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Welcome to the haddock-runner docs

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The haddock-runner is a powerful tool for running large-scale HADDOCK docking experiments. It automates the execution of HADDOCK3 workflows across multiple protein complexes, enabling comprehensive benchmarking and performance evaluation.

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is a widely-used software suite for flexible docking of biomolecular complexes, particularly useful for studying protein-protein interactions.

Key Features

  • Large-scale Benchmarking: Execute HADDOCK workflows on multiple molecular complexes simultaneously
  • Scenario Testing: Run different docking scenarios (workflows, parameters) on the same datasets
  • Concurrent Execution: Process multiple targets concurrently for efficient resource utilization
  • Input Validation: Automatic checksum validation to ensure data integrity
  • Flexible Configuration: YAML-based configuration for complex benchmarking setups

How It Works

haddock-runner takes a YAML configuration file that defines:

  • General settings: Maximum concurrent jobs, core allocation, working directory
  • Input datasets: List of molecular structures and associated files
  • Docking scenarios: Different HADDOCK workflows and parameters to test

The tool then automatically:

  1. Validates all input files using checksums
  2. Creates individual HADDOCK jobs for each target-scenario combination
  3. Executes jobs concurrently according to resource constraints
  4. Organizes results in a structured working directory

Quick Start

Prerequisites

  • HADDOCK3 installed and properly configured
  • Input molecular structures in PDB format
  • Optional restraint files (TBL format) for guided docking

Basic Usage

haddock-runner benchmark_config.yaml

Common Options

Setup mode (validate and prepare without execution):

haddock-runner --setup benchmark_config.yaml

Debug mode (verbose logging):

haddock-runner --debug benchmark_config.yaml

Typical Use Cases

When running benchmarks, researchers typically investigate:

  • Parameter Optimization: How different sampling parameters affect docking quality
  • Workflow Comparison: Performance of different docking protocols
  • Method Validation: Testing new restraint strategies or scoring functions
  • Performance Benchmarking: Execution time and resource usage patterns
  • Reproducibility Studies: Consistent results across different computational environments

Example Workflow

A typical benchmark might include:

  • 5-10 different protein complexes
  • 3-5 different docking scenarios (true interface, center-of-mass, random restraints)
  • 100-1000 docking runs per scenario
  • Concurrent execution on 4-8 CPU cores

Results are organized by scenario and target, making it easy to compare performance across different conditions.

Getting Started with Your Own Benchmark

  1. Prepare your molecular structures in PDB format
  2. Create restraint files if using guided docking
  3. Write a configuration file defining your scenarios
  4. List your input files in the required format
  5. Run the benchmark and analyze results

See the Setting Up a Benchmark and Writing a Benchmark YAML File sections for detailed instructions.

Getting Help

If you encounter any issues or have questions:

The HADDOCK team and community are available to help with setup, configuration, and analysis of your benchmarks.