{"id":13733823,"url":"https://github.com/kuixu/VRmol","last_synced_at":"2025-05-08T10:30:35.177Z","repository":{"id":89422641,"uuid":"136023703","full_name":"kuixu/VRmol","owner":"kuixu","description":"VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure","archived":false,"fork":false,"pushed_at":"2020-12-24T09:18:43.000Z","size":483949,"stargazers_count":35,"open_issues_count":2,"forks_count":10,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-07T08:45:19.654Z","etag":null,"topics":["autodock-vina","genomic-variation","molecular-structure-visualization","virtual-reality","visualization","vr-device","web-based","webvr","webxr"],"latest_commit_sha":null,"homepage":"https://VRmol.net","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kuixu.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-06-04T12:44:42.000Z","updated_at":"2024-06-30T21:56:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"264bdacb-dca8-4e0b-9da1-88af8bb31386","html_url":"https://github.com/kuixu/VRmol","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kuixu%2FVRmol","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kuixu%2FVRmol/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kuixu%2FVRmol/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kuixu%2FVRmol/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kuixu","download_url":"https://codeload.github.com/kuixu/VRmol/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253045516,"owners_count":21845718,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["autodock-vina","genomic-variation","molecular-structure-visualization","virtual-reality","visualization","vr-device","web-based","webvr","webxr"],"created_at":"2024-08-03T03:00:49.568Z","updated_at":"2025-05-08T10:30:33.551Z","avatar_url":"https://github.com/kuixu.png","language":"JavaScript","readme":"\u003cp align=\"center\"\u003e \u003cimg src=\"https://github.com/kuixu/VRmol/wiki/figs/misc/logo.png\" width=200px\u003e\u003c/p\u003e\n\n--------------------------------------------------------------------------------\n\n# VRmol: Virtual Reality for Molecular Structures \n\n\n## Introduction\n\nWe 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. \n\n## News\n - 08/17/2020: VRmol is back to normal.\n - 08/16/2020: Cloud Server migration. Most features are functioning normally except drug docking.\n - 07/25/2020: VRmol accepted to Bioinformatics.\n - 06/03/2020: [Wiki](https://github.com/kuixu/VRmol/wiki) is online.\n - 05/18/2020: Upgrade based on the WebXR core API, which supports Chrome(\u003e=81), Microsoft Edge (\u003e=81). \n - 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)\n - 05/17/2019: VRmol is back to normal.\n - 05/16/2019: The service provider is sufferring of Network Rounte Issue, VRmol server is outage.\n - 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)\n - 02/27/2019: VRmol is applied in teaching structural biology cource at Tsinghua University.\n\n## Demo\n\n\u003cimg src=\"https://github.com/kuixu/VRmol/wiki/figs/misc/entervr-320.gif\" width=50%\u003e\n\n\n## Documentation\n\nTutorials of VRmol can be accessed at [here](https://vrmol.net/docs).\n\nVRmol provides two modes:\n- [**VR Mode**](https://vrmol.net/docs/#header-n5340) will guide you to experience VRmol in Virtual Reality environment.\n- [**nonVR Mode**](https://vrmol.net/docs/#header-n5609) will guide you to experience VRmol on the desktop.