examples

BondForge Examples

This directory contains comprehensive examples demonstrating how to use BondForge.

Available Examples

CLI Examples

cli_examples.sh - Shell script with CLI command examples

• Basic analysis
• Specific interaction types
• Advanced energy calculations
• Batch processing
• Structure comparison
• Custom configuration
• And more!

Usage:

chmod +x cli_examples.sh
./cli_examples.sh  # View all examples

Python API Examples

example_demo.py - Basic demonstration script

• Core analyzer (7 interaction types)
• Hub residue identification
• Result export
• Visualization

Usage:

python example_demo.py protein.pdb

comprehensive_example.py - Complete demonstration

• Core analyzer (7 types)
• Extended analyzer (20 types)
• Interface analysis
• Visualization generation
• All features demonstrated

Usage:

python comprehensive_example.py protein.pdb

Quick Start

1. Get Test Data

Download sample PDB files:

# Small protein for testing
wget https://files.rcsb.org/download/1ABC.pdb

# Or use any of your own PDB files

2. Run CLI Examples

# Basic analysis
bondforge analyze 1ABC.pdb

# With advanced features
bondforge analyze 1ABC.pdb --energy --parallel

3. Run Python Examples

# Simple demo
python example_demo.py 1ABC.pdb

# Comprehensive demo
python comprehensive_example.py 1ABC.pdb

Example Categories

Basic Usage

• cli_examples.sh - Example 1: Basic analysis
• example_demo.py - Simple workflow

Advanced Features

• cli_examples.sh - Example 3: Energy calculations
• comprehensive_example.py - All 20 interaction types

Batch Processing

• cli_examples.sh - Example 4: Batch processing
• Multiple structure analysis

Configuration

• cli_examples.sh - Example 6: Custom config
• YAML configuration examples

Comparison Analysis

• cli_examples.sh - Example 5: Structure comparison
• Wild-type vs mutant

🎯 Example Outputs

All examples generate results in organized directories:

results/
├── interactions.csv          # All detected interactions
├── hubs.csv                  # Hub residues
├── critical_interactions.csv # Critical interactions
├── interaction_network.png   # Network visualization
└── visualize.pml             # PyMOL script

Creating Your Own Examples

Template: Basic Analysis

from bondforge import ExtendedProteinInteractionAnalyzer

# Load and analyze
analyzer = ExtendedProteinInteractionAnalyzer('protein.pdb')
results = analyzer.analyze_all_interactions()

# Print summary
print(f"Total interactions: {results['total_interactions']}")

# Export
analyzer.export_to_csv('results/')

Template: Advanced Energy

from bondforge import ExtendedProteinInteractionAnalyzer
from bondforge.energy_calculator import AdvancedEnergyCalculator

# Analyze
analyzer = ExtendedProteinInteractionAnalyzer('protein.pdb')
h_bonds = analyzer.find_hydrogen_bonds()

# Calculate energies
calc = AdvancedEnergyCalculator()
for bond in h_bonds:
    energy = calc.calculate_hydrogen_bond_energy(
        donor_atom=bond['donor_type'],
        acceptor_atom=bond['acceptor_type'],
        distance=bond['distance'],
        angle=bond['angle']
    )
    print(f"Energy: {energy.total:.2f} kcal/mol")

Template: Statistical Validation

from bondforge.statistical_validator import StatisticalValidator

validator = StatisticalValidator()

# Validate interaction
result = validator.calculate_zscore(
    'hydrogen_bond',
    observed_distance=2.9,
    observed_angle=165
)

print(f"Z-score: {result['z_score_distance']:.2f}")
print(f"Typical: {result['is_typical']}")
print(f"Confidence: {result['confidence']}")

🔧 Customization Examples

Custom Distance Cutoffs

analyzer = ExtendedProteinInteractionAnalyzer('protein.pdb')

# Custom hydrogen bond cutoff
h_bonds = analyzer.find_hydrogen_bonds(distance_cutoff=3.2)

# Custom salt bridge cutoff
salt_bridges = analyzer.find_salt_bridges(distance_cutoff=3.8)

Custom Configuration File

# my_config.yaml
analysis:
  distance_cutoffs:
    hydrogen_bond: 3.2
    salt_bridge: 3.8
  energy_calculation:
    method: advanced
    force_field: amber

Then use:

bondforge analyze protein.pdb --config my_config.yaml

📊 Example Use Cases

1. Drug Discovery

Analyze protein-ligand interactions for drug design

2. Protein Engineering

Compare wild-type vs mutant to guide mutations

3. Stability Analysis

Identify critical interactions for stability

4. Interface Characterization

Study protein-protein binding interfaces

5. Quality Control

Validate structure quality and completeness

🎓 Learning Path

Beginners:

1. Start with cli_examples.sh Example 1
2. Try example_demo.py
3. Explore basic CLI commands

Intermediate:

1. Run comprehensive_example.py
2. Try custom configurations
3. Experiment with different interaction types

Advanced:

1. Use advanced energy calculations
2. Implement statistical validation
3. Create custom analysis workflows
4. Batch process multiple structures

🐛 Troubleshooting

PDB file not found:

# Download test structures
wget https://files.rcsb.org/download/1ABC.pdb

Module not found:

# Install BondForge
pip install -e .

CLI command not found:

# Reinstall with entry points
pip install -e .

📞 Need Help?

• 📚 Documentation: See docs/ directory
• 💬 Discussions: GitHub Discussions
• 🐛 Issues: GitHub Issues
• 📧 Email: ayehbolouki1988@gmail.com

🎉 Contribute Examples

Have a cool use case? Share it!

1. Create your example script
2. Add documentation
3. Submit a pull request

See CONTRIBUTING.md for guidelines.

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Happy Forging! 🔥

These examples help you get started quickly with BondForge