Libmol.org

Molecular visualization made easy for beginners

Web Application

Libmol.org is a single page web application designed to provide students starting structural biology with simplified self explanatory tools to view and interact with biological macromolecules.

Acknowledgments

Contributors

Thanks to Hervé Furstoss for creating and contributing to the interactive documentation. Arose for developing and continuously improving NGL Philippe, Gilles, Jacques, Thomas, Eric and other members of the Forum National de SVT for their support and insightful inputs.

Libraries and other resources

This application could not have been written nor deployed without the following open source libraries:

• NGL: Javascript molecular visualization library leveraging WebGL browsers capacities and tuned for performance
  • AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. Web-based molecular graphics for large complexes. ACM Proceedings of the 21st International Conference on Web3D Technology (Web3D '16): 185-186, 2016. doi:10.1145/2945292.2945324
  • AS Rose and PW Hildebrand. NGL Viewer: a web application for molecular visualization. Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. doi:10.1093/nar/gkv402
• Vue.js, Vuex: Progressive JS framework
• Vuei18n: Vue plugin for internationalization
• ElementUI: UI Library for desktop application using Vue
• screenfull: wrapper to the fullscreen API for cross-browser compatibility
• Fontello: icon fonts generator

Fonts

• Font Awesome Copyright (C) 2016 by Dave Gandy Author: Dave Gandy License: SIL
• Elusive: Copyright (C) 2013 by Aristeides Stathopoulos Author: Aristeides Stathopoulos License: SIL

Special thanks to Netlify.com for hosting open source projects such as Libmol.org for free.

i18n effort

Should you be interested in translating Libmol.org to your language, your contribution is most welcome! First part of the translation process deals with the user interface. It requires completing an online Google spreadsheet with your locale keywords. The second part of the process is more involving and requires forking this repository, duplicating one of the folders in locales/ and translating all the markdown files in it. Please do not hesitate to contact me if interested.

Development and Build Setup

You don't need this to use LibMol.org The source code is distributed from this repository and can be downloaded to your computer using Git or the complete archive. Once the source code is downloaded and extracted, you'll have to install all dependencies required to build the project.

# install dependencies
npm install

# serve with hot reload at localhost:8081
npm run serve

# build for production with minification
npm run build

ToDo

• Files :
  • handle mega files
• Errors/warnings : send messages
  • when file could not be loaded
  • when network is not available --> online/offline api
• Commands :
  • add/remove labels
  • provide choices for selecting hetero (e.g. : in cox2 ara and hem)
• Sequences :
  • search (user selection ?)
• 3D View:
  • change cursor when rotating, zooming, panning, selecting
  • rotating around z-axis
• known bugs :
  • polymer size should exceed 3 for ribbon/backbone