rdkit-provider

Initialises a web worker with RDKitModule instance from @rdkit/rdkit and exposes it via a react context

Setup

Assets

The project using this package needs to provide it with RDKit package assets

After installing @rdkit/rdkit copy to your public folder node_modules/@iktos-oss/rdkit-provider/lib/rdkit-worker*.js node_modules/@rdkit/rdkit/dist/RDKit_minimal.js node_modules/@rdkit/rdkit/dist/RDKit_minimal.wasm

Usage

Wrap your components/App with RDKitProvider

import { RDKitProvider } from '@iktos/rdkit-provider';
<RDKitProvider>
  <Component />
</RDKitProvider>

you can also enable caching for molecule, which would enhance performance

import { RDKitProvider } from '@iktos/rdkit-provider';
<RDKitProvider cache={{ enableJsMolCaching: true, maxJsMolsCached: 50 }}>
  <Component />
</RDKitProvider>

Options that can be passed to RDKitProvider :

prop	type	functionality	required/optional
cache	RDKitProviderCacheOptions = { enableJsMolCaching?: boolean; maxJsMolsCached?: number; }	enables JSMol caching for better performance	optional
preferCoordgen	boolean	will be passed to @rdkit/rdkitjs prefer_coordgen to use Schrodinger’s open-source Coordgen library to generate 2D coordinates of molecules	optional
removeHs	boolean	toggles removing hydrogens molecules. Defaults to true	optional
kekulize	boolean	toggles kekulization of molecules during instantiation. Defaults to true. Set to false to handle molecules that fail kekulization (e.g. some aromatic SMILES)	optional
initialWorkerInstance	Worker instance of rdkit-worker.js	pass an rdkit worker instance, if not passed rdkit-provider creates one for you	optional
rdkitPath	string default to /RDKit_minimal.js in initRDKit.ts	pass a custom path to rdkit module	optional
rdkitWorkerPublicFolder	string, default is '', meaning the file is at the root level of the public folder	path to the folder containing the rdkit-worker-[version].js relative to the public folder	optional

You can make use of a set of helper functions exposed by the package

import { useRDKitUtils, useRDKit } from '@iktos/rdkit-provider';

const Component = () => {
  const { worker } = useRDKit();
  const { isValidSmiles } = useRDKitUtils();
  const submit = useCallback(
    async (smiles) => {
      const { isValid } = await isValidSmiles({ smiles });
      if (!isValid) return;
      // ...
    },
    [isValidSmiles],
  );

  if (!worker) return 'loading ...';
  return <>...</>;
  //...
};

Example of usage can be found in github.com/iktos/molecule-representation