Index

# 3Dmol.js

## Overview

3Dmol.js is an object-oriented, WebGL based JavaScript library for online molecular visualization - No Java required!
With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications. Features include:

- support for pdb, sdf, mol2, xyz, and cube formats
- parallelized molecular surface computation
- sphere, stick, line, cross, cartoon, and surface styles
- atom property based selection and styling
- labels
- clickable interactivity with molecular data
- geometric shapes including spheres and arrows

## Getting Started

Molecular data can be shared and visualized without writing any HTML
using only a declarative URL specification and our hosted viewer (see Viewing Molecules with the 3Dmol Server).

Viewers can be quickly embedded in any HTML document using just two lines of source code (see Embedding a 3Dmol Viewer).

#### Mouse Controls

Movement | Mouse Input | Touch Input
--- | --- | ---
Rotation | Primary Mouse Button | Single touch
Translation | Middle Mouse Button or Ctrl+Primary | Triple touch
Zoom | Scroll Wheel or Second Mouse Button or Shift+Primary | Pinch (double touch)
Slab | Ctrl+Second | Not Available

## Using 3Dmol.js

3Dmol.js provides a full-featured API for manipulating and styling molecular data.

### Including it in your web project

#### Method 1: using the latest version

The library is available as a single minified JavaScript file bundled with jQuery:

    {@lang xml}<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>

An un-minified file is also provided for debugging purposes:

    {@lang xml}<script src="https://3Dmol.csb.pitt.edu/build/3Dmol.js"></script>

There is also an unminified version provided without jQuery for use when compiling your own minified libraries:

    {@lang xml}<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-nojquery.js"></script>

#### Method 2: using a CDN

The files hosted by 3Dmol.csb.pitt.edu closely track the development version and so will change frequently. If you desire more stability you may copy the files into your own project or, alternatively, we host release snapshots on the cdnjs content delivery network (note that you must specify the release version).

    {@lang xml}<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/1.4.0/3Dmol-min.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/1.4.0/3Dmol-nojquery.js"></script>

Using the CDN will likely provide the best network performance to your users, but features will lag behind the development branch as we only plan to tag new releases a few times a year.

It is highly recommended to include a Subresource Integrity tag to your script to protect your users from malicious manipulations.

Example for calculating the sha384sum with openssl for 3Dmol-min.js:

    {@lang bash}cat 3Dmol-min.js | openssl dgst -sha384 -binary | openssl base64 -A
    # prints: G/ktMxNGQtSajNFY+7He9WGWTfkmMrPlEbZbCjtjWLYXpsgvuAkS8Aj8IBjs13yc

Now add it to the `script` tag:

    {@lang xml}<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/1.4.0/3Dmol-min.js" integrity="sha384-G/ktMxNGQtSajNFY+7He9WGWTfkmMrPlEbZbCjtjWLYXpsgvuAkS8Aj8IBjs13yc"></script>

#### Method 3: using an ES6 style import

If you are using a bundler such as Webpack or Parcel and your code is in TypeScript or using ES6 imports (and after maybe using Babel to transpile it), then you will want to import it like this:

First add the library to your dependencies:

    {@lang bash}npm install 3dmol
    # or yarn add 3dmol

Next, use this import line in your code:

    {@lang javascript}import jquery;
    // note the different capitalization of 3dmol
    import * as $3Dmol from 3dmol/build/3Dmol-nojquery.js';

### Using the source code

The full source distribution is available from github.

    {@lang bash}git clone https://github.com/3dmol/3Dmol.js
    cd 3Dmol.js
    npm install

The `npm install` command will take care of building the project with gulp. To rebuild it again use `gulp` or `npm run build`. This will allow you to access the completely built file at `build/3Dmol.js`.

Since 3Dmol.js is licensed under the permissive BSD open-source license, you are free
to copy this code and use it any any project, as long the code is properly acknowledged.

Every 3Dmol.js viewer canvas corresponds to a $3Dmol.GLViewer object. The viewer object
includes methods for setting viewer properties and for creating and manipulating molecular models, surfaces
and custom geometric shapes within the view.

A $3Dmol.GLModel object represents molecular data. Each model object stores its own
rendering data and provides a convient way to reference a defined part of the scene.

Models are manipulated and styled using AtomSpec JavaScript objects.

An example of a viewer that manipulates the styles of the embedded objects is shown below. View the source code for the implementation details.

### Citing 3Dmol.js

If this software is useful in your work, please use the following citation:

> Nicholas Rego and David Koes
> 3Dmol.js: molecular visualization with WebGL
> Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

## FAQ

### What are your future plans for 3Dmol.js?

Due to limited resources, our focus is on developing 3Dmol.js as a molecular viewer library, rather than a full featured cheminformatics/bioinformatics toolkit.

For example, adding support for WebGL 2.0 has a higher priority than adding editing functionality to the hosted viewer.

We hope others use 3Dmol.js as a building block for such web applications and look forward to collaborating with web developers to deliver the visualization functionality needed to enable them. Of course, if additional resources become available we may expand the scope of our efforts. However, the goal is to keep the core of 3Dmol.js as small as possible and focused on visualization.

### Are you planning on supporting additional file formats?

Time permitting, we will add support for additional formats as they are requested. We also hope to integrate with other cheminformatics libraries to automatically provide additional formats and analysis.

### Does 3Dmol.js work with touch devices?

Yes, as long as they support WebGL. For example, it runs great in Safari on an iPad running iOS 8.

## Contact

Please address any questions or concerns to dkoes@pitt.edu.
You may also submit an issue on github.

## Funding

3DMol.js is funded through R01GM108340 from the National Institute of General Medical Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.