\n\n### Video Tutorials\n\n- [**Entering VR Scene**](https://vrmol.net/docs/#header-n59) [[YouTube]](https://www.youtube.com/watch?v=k-qsnA9e5-o)\n- [**Loading Structure**](https://vrmol.net/docs/#header-n72) [[YouTube]](https://www.youtube.com/watch?v=qAvqJ8WrTKA)\n- [**Measurement**](https://vrmol.net/docs/#header-n227) \n- [**Drag Structure elements**](https://vrmol.net/docs/#header-n237) \n- [**Structure Editing**](https://vrmol.net/docs/#header-n251) \n- [**Genome Variations**](https://vrmol.net/docs/#header-n259) \n- [**Interactive Docking**](https://vrmol.net/docs/#header-n267) [[YouTube]](https://www.youtube.com/watch?v=iblEtcxJTos)\n- [**Entering VR Scene**](https://vrmol.net/docs/#header-n59) \n- [**Fragmentation  in nonVR mode**](https://vrmol.net/docs/#header-n459)\n- [**Structure Editing  in nonVR mode**](https://vrmol.net/docs/#header-n468)\n- [**Genome Variations  in nonVR mode**](https://vrmol.net/docs/#header-n476)\n- [**Interactive Docking in nonVR mode**](https://vrmol.net/docs/#header-n489)\n\n\n## Practice VRmol\n\nYou could practice VRmol with VR device on [WebXR supported browsers](https://caniuse.com/#search=webxr) below:\n  - Google Chrome(\u003e=81)\n  - Microsoft Edge (\u003e=81) [Download](https://www.microsoft.com/en-us/edge)\n  - Firefox Reality Android standalones and PC in (Q1 2020)\n\nSupported VR devices:\n  - Windows Mixed Reality*\n  - HTC Vive*\n  - Oculus Rift\n\n\u003e *: indicates well tested devices.\n\nOperation System:\n  - Windows 10 (build verion: 1903+)\n\nAlso 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:\n  - [Google Chrome](https://chrome.google.com/webstore/detail/webxr-api-emulator/mjddjgeghkdijejnciaefnkjmkafnnje)\n  - [Mozilla Firefox](https://addons.mozilla.org/en-US/firefox/addon/webxr-api-emulator/)\n\nThe [source code](https://github.com/MozillaReality/WebXR-emulator-extension) for the extension is also available.\n\n\u003e For Firefox: Solving the problem of `CORS request did not succeed` when accessing web services (genomic variation, drug docking) by setting below in firefox.\n```\nabout:config: security.ssl.enable_ocsp_stapling --\u003e False\n```\n\n\n## Framework\n\nThe framework of VRmol.\n\n\u003cimg src=\"https://github.com/kuixu/VRmol/wiki/figs/misc/framework.png\" width=50%\u003e\n\n## Screenshot\n\nA screenshot of structure visualization with stereo view.\n\u003cimg src=\"https://github.com/kuixu/VRmol/wiki/figs/misc/screenshot.png\" width=80%\u003e\n\n\n\n## Sharing by URL\n\n\n### URL Options\nYou 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\n\n```html\n\u003ciframe src=\"https://vrmol.net/?id=1dfb\" /\u003e\n```\n\n\nThe options and their data types supported in VRmol are shown in the table below.\n\n| Options    | Data Type |Value  |Comment|\n| :------ | :------ |:------ |:------ |\n| id | String|PDB code|4 charactors|\n|panelShow|Integer|Show:1, Hide:0|Show menu panel or not|\n|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|\n|showSurface|Integer|Show:1, Hide:0|Show surface panel or not|\n|surfaceOpc|Float|0~1|Transparency of surface|\n|surfaceType|Integer|Van der Waals surface:1, solvent excluded surface:2, solvent accessible surface:3, molecular surface:4|Surface type|\n|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|\n|travel|Integer|Show:1, Hide:0|Enter travel mode or not|\n|vmode|String|nonvr, vr|Visualization Mode|\n|fragment|String|['a', 7, 6]|Fragmentation, label the 7th residue with `Ball \u0026 Rod` style|\n\n\n### Examples for API \n\n\n  1. Present structure (PDB code:`1MBS`) with `Ball \u0026 Rod` style and hide the menu panel.  [Try it](https://vrmol.net/index.html?id=1mbs\u0026panelShow=0\u0026mainMode=6)\n```html\n\u003ciframe src=\"https://vrmol.net/index.html?id=1mbs\u0026panelShow=0\u0026mainMode=6\" /\u003e\n```\n\n\n  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\u0026panelShow=0\u0026mainMode=7\u0026showSurface=1\u0026surfaceOpc=0.5\u0026surfaceType=1)\n```html\n\u003ciframe src=\"https://vrmol.net/index.html?id=1dfb\u0026panelShow=0\u0026mainMode=7\u0026showSurface=1\u0026surfaceOpc=0.5\u0026surfaceType=1\"  /\u003e\n```\n\n  3. Present structure (PDB code:`1F5X`) with the 7th residue labeled with `Ball \u0026 Rod` style in VR mode. [Try it](https://vrmol.net/?id=1f5x\u0026fragment=['a',7,6]\u0026vmode=vr)\n```html\n\u003ciframe src=\"https://vrmol.net/?id=1f5x\u0026fragment=['a',7,6]\u0026vmode=vr\"  /\u003e\n```\n\n  4. Present structure (PDB code:`2HYY`) with surface