Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/kuixu/VRmol
VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure
https://github.com/kuixu/VRmol
autodock-vina genomic-variation molecular-structure-visualization virtual-reality visualization vr-device web-based webvr webxr
Last synced: 28 days ago
JSON representation
VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure
- Host: GitHub
- URL: https://github.com/kuixu/VRmol
- Owner: kuixu
- License: mit
- Created: 2018-06-04T12:44:42.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-12-24T09:18:43.000Z (almost 4 years ago)
- Last Synced: 2024-05-13T16:32:34.854Z (7 months ago)
- Topics: autodock-vina, genomic-variation, molecular-structure-visualization, virtual-reality, visualization, vr-device, web-based, webvr, webxr
- Language: JavaScript
- Homepage: https://VRmol.net
- Size: 462 MB
- Stars: 34
- Watchers: 6
- Forks: 10
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- vr-resources - VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure
README
--------------------------------------------------------------------------------
# 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.
## 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
```
The options and their data types supported in VRmol are shown in the table below.
| Options | Data Type |Value |Comment|
| :------ | :------ |:------ |:------ |
| id | String|PDB code|4 charactors|
|panelShow|Integer|Show:1, Hide:0|Show menu panel or not|
|mainMode|Integer|LINE:1, DOT:2, BACKBONE:3, SPHERE:4, STICK:5, BALL_AND_ROD:6, TUBE:7, RIBBON_FLAT:8, RIBBON_ELLIPSE:9, RIBBON_RECTANGLE:10, RIBBON_STRIP:11, RIBBON_RAILWAY:12, CARTOON_SSE:13, SURFACE:14|Main Structure Representation|
|showSurface|Integer|Show:1, Hide:0|Show surface panel or not|
|surfaceOpc|Float|0~1|Transparency of surface|
|surfaceType|Integer|Van der Waals surface:1, solvent excluded surface:2, solvent accessible surface:3, molecular surface:4|Surface type|
|colorMode|Integer|Element:601, Residue:602, Secondary Structure:603, Chain:604, Representation:605, B-Factor:606, Spectrum:607, Chain Spectrum:608, Hydrophobicity:609|Color schemes|
|travel|Integer|Show:1, Hide:0|Enter travel mode or not|
|vmode|String|nonvr, vr|Visualization Mode|
|fragment|String|['a', 7, 6]|Fragmentation, label the 7th residue with `Ball & Rod` style|
### 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
```
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
```
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
```
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