Molecule Visualization with 3Dmol.js - acelot-inc/boltzmann GitHub Wiki

3D Molecule Visualization with 3Dmol.js

Related Files

  • boltzmann/static/ext/3dmol/3Dmol-min.js
  • boltzmann/static/ext/3dmol/3Dmol.ui-min.js

Related Pages

Related topics: JSME Integration

3D Molecule Visualization with 3Dmol.js

Introduction

3Dmol.js is a modern, open-source JavaScript library for visualizing molecular structures in 3D. It's designed to be easily embedded in web pages, providing interactive rendering of molecules from various data formats. In the acelot-inc/boltzmann repository, 3Dmol.js is used to enhance the user experience by allowing interactive visualization of molecular dynamics simulations and other chemical data.

Purpose and Functionality

The primary purpose of integrating 3Dmol.js into the Boltzmann project is to provide users with a clear, interactive view of molecular structures and simulations. Key functionalities include:

  • Rendering: Displaying molecules in 3D with customizable rendering styles (e.g., sticks, spheres, cartoons).
  • Interaction: Allowing users to rotate, zoom, and pan the molecular view.
  • Data Loading: Supporting various molecular data formats such as PDB, SDF, and XYZ.
  • Animation: Animating molecular dynamics trajectories to visualize simulations over time.
  • Customization: Providing options to customize the appearance of molecules, including colors, styles, and labels.

The core files are:

  • boltzmann/static/ext/3dmol/3Dmol-min.js: The minified core library of 3Dmol.js, containing the main rendering and interaction functionalities.
  • boltzmann/static/ext/3dmol/3Dmol.ui-min.js: Provides UI components and utilities to simplify integration with web applications.

Sources:

Code Snippets

Here's a basic example of how to initialize a 3Dmol.js viewer:

var element = $('#viewer_3dmol');
var config = {
    backgroundColor: 'white',
};

var viewer = $3Dmol.createViewer(element, config);
viewer.addModel(pdbString, "pdb");
viewer.setStyle({}, {stick:{}}); 
viewer.zoomTo();
viewer.render();

This snippet demonstrates creating a viewer, loading a PDB file, setting the rendering style to "sticks", and zooming to fit the molecule in the view.

Integration with Overall Architecture

3Dmol.js integrates into the Boltzmann project by providing a visual interface for molecular data. The typical workflow involves:

  1. Data Acquisition: Molecular data (e.g., from simulations or experimental results) is obtained in a supported format.
  2. Data Processing: The data is processed and prepared for visualization.
  3. Rendering: 3Dmol.js is used to render the molecular structure in an HTML element.
  4. User Interaction: Users can interact with the rendered molecule, changing the view, style, and other parameters.

Mermaid Diagram

Here's a sequence diagram illustrating the interaction between the user, Boltzmann application, and 3Dmol.js:

sequenceDiagram
    participant User
    participant BoltzmannApp
    participant 3Dmol.js

    User->>BoltzmannApp: Request Molecular View
    activate BoltzmannApp
    BoltzmannApp->>BoltzmannApp: Retrieve Molecular Data
    BoltzmannApp->>3Dmol.js: Load Data & Render
    activate 3Dmol.js
    3Dmol.js-->>BoltzmannApp: Rendered View
    deactivate 3Dmol.js
    BoltzmannApp-->>User: Display Interactive View
    deactivate BoltzmannApp
    User->>3Dmol.js: Interact with Molecule
    activate 3Dmol.js
    3Dmol.js-->>User: Update View
    deactivate 3Dmol.js

Conclusion

3Dmol.js offers a powerful and flexible way to visualize molecular structures within the acelot-inc/boltzmann project. Its ease of integration and rich feature set make it an invaluable tool for researchers and users seeking to explore molecular data in an interactive and intuitive manner.