VRmol

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VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure

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# VRmol: Virtual Reality for Molecular Structures

## Introduction

We leverage the most cutting-edge computational technologies to develop a virtual reality (VR) system - VRmol - that provides the visualization and analysis of macromolecule structures in an infinite virtual environment on the web. VRmol is natively built with WebVR technology, providing all structural analysis functions in a fully immersive, inspiring virtual environment. It is convenient to use, runs on internet and requires no software downloading and installation. And by connecting to a number of cloud-based genomic and drug databases, it provides an integrative platform to perform advanced structural and translational research. It can be freely accessed online by typing [https://VRmol.net](https://VRmol.net?from=github) in VR-supported browser.

## News
 - 08/17/2020: VRmol is back to normal.
 - 08/16/2020: Cloud Server migration. Most features are functioning normally except drug docking.
 - 07/25/2020: VRmol accepted to Bioinformatics.
 - 06/03/2020: [Wiki](https://github.com/kuixu/VRmol/wiki) is online.
 - 05/18/2020: Upgrade based on the WebXR core API, which supports Chrome(>=81), Microsoft Edge (>=81). 
 - 02/21/2020: `Special Vis` for COVID-19 from [Tsinghua Univ.](https://mp.weixin.qq.com/s/J6j7Ya6Z7zOiLWufy_HApQ): [[Click to Vis]](https://vrmol.net/?id=https://vrmol.net/data/2019-nCoV-RBD-ACE2-sse.pdb), [NMDC](http://nmdc.cn/?from=groupmessage#/resource/detail?no=NMDCS0000001): [[Click to Vis]](https://vrmol.net/?id=https://vrmol.net/data/2019nCoV-S_RBD_ACE2-sse.pdb) and [West Lake Univ.](https://mp.weixin.qq.com/s/84jx6ggh-7VmFNK5it7O0g): [[Click to Vis]](https://vrmol.net/?id=https://vrmol.net/data/RBD-ACE2-B0AT1-sse.pdb), [[Open Conformation]](https://vrmol.net/?id=https://vrmol.net/data/ACE2_B0AT1_open_conformation-sse.pdb), [[Closed Conformation]](https://vrmol.net/?id=https://vrmol.net/data/ACE2_B0AT1_closed_conformation-sse.pdb)
 - 05/17/2019: VRmol is back to normal.
 - 05/16/2019: The service provider is sufferring of Network Rounte Issue, VRmol server is outage.
 - 04/27/2019: VRmol is being on show at Tsinghua's 108th anniversary. [News](http://life.tsinghua.edu.cn/publish/smkx/11192/2019/20190429100026441636257/20190429100026441636257_.html)
 - 02/27/2019: VRmol is applied in teaching structural biology cource at Tsinghua University.

## Demo

## Documentation

Tutorials of VRmol can be accessed at [here](https://vrmol.net/docs).

VRmol provides two modes:
- [**VR Mode**](https://vrmol.net/docs/#header-n5340) will guide you to experience VRmol in Virtual Reality environment.
- [**nonVR Mode**](https://vrmol.net/docs/#header-n5609) will guide you to experience VRmol on the desktop.

### Video Tutorials

- [**Entering VR Scene**](https://vrmol.net/docs/#header-n59) [[YouTube]](https://www.youtube.com/watch?v=k-qsnA9e5-o)
- [**Loading Structure**](https://vrmol.net/docs/#header-n72) [[YouTube]](https://www.youtube.com/watch?v=qAvqJ8WrTKA)
- [**Measurement**](https://vrmol.net/docs/#header-n227) 
- [**Drag Structure elements**](https://vrmol.net/docs/#header-n237) 
- [**Structure Editing**](https://vrmol.net/docs/#header-n251) 
- [**Genome Variations**](https://vrmol.net/docs/#header-n259) 
- [**Interactive Docking**](https://vrmol.net/docs/#header-n267) [[YouTube]](https://www.youtube.com/watch?v=iblEtcxJTos)
- [**Entering VR Scene**](https://vrmol.net/docs/#header-n59) 
- [**Fragmentation  in nonVR mode**](https://vrmol.net/docs/#header-n459)
- [**Structure Editing  in nonVR mode**](https://vrmol.net/docs/#header-n468)
- [**Genome Variations  in nonVR mode**](https://vrmol.net/docs/#header-n476)
- [**Interactive Docking in nonVR mode**](https://vrmol.net/docs/#header-n489)

