Mol* Documentation

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Building a Custom Library ​

This page goes over creating a custom Mol* based library usable inside a <script> tag in an HTML page.

Setup ​

  • Create a new npm/yarn package
  • Install molstar and esbuild packages
mkdir molstar-lib
cd molstar-lib
npm init
npm install molstar
npm install esbuild --save-dev

Example Library Code ​

Create new file src/index.ts (or .js if you don't want to use TypeScript):

ts
import { DefaultPluginSpec, PluginSpec } from 'molstar/lib/mol-plugin/spec';
import { PluginContext } from 'molstar/lib/mol-plugin/context';

export async function initViewer(element: string | HTMLDivElement, options?: { spec?: PluginSpec }) {
    const parent = typeof element === 'string' ? document.getElementById(element)! as HTMLDivElement : element;
    const canvas = document.createElement('canvas') as HTMLCanvasElement;
    parent.appendChild(canvas);

    const spec = options?.spec ?? DefaultPluginSpec();

    const plugin = new PluginContext(spec);
    await plugin.init();

    plugin.initViewer(canvas, parent);

    return plugin;
}

export async function loadStructure(
    plugin: PluginContext,
    url: string,
    options?: { format?: string, isBinary?: boolean }
) {
    const data = await plugin.builders.data.download(
        { url, isBinary: options?.isBinary }
    );
    const trajectory = await plugin.builders.structure.parseTrajectory(
        data,
        options?.format ?? 'mmcif' as any
    );
    const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
    return preset;
}

Building the Library ​

Add new commands to the scripts section of the package.json file

json
"scripts": {
  "build": "esbuild src/index.ts --bundle --outfile=./build/js/index.js --global-name=molstarLib",
  "watch": "esbuild src/index.ts --bundle --outfile=./build/js/index.js --global-name=molstarLib --watch"
}

and run the command npm run build (or watch for interactive development experience). This will create build/js/index.js file which can be imported with a <script> tag and the exported functions called view the molstarLib prefix (you can customize this parameter).

Using the Library ​

Create file build/index.html:

html
<!DOCTYPE html>
<html lang="en">
    <head>
        <meta charset="utf-8" />
        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
        <title>Mol* Library Example</title>
    </head>
    <style>
        #viewer {
            position: absolute;
            width: 800px;
            height: 600px;
        }
    </style>
    <script type="text/javascript" src="./js/index.js"></script>
    <body>
        <div id="viewer"></div>
        <script type="text/javascript">
            async function init() {1
                const plugin = await molstarLib.initViewer("viewer");
                await molstarLib.loadStructure(
                    plugin,
                    "https://models.rcsb.org/4hhb.bcif",
                    { isBinary: true }
                );
            }
            init();
        </script>
    </body>
</html>

After opening index.html in a browser, you should see

lib-example

Using Mol* React UI ​

The above example does not make use of the default Mol* React UI and any UI components are therefore the author's responsibility. The below examples show how to (re)use the Mol* React UI.

  • Create src/ui.tsx:
tsx
import React from 'react';
import { createRoot } from 'react-dom/client';

import { DefaultPluginUISpec, PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
import { Plugin } from 'molstar/lib/mol-plugin-ui/plugin';

export async function initViewerUI(element: string | HTMLDivElement, options?: { spec?: PluginUISpec }) {
    const parent = typeof element === 'string' ? document.getElementById(element)! as HTMLDivElement : element;
    const spec = { ...DefaultPluginUISpec(), ...options?.spec };
    const plugin = new PluginUIContext(spec);
    await plugin.init();

    createRoot(parent).render(<Plugin plugin={plugin} />)

    return plugin;
}

export async function loadStructure(plugin: PluginUIContext, url: string, options?: { format?: string, isBinary?: boolean }) {
    const data = await plugin.builders.data.download({ url, isBinary: options?.isBinary });
    const trajectory = await plugin.builders.structure.parseTrajectory(data, options?.format ?? 'mmcif' as any);
    await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
}
  • Create src/style.scss:
scss
@import '../node_modules/molstar/lib/mol-plugin-ui/skin/light.scss';
  • Create build/ui.html:
html
<!DOCTYPE html>
<html lang="en">
    <head>
        <meta charset="utf-8" />
        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
        <title>Mol* UI Library Example</title>
    </head>
    <link rel="stylesheet" type="text/css" href="css/style.css" />
    <style>
        #viewer {
            position: absolute;
            inset: 0;
        }
    </style>
    <script type="text/javascript" src="./js/ui.js"></script>
    <body>
        <div id="viewer"></div>
        <script type="text/javascript">
            async function init() {
                const plugin = await molstarLib.initViewerUI("viewer", {
                    spec: {
                        layout: {
                            initial: {
                                isExpanded: true,
                                showControls: true,
                            },
                        },
                    }
                });
                await molstarLib.loadStructure(plugin, "https://models.rcsb.org/4hhb.bcif", { isBinary: true });
            }
            init();
        </script>
    </body>
</html>
  • Install sass: npm install sass -save-dev (or use esbuild plugin and import the scss file in ui.tsx)
  • Add scripts to package.json:
json
"build-ui": "esbuild src/ui.tsx --bundle --outfile=./build/js/ui.js --global-name=molstarLib",
"css": "sass src/style.scss ./build/css/style.css"
  • Run npm run build-ui and npm run css (skip if using esbuild-sass-plugin)
  • Opening build/ui.html: ui-example