Quetzal

 

Code for Scalable Autoregressive 3D Molecule Generation

Setup:

mamba create -f environment.yml

This environment was prepared via:

mamba create -n quetzal python=3.10
mamba activate quetzal
mamba install c-compiler cxx-compiler # needed for torch.compile
pip install torch==2.6 lightning==2.5.0.post0 rdkit==2023.03.3 jupyter notebook ipywidgets scipy "numpy<2" matplotlib tqdm pandas wandb==0.18.7 seaborn msgpack py3Dmol torchdata

rdkit==2023.03.3 is important to have consistent validity metrics

Optional W&B setup:

export WANDB_ENTITY=<your_entity>

Create a folder for SLURM logs (required):

mkdir -p slurm

Download checkpoint(s):

mkdir -p checkpoints
cd checkpoints
wget https://huggingface.co/auhcheng/quetzal/resolve/main/original.ckpt # best qm9 model
wget https://huggingface.co/auhcheng/quetzal/resolve/main/geom.ckpt # best geom model

You can find the rest of the checkpoints for ablation studies here.

Start playing around with the model in play.ipynb!

Training and evaluation

Directly download the preprocessed data:

wget https://huggingface.co/auhcheng/quetzal/resolve/main/data.tar.gz
tar -xf data.tar.gz

Or download and preprocess data from raw:

python qm9.py # less than a minute
python geom.py # 30-60 minutes, ~100G space

The command for training on QM9:

python train.py --name=qm9_run

Add --debug for a progress bar. See train.py for more options.

The command for evaluating on QM9: (change --ckpt if needed)

python generate.py --ckpt=logs/quetzal/qm9_run/checkpoints/epoch=1999-step=188000.ckpt --name=qm9_samples --device=cuda --num_samples=10000 --num_chunks=1 --diff_steps=60 --max_len=32
python metrics.py --samples_dir=samples/gen/qm9_samples --dataset=qm9

The command for training on GEOM:

sbatch 4run.sh

To continue the run for longer than 24 hours, simply run the same training command and make sure the run has the same --name, or pass --resume_path=<path>.ckpt.

The command for evaluating on GEOM:

python generate.py --ckpt=logs/quetzal/geom_run/checkpoints/epoch=201-step=734272.ckpt --name=geom_samples --device=cuda --num_samples=10000 --num_chunks=10 --diff_steps=120 --max_len=192
python metrics.py --samples_dir=samples/gen/geom_samples --dataset=geom

To submit multiple jobs, specify commands in the jobs file, and run ./submit.sh to submit each line in the jobs file.

You can find almost all figures and how they were generated in figures/. First, download the generated samples:

wget https://huggingface.co/auhcheng/quetzal/resolve/main/samples.tar.gz
tar -xf samples.tar.gz

The samples in samples/ may be in .xyz format, or batched together as Molecule objects stored with their diffusion traces as gen.pt. You can see how these are loaded in figures/uncurated/show.ipynb or figures/anim/anim.ipynb. For automating conversion of html to png, figures/render.py may be useful.

Hydrogen decoration

Evaluate Quetzal on hydrogen decoration:

python hdeco.py

The progress bar may appear to hang due to torch.compile.

For OpenBabel+Hydride:

mamba install openbabel
pip install hydride

Use addH.sh. You will need to prepare some .xyz files of the test set without hydrogens. You also need to rewrite hdeco.py to calculate RMSD for these generated .xyz files.

For Olex2, you may find run_olex2.scpt useful.

Some of the samples are flipped along the x/y/z axes, because the QM9 test data were reprocessed using PCA at some point.

Exact log-likelihood computation

python density.py --ckpt=checkpoints/original.ckpt --name=qm9_density
python density.py --ckpt=checkpoints/geom.ckpt --name=geom_density

---

This work was made possible by several previous works, including but not limited to:

• Autoregressive Image Generation without Vector Quantization
• nanoGPT
• Elucidating Diffusion Models
• Equivariant Diffusion Models
• Symphony

If you find any of the code in this repo useful, please cite!

@article{cheng2025scalable,
  title={Scalable Autoregressive {3D} Molecule Generation},
  author={Cheng, Austin H and Sun, Chong and Aspuru-Guzik, Al{\'a}n},
  journal={arXiv preprint arXiv:2505.13791},
  year={2025}
}