## Practice VRmol

You could practice VRmol with VR device on [WebXR supported browsers](https://caniuse.com/#search=webxr) below:
  - Google Chrome(>=81)
  - Microsoft Edge (>=81) [Download](https://www.microsoft.com/en-us/edge)
  - Firefox Reality Android standalones and PC in (Q1 2020)

Supported VR devices:
  - Windows Mixed Reality*
  - HTC Vive*
  - Oculus Rift

> *: indicates well tested devices.

Operation System:
  - Windows 10 (build verion: 1903+)

Also you could practice VRmol without VR device by using [WebXR API Emulator extension](https://blog.mozvr.com/webxr-emulator-extension/), download the WebXR API Emulator for your supported browser below:
  - [Google Chrome](https://chrome.google.com/webstore/detail/webxr-api-emulator/mjddjgeghkdijejnciaefnkjmkafnnje)
  - [Mozilla Firefox](https://addons.mozilla.org/en-US/firefox/addon/webxr-api-emulator/)

The [source code](https://github.com/MozillaReality/WebXR-emulator-extension) for the extension is also available.

> For Firefox: Solving the problem of `CORS request did not succeed` when accessing web services (genomic variation, drug docking) by setting below in firefox.
```
about:config: security.ssl.enable_ocsp_stapling --> False
```

## Framework

The framework of VRmol.

## Screenshot

A screenshot of structure visualization with stereo view.
<img src="https://github.com/kuixu/VRmol/wiki/figs/misc/screenshot.png" width=80%>

## Sharing by URL

### URL Options
You can save a specific structural representation scene by saving operation options setting in VRmol as a URL, like `https://vrmol.net/index.html?id=1dfb`. And then you can load and share the scene by opening this previously-saved URL in the web browser or embedding it into your own website by using `iframe`, such as

```html
<iframe src="https://vrmol.net/?id=1dfb" />
```

The options and their data types supported in VRmol are shown in the table below.

### Examples for API

1. Present structure (PDB code:`1MBS`) with `Ball & Rod` style and hide the menu panel.  [Try it](https://vrmol.net/index.html?id=1mbs&panelShow=0&mainMode=6)
```html
<iframe src="https://vrmol.net/index.html?id=1mbs&panelShow=0&mainMode=6" />
```

2. Present structure (PDB code:`1DDB`) with `Tube` style and show its Van der Waals surface with transparency (0.5), and hide the menu panel. [Try it](https://vrmol.net/index.html?id=1dfb&panelShow=0&mainMode=7&showSurface=1&surfaceOpc=0.5&surfaceType=1)
```html
<iframe src="https://vrmol.net/index.html?id=1dfb&panelShow=0&mainMode=7&showSurface=1&surfaceOpc=0.5&surfaceType=1"  />
```

3. Present structure (PDB code:`1F5X`) with the 7th residue labeled with `Ball & Rod` style in VR mode. [Try it](https://vrmol.net/?id=1f5x&fragment=['a',7,6]&vmode=vr)
```html
<iframe src="https://vrmol.net/?id=1f5x&fragment=['a',7,6]&vmode=vr"  />
```

4. Present structure (PDB code:`2HYY`) with surface in VR. [Try it](https://vrmol.net/index.html?id=https://vrmol.net/data/2hyy.pdb&panelShow=1&mainMode=13&showSurface=1&surfaceOpc=1&surfaceType=1&colorMode=609&vmode=vr)
```
https://vrmol.net/index.html?id=2hyy&panelShow=1&mainMode=13&showSurface=1&surfaceOpc=1&surfaceType=1&colorMode=609&vmode=vr
```

