Examples

This page provides comprehensive examples of haddock-runner configurations for various benchmarking scenarios. These examples demonstrate the tool’s flexibility and help you design your own benchmarks.

Basic Examples

Restraint Strategy Comparison

Compare different restraint approaches for the same targets:

general:
  mol_suffixes: [_r_u, _l_u]
  input_list: input_list.txt
  work_dir: ./results/restraint-comparison
  max_concurrent: 2
  ncores: 4
  execution: local

scenarios:
  - name: true-interface-restraints
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 500
        ambig_fname: _ti.tbl
      flexref:
        ambig_fname: _ti.tbl
      caprieval:
        reference_fname: _ref.pdb

  - name: hbond-only-restraints
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 500
        ambig_fname: _hb.tbl
      flexref:
        ambig_fname: _hb.tbl
      caprieval:
        reference_fname: _ref.pdb

  - name: center-of-mass
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 500
        cmrest: true
      flexref:
        cmrest: true
      caprieval:
        reference_fname: _ref.pdb

  - name: random-air-restraints
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 500
        ranair: true
      flexref:
        ranair: true
      caprieval:
        reference_fname: _ref.pdb

Advanced Examples

The purpose of this scenario is to sample antibody-peptide complexes, re-docking experimental structures. Rigid docking, flexible refinement and em refinement. Unambiguous restrains to keep Ab heavy and light chain together and ambiguous for CDR loops and whole peptide.

general:
  input_list: /trinity/csbdevel/jvillave/deeprank-ab-pep/haddock3/2_real/2_config/data_2_cutoff_043/input_test_scenario_0.list
  mol_suffixes: [_antibody, _antigen]
  work_dir: /trinity/csbdevel/jvillave/deeprank-ab-pep/haddock3/2_real/3_2_results/scenario_0_results
  execution: slurm 
  max_concurrent: 100
  ncores: 24

scenarios:
  # ------------------------------------------------------------
  # 1) scenario 0, ab initio ground truth
  # ------------------------------------------------------------
  - name: ground-truth
    workflow:
      topoaa:
        tolerance : 20
      rigidbody:
        tolerance : 20
        crossdock: false
        sampling: 10000
        ambig_fname: _ti.tbl
        unambig_fname: _antibody-unambig.tbl
      clustfcc:
        plot_matrix: true
      # select up to 100 clusters per target,
      # keeping 5 top models each (max 500 models)
      seletopclusts:
        top_clusters: 100
        top_models: 5
      flexref:
        tolerance : 20
        ambig_fname: _ti.tbl
        unambig_fname: _antibody-unambig.tbl
      # final energy minimisation
      emref:
        tolerance : 20
        ambig_fname: _ti.tbl
        unambig_fname: _antibody-unambig.tbl
      caprieval:
        reference_fname: _matched.pdb
        fnat_cutoff: 4.0
        irmsd_cutoff: 8.0
      emscoring:
        tolerance : 20
        per_interface_scoring: true

…

Configuration Variations

HPC Cluster Configuration

Optimized for SLURM workload manager:

general:
  mol_suffixes: [_r_u, _l_u]
  input_list: large_input_list.txt
  work_dir: /scratch/results/large-benchmark
  max_concurrent: 20
  ncores: 8
  execution: slurm

scenarios:
  - name: hpc-optimized
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 2000
        ambig_fname: _ti.tbl
      flexref:
        ambig_fname: _ti.tbl
      caprieval:
        reference_fname: _ref.pdb

Minimal Configuration

Simple setup for quick testing:

general:
  mol_suffixes: [_r_u, _l_u]
  input_list: test_input.txt
  work_dir: ./test-results
  max_concurrent: 2
  ncores: 2
  execution: local

scenarios:
  - name: quick-test
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 100
        cmrest: true

Real-world Example: BM5 Benchmark

A configuration similar to the BM5 benchmark setup:

general:
  mol_suffixes: [_r_u, _l_u]
  input_list: bm5_input_list.txt
  work_dir: ./results/bm5-style
  max_concurrent: 10
  ncores: 4
  execution: local

scenarios:
  - name: bm5-true-interface
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 1000
        ambig_fname: _ti.tbl
        unambig_fname: _unambig.tbl
      seletop:
        select: 200
        sort_by: score
      semiflexref:
        ambig_fname: _ti.tbl
        unambig_fname: _unambig.tbl
      emref:
        mdsteps: 500
      caprieval:
        reference_fname: _ref.pdb
        clusters: 4

  - name: bm5-center-mass
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 1000
        cmrest: true
      seletop:
        select: 200
        sort_by: score
      semiflexref:
        cmrest: true
      emref:
        mdsteps: 500
      caprieval:
        reference_fname: _ref.pdb
        clusters: 4

Input List Examples

Simple Input List

# Target 1A2K
structures/1A2K/1A2K_r_u.pdb
structures/1A2K/1A2K_l_u.pdb
structures/1A2K/1A2K_ti.tbl
structures/1A2K/1A2K_ref.pdb

# Target 1GGR
structures/1GGR/1GGR_r_u.pdb
structures/1GGR/1GGR_l_u.pdb
structures/1GGR/1GGR_ti.tbl
structures/1GGR/1GGR_ref.pdb

Complex Input List with Multiple File Types

# Target 1PPE - Protein-protein with multiple restraint types
structures/1PPE/1PPE_r_u.pdb
structures/1PPE/1PPE_l_u.pdb
structures/1PPE/1PPE_ti.tbl
structures/1PPE/1PPE_hb.tbl
structures/1PPE/1PPE_unambig.tbl
structures/1PPE/1PPE_ref.pdb

# Target 2OOB - With ligand files
structures/2OOB/2OOB_r_u.pdb
structures/2OOB/2OOB_l_u.pdb
structures/2OOB/2OOB_x_u.pdb
structures/2OOB/2OOB_ti.tbl
structures/2OOB/2OOB_hb.tbl
structures/2OOB/2OOB_ligand.top
structures/2OOB/2OOB_ligand.param
structures/2OOB/2OOB_ref.pdb

Best Practices for Examples

Starting with Examples

Begin with simple configurations and gradually add complexity
Test with small datasets before scaling up
Use --setup mode to validate configurations before full runs
Start with low sampling numbers for initial testing

Adapting Examples

Modify scenarios to match your research questions
Adjust resource settings based on your hardware
Customize workflows for your specific docking needs
Scale parameters appropriately for your system size

Creating Your Own

Use these examples as templates and:

Replace file paths with your actual data
Adjust sampling parameters for your needs
Add or remove workflow steps as required
Configure resource limits for your environment

Troubleshooting Examples

Common Configuration Issues

Problem: Jobs fail with missing file errors Solution: Verify all files in input list exist and paths are correct

Problem: Out of memory errors Solution: Reduce max_concurrent or increase ncores per job

Problem: HADDOCK module not found Solution: Ensure HADDOCK3 is properly installed and in PATH

Problem: Slow execution Solution: Adjust max_concurrent and ncores for optimal resource usage

Additional Resources

Complete configuration reference: Writing a Benchmark YAML File
Input list format guide: Writing an Input List File
Running benchmarks: Running Haddock Runner
Real-world setup: Setting Up a Benchmark

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