
Introduction
RDKit.js is a powerful cheminformatics and molecule rendering toolbelt for JavaScript.
It is the official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.
The project is leveraging web assembly to rollout a subset of the RDKit functionality that is relevant in any javascript context. The WASM module bundled with this package is compiled directly from the RDKit source code.
The functionality included in RDKit.js is decided by the RDKit core team and its community. Thus, if you use this package, your voice matters.
What is the scope of this repository
This repository is currently dedicated to:
- NPM builds and releases of the RDKit core wasm module
- Website deployment of examples using the RDKit core wasm module in JavaScript and web frameworks
- Any additional functionalities built on top of the RDKit core wasm module.
The scope of the project may change over time.
What is NOT the scope of this repository
Any changes to the core RDKit wasm module (also known as RDKit's MinimalLib) is out of scope of this project.
To contribute or keep track of the changes to the core RDKit wasm module, go here.
Install
npm i @rdkit/rdkit
# or yarn add @rdkit/rdkitUsage
Using RDKit.js package assets
Option 1: Use the npm package distribution files
Once you have the RDKit package installed in your node modules, copy the following distribution files anywhere in your deployed assets.
node_modules/@rdkit/rdkit/dist/RDKit_minimal.jsnode_modules/@rdkit/rdkit/dist/RDKit_minimal.wasm
NOTE: By default, both files must be copied at the same location in your deployed assets for the library to work properly. If you need the RDKIT_minimal.wasm file to be loaded from another location, use the locateFile option when invoking initRDKitModule.
// Load the RDKit WASM module from a specific path on your server.
window.initRDKitModule({ locateFile: () => '/path/to/RDKit_minimal.wasm' }).then(/* ... */);Option 2: Use the remote distribution files from unpkg.com
https://unpkg.com/@rdkit/rdkit/dist/RDKit_minimal.jshttps://unpkg.com/@rdkit/rdkit/dist/RDKit_minimal.wasm
Running RDKit.js in your JavaScript code
To use RDKit.js, load the javascript file and instantiate the wasm module inside the head tag of your index.html, before you run your application code:
<head>
<!-- ...other files and HTML tags... -->
<!-- Load the RDKit JS file -->
<script src="https://unpkg.com/@rdkit/rdkit/dist/RDKit_minimal.js"></script>
<!-- Instantiate the WASM module. The inline script below could live elsewhere inside your application code. -->
<script>
window
.initRDKitModule()
.then(function (RDKit) {
console.log("RDKit version: " + RDKit.version());
window.RDKit = RDKit;
/**
* The RDKit module is now loaded.
* You can use it anywhere.
*/
})
.catch(() => {
// handle loading errors here...
});
</script>
<!-- ...your application code goes here... -->
</head>Using RDKit.js with JavaScript
It is recommended to go through all the JavaScript examples available on the official website rdkitjs.com.
Using RDKit.js with React.js
If you are using React.js, several additional examples using React.js are available at react.rdkitjs.com.
Using RDKit.js with Next.js
If you are using Next.js, you can use a modified webpack config to build your app.
Using RDKit.js with Vue.js
If you are using Vue.js, several additional examples using Vue.js are available at vue.rdkitjs.com.
Using RDKit.js with Angular
If you are using Angular, several additional examples using Angular are available at angular.rdkitjs.com.
Usage in TypeScript
To see how to use RDKit.js with TypeScript, please go through the walkthrough here.
The full documentation related to type definitions is at docs.rdkitjs.com.
Note: This is still at an experimental stage.
Contributing
You are welcome to contribute to any GitHub issue currently open.
You are also welcome to log any issue or start a discussion on any topic related to RDKit.js.
To contribute to the plain javascript examples, read this sub-repository README.
To contribute to the React.js examples, read this sub-repository README.
To contribute to the Vue.js examples, read this sub-repository README.
To contribute to the Angular.js examples, read this sub-repository README.
Release process
NPM releases are currently semi-automated with the following azure pipeline:
https://dev.azure.com/rdkit-js/rdkit-js/_build?definitionId=1
Here are the guidelines to respect when releasing a new version of the package:
- Always release a new package from the master branch
- Use the following commit message format: "RDKit release <version of the main rdkit release>"
Example commit message: "RDKit release 2022.3.3-1.0.0"
- In Azure pipeline parameters, specify the RDKit version with underscores seperating major, minor, and patch version
Example: 2022_03_3
- In Azure pipeline parameters, specify the semver version with dots seperating major, minor, and patch version
Example: 1.0.0
- If you are releasing an official release, do not forget to uncheck the Is beta? checkbox in the Azure pipeline parameters.
Important note on npm versioning
The scope of this repository goes beyond the release of the RDKit wasm core module. Other utilities may eventually be included on top of the core module in the RDKit.js npm release.
Because of that, we need a versioning system that will keep track of
- The RDKit wasm core module version (exact match with its parent RDKit release)
- Multiple npm release versions that can be published on top of a same wasm core module version.
With this in mind, we will attempt the following versioning scheme of the package:
- For each RDKit release, a new version of the npm package will be released as -.
Example: when the 2022.03.3 version of RDKit is released, its first NPM release will be
2022.03.3-1.0.0. - On each subsequent npm release using the same core module, only the semver version will be modified according to semver conventions.
Example: when a bug fix is made in a React component built on top of RDKit for version 2022.03.3, a new npm release
2022.03.3-1.0.1will be published. Example: when a new React component is built on top of RDKit for version 2022.03.3, a new npm release2022.03.3-1.1.0will be published.
Website deployment
Website deployments for rdkitjs.com are automated via Vercel for each commit merged or pushed to the master branch.
Live demo URLs are also generated on each pull requests made to easily visualize changes before merging.
Maintainers
- Michel Moreau @MichelML & the RDKit community