rxnemb 1.0.0

A reaction-level embedding descriptor.

🚀 Overview

RXNEmb is a novel reaction-level embedding descriptor generated via the pre-trained model RXNGraphormer. It captures chemical bond formation and cleavage patterns, enabling data-driven reaction classification, mechanistic interpretation, and reaction space visualization.

The preprint paper is available at https://arxiv.org/pdf/2601.03689 .

🔧 Installation

pip install rxnemb

💡 Generate RXNEmb Descriptor

Example: Generate reaction embeddings from SMILES list

from rxnemb import RXNEMB

generator = RXNEMB()

# prepare reaction SMILES
# here are some examples
rxn_smiles_lst = [
    "O=C(O)c1ccccc1.[Cl-]>>O=C(Cl)c1ccccc1",  
    "C1CCOC1.C1CCOC1.O.O=C(O)C(Br)c1ccccc1>>OCC(Br)c1ccccc1",
    # ... more 
]

# output
rxn_emb = generator.gen_rxn_emb(rxn_smiles_lst)
print(rxn_emb.shape) # torch.Size([2, 768])

📚 Citation

If you use RXNEmb in your research, please cite:

@misc{RXNEmb_liu2026,
      title={A Pre-trained Reaction Embedding Descriptor Capturing Bond Transformation Patterns}, 
      author={Weiqi Liu and Fenglei Cao and Yuan Qi and Li-Cheng Xu},
      date = {2026-01-07},
      eprint={2601.03689},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      doi = {10.48550/arXiv.2601.03689},
      url={https://arxiv.org/abs/2601.03689}, 
      pubstate = {prepublished},
}