@rdkit/rdkit-temporary-testing

v2022.3.6-beta

Published

2 years ago

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

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ptosco

michelml

greglandrum

javascript c-plus-plus cheminformatics rdkit wasm

New demos in progress at rdkitjs.com & react.rdkitjs.com

Please ⭐ this repo to show interest and support ongoing development!

Read original discussion on RDKit's official repository for more context.

RDKit for JavaScript (Official)

Introduction

Note: This package should be considered experimental. The API is not yet stable and may change from release to release.

The idea of this package is to allow the RDKit to be used from JavaScript so that we can add chemical capabilities to web applications.

Rather than attempting a comprehensive wrapper (like the old RDKitJS), this exposes a small set of key functionality. I think the general approach, including this actual library, can be useful for other wrapper projects in the future.

This initial set of functionality is not complete, but it is intended to already be directly useful.

Install

npm i @rdkit/rdkit

Using the RDKit 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/CodeMinimalLib/dist/RDKit_minimal.js
node_modules/@rdkit/rdkit/CodeMinimalLib/dist/RDKit_minimal.wasm

NOTE: Both files must be copied at the same location in your deployed assets for the library to work properly.

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

https://unpkg.com/@rdkit/rdkit/Code/MinimalLib/dist/RDKit_minimal.js
https://unpkg.com/@rdkit/rdkit/Code/MinimalLib/dist/RDKit_minimal.wasm

Running RDKit in your JavaScript code

To use RDKit, 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/Code/MinimalLib/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>

Usage

See the getting started demo at https://unpkg.com/@rdkit/rdkit/Code/MinimalLib/dist/GettingStartedInJS.html .

Follow the examples of this page to see the various ways to use the JavaScript release of RDKit.

Live demos

From this npm package: https://unpkg.com/@rdkit/rdkit/Code/MinimalLib/dist/GettingStartedInJS.html
From this npm package: https://unpkg.com/@rdkit/rdkit/Code/MinimalLib/dist/demo.html

Contributing

Preparing a new release of the package

Make sure you are at the root of the RDKit GitHub project, and on the branch and version of the project you want to release. Note that no commits should occur during the release process.

Step 1: Set the release version in package.json

npm --no-git-tag-version version <semver version matching an RDKit release>
# Example npm --no-git-tag-version version 2021.3.1

Step 2: Build the distribution files

npm run build -- <RDKit git release tag name>
# Example: npm run build -- Release_2021_03_1

This command will default to using the master branch if no version is provided. Also, checkout the build_rdkitjs.sh file and the minimallib Dockerfile to see how things are tied together.

Step 3: Publish the package to npm

Once you have verified that the distribution files have been properly added in Code/MinimalLib/dist, publish the package:

npm publish --access public

Step 4: Set back the placeholder version in package.json

npm run resetVersion

And you're done!

Releasing a new beta version of the package

The process is the same as publishing a regular version, but the version specified and the npm publish command change slightly:

npm --no-git-tag-version version 2021.3.1-beta.0 # specify beta number in version here
npm publish --beta --access public # specify npm that it's a beta version