OXtal (Organic X "Crys-" tal) is an all-atom diffusion model for molecular crystal structure prediction (CSP). Unlike traditional quantum-chemical approaches, which rely on expensive energy oracles, OXtal generates fast and accurate zero-shot predictions at a fraction of the cost. Specifically, OXtal recovers experimental crystal structures for both rigid and flexible molecules, as well as co-crystals, with conformer RMSD1 < 0.5 Å and attains over 80% packing similarity rate, demonstrating its ability to model both thermodynamic and kinetic regularities of molecular crystallization.

⚙️ Installation and Setup

OXtal was developed with Python 3.11.0, CUDA 12.6, and PyTorch 2.5.0, but you may need to adjust these accordingly to match your own compute resources. To set up the environment, run the following commands from the top-level OXtal directory, which should create the oxtal-env environment in .venv/

# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# Install oxtal-env
uv sync

After installing the environment through uv, you can activate it using:

source .venv/bin/activate

[Optional] CUTLASS Installation

OXtal also supports using DeepSpeed4Science EvoformerAttention for memory-efficient attention, which significantly reduces GPU memory usage and enables inference on longer sequences. This requires NVIDIA CUTLASS to be available on disk and a GPU with Ampere or newer architecture (e.g. A100, L40S, H100, H200, B100, B200). To enable this functionality, add deepspeed>=0.18.3 to the list of dependencies in pyproject.toml, and update your environment using the steps above. CUTLASS can be installed as follows:

# First clone the cutlass repo
git clone -b v3.5.1 https://github.com/NVIDIA/cutlass.git

# Then, set the environment variable CUTLASS_PATH to point there
cd cutlass
pwd
export CUTLASS_PATH=<path_from_pwd>

You can also add CUTLASS_PATH to your shell profile so it persists across sessions. The attention kernels will be compiled the first time they are invoked. To invoke evoformer attention during inference, remove use_deepspeed_evo_attention=false from run_inference.sh.

🚀 Inference

This project uses hydra to manage model configuration files, which allows easy command-line overrides and structured configs. You can find all the configuration files in the configs folder. We also use HuggingFace in order to manage our model checkpoint and data files.

To generate samples with OXtal, run the following command:

# Run OXtal inference:
bash run_inference.sh

To run inference on different sets of molecules, simply update the input_json_path parameter in run_inference.sh. We have provided all of our evaluation datasets in the examples folder. To run inference on all 5 evaluation datasets from the paper together, use the examples/all_inference.json file.

Parameter	Description
input_json_path	Path to the input JSON file detailings which crystals to generate.
sample_diffusion.N_sample	Number of samples to generate. For example, num_inference_seeds=10 produces 10 samples per job.
seeds	List of random seeds, e.g. [0,1,2]. Each seed produces sample_diffusion.N_sample outputs for each crystal in the input JSON, so the total number of generated samples equals len(seeds) * sample_diffusion.N_sample.
dump_dir	Output directory for generated structures.
use_deepspeed_evo_attention	Flag to enable/disable EvoformerAttention.

You can also run OXtal with your own molecules by adding a new .json file to the examples folder. The code supports both SMILES strings as well as input .sdf files (specified by adding FILE_ prefix to the file name). For co-crystals, all component parts must be specified individually, with the desired ratios provided. Example .json entries are provided below for reference:

[
    {
        "sequences": [
            {
                "ligand": {
                    "ligand": "CC1=CC(C#N)=C(S1)Nc2c([N+]([O-])=O)cccc2", # SMILES string
                    "count": 30, # How many copies of the molecule to generate
                    "id_key": "ligand"
                }
            }
        ],
        "modelSeeds": [],
        "assembly_id": "1",
        "name": "QAXMEH"
    },
    {
        "sequences": [
            {
                "ligand": {
                    "ligand": "N#CC(C#N)=C1C=CC(C=C1)=C(C#N)C#N",
                    "count": 30,
                    "id_key": "ligand"
                }
            },
            {
                "ligand": {
                    "ligand": "c1cc2cccc3c4cccc5cccc(c(c1)c23)c45",
                    "count": 30,
                    "id_key": "ligand"
                }
            }
        ],
        "modelSeeds": [],
        "assembly_id": "1",
        "name": "PERTCQ01" # Co-Crystal with 1:1 ratio
    },
    {
        "sequences": [
            {
                "ligand": {
                    "ligand": "FILE_./examples/BIPY.sdf", # Input .sdf instead of SMILES string
                    "count": 30,
                    "id_key": "ligand"
                }
            }
        ],
        "modelSeeds": [],
        "assembly_id": "1",
        "name": "UWEQUL"
    },
  ...
]

📊 Evaluation

We use the COMPACK software from CCDC to compare OXtal generated crystal packings to experimentally observed structures in our test datasets. You can install the csd-python-api into your envioronment using the following command:

uv pip install --extra-index-url https://pip.ccdc.cam.ac.uk/ csd-python-api

After installing, ensure that you have properly installed the CCDC dataset and activated your license. For reference, setup instructions using the command line on a Linux machine can be found here.

After running inference and setting up CCDC, you can simply run:

bash run_eval.sh

and the evaluation summary report will be generated in evaluation/metric_summary.txt. You can modify paths and file names as necessary in run_eval.sh.

🙏 Acknowledgements

This code heavily relies on and builds off of the Protenix code base, and we thank the authors of that work for their efforts.

We'd also like to thank CCDC for their support in helping us maintain our commitment to open science.

📖 Cite

If you make use of this code or its accompanying paper, please cite this work as follows:

@inproceedings{jin2025oxtal,
  title={OXtal: An All-Atom Diffusion Model for Organic Crystal Structure Prediction},
  author={Jin, Emily and Nica, Andrei Cristian and Galkin, Mikhail and Rector-Brooks, Jarrid and Lee, Kin Long Kelvin and Miret, Santiago and Arnold, Frances H and Bronstein, Michael and Bose, Avishek Joey and Tong, Alexander and Liu, Cheng-Hao},
  booktitle={ICLR},
  year={2026}
}

📄 License

The source code for OXtal is released under an MIT License (see LICENCE-SOURCE-CODE). However, since OXtal was trained on data from CCDC's Cambridge Structural Database, the model weights are released under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) License (see LICENCE-MODEL-WEIGHTS). For commercial use of the model weights, please ensure that you have a proper CCDC License.