ppillot/libmol

Single Page Web Application for displaying and studying molecular models

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

libmol's Issues

Liaisons H, liaisons Pi, etc

Voir fonction contact dans NGL

Barre de redimensionnement visible en mode "embedded"

Barre de redimensionnement s'affiche à droite du modèle moléculaire présenté. Après passage en plein écran, elle reste à cet endroit au lieu d'être affichée entre la barre latérale et le panneau de visualisation

Comparaison de modèles

Bouton fermeture aide en superposition avec barre de défilement

Solution possible : créer une barre de titre incluant le bouton de fermeture et n'avoir le défilement que dans la zone inférieure.

Action required: Greenkeeper could not be activated 🚨

🚨 You need to enable Continuous Integration on Greenkeeper branches of this repository. 🚨

To enable Greenkeeper, you need to make sure that a commit status is reported on all branches. This is required by Greenkeeper because it uses your CI build statuses to figure out when to notify you about breaking changes.

Since we didn’t receive a CI status on the greenkeeper/initial branch, it’s possible that you don’t have CI set up yet. We recommend using Travis CI, but Greenkeeper will work with every other CI service as well.

If you have already set up a CI for this repository, you might need to check how it’s configured. Make sure it is set to run on all new branches. If you don’t want it to run on absolutely every branch, you can whitelist branches starting with greenkeeper/.

Once you have installed and configured CI on this repository correctly, you’ll need to re-trigger Greenkeeper’s initial pull request. To do this, please click the 'fix repo' button on account.greenkeeper.io.

Bloquer IE

Renvoyer les utilisateurs d'IE vers un autre navigateur ou bien le téléchargement de l'application

Ajout de nouveaux modèles dans la banque de données

Passer à une gestion par tableur entièrement, simplifier l'utilisation de la BDD (pas besoin de tous les champs actuels si l'on n'écrit plus d'articles)

Envoyer un message d'erreur en cas de problème de chargement de modèle

Weird shapes in "ADN 14 paires de bases"

Are the rounded shapes normal in a DNA molecule, or is it an error?