BondXtract ✼

A browser-based tool for exploring and analyzing atomic bonds in crystal structures from CIF (Crystallographic Information File) format.

Overview

BondXtract is a browser-based tool that helps researchers and crystallographers analyze atomic bonding patterns in crystal structures. The application reads CIF files and performs bond analysis with customizable search parameters.

Features

🔍 Advanced Bond Analysis

• Dual-atom bond search: Specify two different atom types to find bonds between them
• Distance-based filtering: Set minimum and maximum distance ranges (in Angstroms)
• Real-time progress tracking: Monitor search progress with detailed status updates

📊 Crystal Structure Support

• CIF file parsing: Full support for Crystallographic Information File format
• Space group symmetry: Automatic detection and application of crystallographic symmetry operations
• Embedded symmetry data: Built-in space group data for 230 crystallographic space groups

🎨 User-Friendly Interface

• Drag & drop support: Easy file upload with visual feedback
• Export functionality: Download results as CSV files for further analysis

⚡ Performance Features

• Progress monitoring: Real-time search progress with ability to stop mid-process
• Offline capable: Works completely offline without internet connection

👜 Portability

• Simple deployment: Just place all application files in the same directory
• No installation required: Works immediately without any setup or configuration
• Cross-platform: Runs on any operating system with a modern web browser

Usage

Getting Started

1. Setup the Application

   • Place all application files (BondXtract.html and embedded_spacegroups.js) in the same directory
   • Open BondXtract.html in any modern web browser
   • No installation or server setup required

2. Upload CIF File

   • Drag and drop a CIF file onto the upload area, or
   • Click "Select File" to browse and select a CIF file

3. Configure Search Parameters

   • Atom Types: Select the two atom types you want to analyze
   • Distance Range: Set minimum and maximum bond distances

4. Run Analysis

   • Click "Search Bonds" to start the analysis
   • Monitor progress in real-time
   • Use "Stop Search" or press Esc to stop mid-process

5. Review Results

   • View detected bonds in the results table
   • Each bond shows atom types, coordinates, distance, and bond classification
   • Download results as CSV for external analysis

Output Information

The tool provides detailed information for each discovered bond:

• Atom 1 & Atom 2: Element symbols and coordinates
• Distance: Bond length in Ångströms
• Relative Position: Spatial relationship between atoms
• Bond Type: Classification based on covalent radii

Bond Classification Methodology

BondXtract includes a feature to determine bond types based on standard covalent radii of ions. This feature should be used as a guideline only. The classification follows these criteria:

• Strong_Bond: Distance ≤ sum(covalent_radii) × 1.2

  • Includes typical covalent and ionic bonds
  • Based on Pauling's covalent radius theory and standard crystallographic databases

• Weak_Bond: sum(covalent_radii) × 1.2 < Distance ≤ sum(covalent_radii) × 1.5

  • Includes hydrogen bonds and van der Waals interactions
  • Common in molecular crystals and biological structures

• Non_Bond: Distance > sum(covalent_radii) × 1.5

  • No significant chemical interaction between atoms

Scientific Basis: The classification thresholds are based on standard crystallographic criteria used in:

• Cambridge Structural Database (CSD)
• Pauling's covalent radius theory
• Common molecular mechanics force fields

The covalent radius data is based on standard crystallographic databases (CRC Handbook, WebElements, etc.). For elements without available covalent radius data, estimated values based on atomic number are used.

Important Note on Space Group Symmetry

When a space group number is detected but the corresponding symmetry operations are not found in the CIF file, BondXtract automatically loads the necessary symmetry operations from embedded data. However, the embedded symmetry operations are based on standard setting and origin choice 1. If your crystal structure uses different axis orientations or origin choices, the symmetry operations may not match exactly. To avoid unexpected inconsistencies, it is recommended to ensure your CIF file contains explicit symmetry operations for accurate analysis.

Technical Details

Supported File Formats

• CIF (Crystallographic Information File): Standard format for crystallographic data
• Space Groups: All 230 crystallographic space groups supported
• Atom Types: All elements from the periodic table

Browser Compatibility

• Tested on: Chrome (confirmed working)
• Other modern browsers: Firefox, Safari, Edge (likely compatible but not tested)
• No plugins required: Pure HTML5, CSS3, and JavaScript
• Offline capable: Works completely offline without internet connection
• No server required: Runs entirely in the browser
• Portable: Simple directory deployment with no dependencies

Current Status

Planned Features:

• Additional file format support
• Batch processing capabilities
• Ligand type identification (local molecular geometry analysis) - low priority
• Enhanced visualization options - low priority

Contributing

Contributions are welcome! Areas for improvement include:

• Additional file format support
• Enhanced visualization features
• Performance optimizations
• Documentation improvements

License

This project is licensed under the MIT License - see the LICENSE file for details.

Author

Hitoshi Mori - 2025