@rdkit/rdkit

v2023.9.2-1.0.0

Published

5 months ago

JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.

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12,211

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ptosco

michelml

greglandrum

javascript c-plus-plus cheminformatics rdkit wasm node-js molecule molecule-visualization molecule-viewer molecule-drawing

| | | :---------------------------: | | Molecule Rendering Examples |

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/rdkit

Usage

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.js
node_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.js
https://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.

Source code

Using RDKit.js with React.js

If you are using React.js, several additional examples using React.js are available at react.rdkitjs.com.

Source code

Using RDKit.js with Next.js

If you are using Next.js, you can use a modified webpack config to build your app.

Source code

Using RDKit.js with Vue.js

If you are using Vue.js, several additional examples using Vue.js are available at vue.rdkitjs.com.

Source code

Using RDKit.js with Angular

If you are using Angular, several additional examples using Angular are available at angular.rdkitjs.com.

Source code

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 2022.03.3-1.0.1 will be published. Example: when a new React component is built on top of RDKit for version 2022.03.3, a new npm release 2022.03.3-1.1.0 will 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

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Readme

Table of contents

Introduction

What is the scope of this repository

What is NOT the scope of this repository

Install

Usage

Using RDKit.js package assets

Option 1: Use the npm package distribution files

Option 2: Use the remote distribution files from unpkg.com

Running RDKit.js in your JavaScript code

Using RDKit.js with JavaScript

Using RDKit.js with React.js

Using RDKit.js with Next.js

Using RDKit.js with Vue.js

Using RDKit.js with Angular

Usage in TypeScript

Contributing

Release process

Important note on npm versioning

Website deployment

Maintainers