## Deploy VRmol on your own server Using VRmol API Services

- Download the code into the apache server web directory
  - Set `SERVERURL` as your URL (like https://example.com) at `libs/core.js`
  - Start the Speech Recognition service by run:
    ```python
    python3 server/speech/sr.py
    ```

## Setup VRmol API Services on your own server

- Installation of external tools
     - [AutoDock Vina](http://vina.scripps.edu/)
     - [MGLTools](http://mgltools.scripps.edu/)
     - [OpenBabel](http://openbabel.org/wiki/Main_Page)
  - Data files used to build the Database
     - [Google Drive](https://drive.google.com/open?id=1HhRsWi7R1oI5pGtVvOYc4TuUFlePCbbh)

Server Tools
  - Linux/Windows/macOS [Apache](https://httpd.apache.org/)
  - Integretive tool for Linux [LAMP](https://github.com/teddysun/lamp)
  - Integretive tool for Windowns [WAMP](http://www.wampserver.com/en/)

## Release Versions
  - [Releases](https://github.com/kuixu/VRmol/releases)
  - [v1.0](https://github.com/kuixu/VRmol/tree/v1.0)
  - [v0.2](https://github.com/kuixu/VRmol/tree/v0.2)
  - [v0.1](https://github.com/kuixu/VRmol/tree/v0.1)

## Citation

Paper: [Bioinformatics](https://doi.org/10.1093/bioinformatics/btaa696) [Biorxiv](https://www.biorxiv.org/content/early/2019/03/27/589366.1)
```
@article{10.1093/bioinformatics/btaa696,
    author = {Xu, Kui and Liu, Nan and Xu, Jingle and Guo, Chunlong and Zhao, Lingyun and Wang, Hong-Wei and Zhang, Qiangfeng Cliff},
    title = "{VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure}",
    journal = {Bioinformatics},
    year = {2020},
    month = {08},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btaa696},
    url = {https://doi.org/10.1093/bioinformatics/btaa696},
    note = {btaa696},
    eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa696/33560033/btaa696.pdf},
}

@article {Xu589366,
	author = {Xu, Kui and Liu, Nan and Xu, Jingle and Guo, Chunlong and Zhao, Lingyun and Wang, Hong-wei and Zhang, Qiangfeng Cliff},
	title = {VRmol: an Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure},
	elocation-id = {589366},
	year = {2019},
	doi = {10.1101/589366},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2019/03/27/589366.1},
	eprint = {https://www.biorxiv.org/content/early/2019/03/27/589366.1.full.pdf},
	journal = {bioRxiv}
}

```

## Acknowledgments

VRmol is developed based on [three.js](https://threejs.org) and [WebXR](https://www.w3.org/TR/webxr/) with the help of Dawei Zhang and Xun Ran, and we would like to express our special thanks to those open-source projects below.
  - [https://immersiveweb.dev/#supporttable](https://immersiveweb.dev/#supporttable)
  - [https://www.w3.org/TR/webxr/](https://github.com/MozillaReality/WebXR-emulator-extension)
  - [Web3DMol](https://web3dmol.net) - for PDB file loading and parsing
  - [GLmol.js](https://github.com/biochem-fan/GLmol) - for calculating surface 
  - [Chroma.js](https://github.com/gka/chroma.js) - for color handling
  - [gunzip.min.js](https://github.com/imaya/zlib.js) - for decompress EM map files
  - [AutoDock vina](http://vina.scripts.edu) - for Docking Drugs in VR scene
  - [MGLTools](http://mgltools.scripps.edu/) - for preparing docking files
  - [OpenBabel](http://openbabel.org/wiki/Main_Page) - for convert docking results

VRmol

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