in VR. [Try it](https://vrmol.net/index.html?id=https://vrmol.net/data/2hyy.pdb\u0026panelShow=1\u0026mainMode=13\u0026showSurface=1\u0026surfaceOpc=1\u0026surfaceType=1\u0026colorMode=609\u0026vmode=vr)\n```\nhttps://vrmol.net/index.html?id=2hyy\u0026panelShow=1\u0026mainMode=13\u0026showSurface=1\u0026surfaceOpc=1\u0026surfaceType=1\u0026colorMode=609\u0026vmode=vr\n```\n\n## Deploy VRmol on your own server Using VRmol API Services\n\n  - Download the code into the apache server web directory\n  - Set `SERVERURL` as your URL (like https://example.com) at `libs/core.js`\n  - Start the Speech Recognition service by run:\n    ```python\n    python3 server/speech/sr.py\n    ```\n\n## Setup VRmol API Services on your own server\n\n  - Installation of external tools\n     - [AutoDock Vina](http://vina.scripps.edu/)\n     - [MGLTools](http://mgltools.scripps.edu/)\n     - [OpenBabel](http://openbabel.org/wiki/Main_Page)\n  - Data files used to build the Database\n     - [Google Drive](https://drive.google.com/open?id=1HhRsWi7R1oI5pGtVvOYc4TuUFlePCbbh)\n\n\nServer Tools\n  - Linux/Windows/macOS [Apache](https://httpd.apache.org/)\n  - Integretive tool for Linux [LAMP](https://github.com/teddysun/lamp)\n  - Integretive tool for Windowns [WAMP](http://www.wampserver.com/en/)\n\n\n\n## Release Versions\n  - [Releases](https://github.com/kuixu/VRmol/releases)\n  - [v1.0](https://github.com/kuixu/VRmol/tree/v1.0)\n  - [v0.2](https://github.com/kuixu/VRmol/tree/v0.2)\n  - [v0.1](https://github.com/kuixu/VRmol/tree/v0.1)\n\n## Citation\n\nPaper: [Bioinformatics](https://doi.org/10.1093/bioinformatics/btaa696) [Biorxiv](https://www.biorxiv.org/content/early/2019/03/27/589366.1)\n```\n@article{10.1093/bioinformatics/btaa696,\n    author = {Xu, Kui and Liu, Nan and Xu, Jingle and Guo, Chunlong and Zhao, Lingyun and Wang, Hong-Wei and Zhang, Qiangfeng Cliff},\n    title = \"{VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure}\",\n    journal = {Bioinformatics},\n    year = {2020},\n    month = {08},\n    issn = {1367-4803},\n    doi = {10.1093/bioinformatics/btaa696},\n    url = {https://doi.org/10.1093/bioinformatics/btaa696},\n    note = {btaa696},\n    eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa696/33560033/btaa696.pdf},\n}\n\n\n\n@article {Xu589366,\n\tauthor = {Xu, Kui and Liu, Nan and Xu, Jingle and Guo, Chunlong and Zhao, Lingyun and Wang, Hong-wei and Zhang, Qiangfeng Cliff},\n\ttitle = {VRmol: an Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure},\n\telocation-id = {589366},\n\tyear = {2019},\n\tdoi = {10.1101/589366},\n\tpublisher = {Cold Spring Harbor Laboratory},\n\tURL = {https://www.biorxiv.org/content/early/2019/03/27/589366.1},\n\teprint = {https://www.biorxiv.org/content/early/2019/03/27/589366.1.full.pdf},\n\tjournal = {bioRxiv}\n}\n\n```\n\n## Acknowledgments\n\nVRmol 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.\n  - [https://immersiveweb.dev/#supporttable](https://immersiveweb.dev/#supporttable)\n  - [https://www.w3.org/TR/webxr/](https://github.com/MozillaReality/WebXR-emulator-extension)\n  - [Web3DMol](https://web3dmol.net) - for PDB file loading and parsing\n  - [GLmol.js](https://github.com/biochem-fan/GLmol) - for calculating surface \n  - [Chroma.js](https://github.com/gka/chroma.js) - for color handling\n  - [gunzip.min.js](https://github.com/imaya/zlib.js) - for decompress EM map files\n  - [AutoDock vina](http://vina.scripts.edu) - for Docking Drugs in VR scene\n  - [MGLTools](http://mgltools.scripps.edu/) - for preparing docking files\n  - [OpenBabel](http://openbabel.org/wiki/Main_Page) - for convert docking results\n\n","funding_links":[],"categories":["Research"],"sub_categories":["Motion Controllers inside Unity!"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkuixu%2FVRmol","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkuixu%2FVRmol","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkuixu%2FVRmol/lists"}