strain-relief 0.5

Calculates ligand strain of small molecules from their docked poses.

StrainRelief 💊

StrainRelief calculates the ligand strain of uncharged docked poses and has a suite of different force fields with which to do this. This includes our own MACE neural network potential trained on SPICE2 but also includes Meta's FairChem models such as e-SEN and UMA.

• 📄 The publication can be found here.
• 📊 All relevant datasets here.
• 💬 RAG chatbot for questions about the paper and references.
• 💻 Chatbot source code.
• 🐍 Published python package.

Update: v0.5

1. Switched to uv for package management.
2. Introduced custom typing (MolsDict, MolPropertiesDict, EnergiesDict and ConfEnergiesDict) to make functions more readable.
3. Updated workflows and MolsDict to include charge and spin. This allows for charge aware NNPs such as eSEN and UMA. A boolean kwarg (include_charged=True) has been added to load_parquets to optionally filter these out.
4. Restructured calling of the main function to make it more intuitive with PyPi packaging.

Installation

Installation from PyPi

pip install strain-relief

Installation from source

Install uv if not already installed. Create a new uv enviroment using:

uv venv
source .venv/bin/activate

From the root directory, run the following commands to install the package and its dependencies in editable mode:

(mace-torch==0.3.x requires e3nn==0.4.4 (only for training, not inference). fairchem-core requires e3nn>=0.5. So until mace-torch==0.4 is released we will have to do this finicky way of installing (GitHub issue).)

git clone https://github.com/prescient-design/StrainRelief.git

uv pip install -e ".[dev]"
uv pip install --force-reinstall e3nn==0.5 fairchem-core
uv run pre-commit install

or if you have a uv.lock file:

uv sync --extra dev --editable

The Protocol

The protocol used in StrainRelief is designed to be simple, fast and model agnostic - all that is needed to apply a new force field is to write an ASE calculator wrapper. Additionally you can use any MACE model, such as these from the MACE-OFF23 repository.

The protocol consists of 5 steps:

1. Minimise the docked pose with a loose convergence criteria to give a local minimum.
2. Generate 20 conformers from the docked ligand pose.
3. Minimise the generated conformers (and the original docked pose) with a stricter convergence criteria.
4. Evaluate the energy of all conformers and choose the lowest energy as an approximation of the global minimum.
5. Calculate E(ligand strain) = E(local minimum) - E(global minimum) and apply threshold.

N.B. energies returned are in kcal/mol.

Usage

StrainRelief runs are configured using hydra configs.

Python Package

from strain_relief import compute_strain

strains = compute_strain(poses: list[RDKit.Mol], config: DictConfig)

for i, r in computed.iterrows():
    print(f"Pose {r['id']} has a strain of {r['ligand_strain']:.2f} kcal/mol")

For a complete example see the tutorial notebook.

Command Line

strain-relief \
    experiment=mmff94s \
    io.input.parquet_path=data/example_ligboundconf_input.parquet \
    io.output.parquet_path=data/example_ligboundconf_output.parquet \

More examples are given here, including the command used for the calculations in the StrainRelief paper.

Configurations

RDKit kwargs

The following dictionaries are passed directly to the function of that name.

• conformers (EmbedMultipleConfs)
• minimisation.MMFFGetMoleculeProperties
• minimisation.MMFFGetMoleculeForceField
• energy_eval.MMFFGetMoleculeProperties
• energy_eval.MMFFGetMoleculeForceField

The hydra config is set up to allow additional kwargs to be passed to these functions e.g. +minimisation.MMFFGetMoleculeProperties.mmffVerbosity=1.

Common kwargs

• threshold (set by default to 16.1 kcal/mol - calibrated using LigBoundConf 2.0)
• conformers.numConfs
• global_min.maxIters/local_min.maxIters
• global_min.fmax/local_min.maxIters
• io.input.include_charged
• hydra.verbose
• seed

Logging

Logging is set to the INFO level by default which logs only aggregate information. hydra.verbose=true can be used to activate DEBUG level logging which includes information for every molecule and conformer.

Unit Tests

• uv run pytest tests/ - runs all tests (unit and integration)
• uv run pytest tests/ -m "not gpu" - excludes all MACE tests
• uv run pytest tests/ -m "not integration" - runs all unit tests

NB Tests requiring a FAIRChem model will be skipped if the OMol25 eSEN small conserving model is not located in tests/models/eSEN.pt. This model can be downloaded here.

Citations

If you use StrainRelief or adapt the StrainRelief code for any purpose, please cite:

@misc{wallace2025strainrelief,
      title={Strain Problems got you in a Twist? Try StrainRelief: A Quantum-Accurate Tool for Ligand Strain Calculations},
      author={Ewan R. S. Wallace and Nathan C. Frey and Joshua A. Rackers},
      year={2025},
      eprint={2503.13352},
      archivePrefix={arXiv},
      primaryClass={physics.chem-ph},
      url={https://arxiv.org/abs/2503.13352},
}

More information

For any questions, please reach out to Ewan Wallace: [e-mail]