RxnScribe

This is the repository for RxnScribe, a sequence generation model for reaction diagram parsing. Try our demo on Hugging Face!

If you use RxnScribe in your research, please cite our paper.

@article{
    RxnScribe,
    author = {Qian, Yujie and Guo, Jiang and Tu, Zhengkai and Coley, Connor W. and Barzilay, Regina},
    title = {RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing},
    journal = {Journal of Chemical Information and Modeling},
    doi = {10.1021/acs.jcim.3c00439}
}

Molecule structure recognition is supported by MolScribe (paper, code, demo).

Quick Start

Run the following command to install the package and its dependencies:

git clone [email protected]:thomas0809/RxnScribe.git
cd RxnScribe
python setup.py install

Download the checkpoint and use RxnScribe to extract reactions from a diagram:

import torch
from rxnscribe import RxnScribe
from huggingface_hub import hf_hub_download

ckpt_path = hf_hub_download("yujieq/RxnScribe", "pix2seq_reaction_full.ckpt")
model = RxnScribe(ckpt_path, device=torch.device('cpu'))

image_file = "assets/jacs.5b12989-Table-c3.png"
predictions = model.predict_image_file(image_file, molscribe=True, ocr=True)

The predictions will be in the following format:

[
    {  # First reaction
        'reactants': [
            {
                'category': '[Mol]', 'category_id': 1, 'bbox': (0.1550, 0.0246, 0.2851, 0.2614),
                'smiles': '*OC(=O)c1ccccc1C#Cc1ccccc1', 'molfile': '(omitted)' 
            }, 
            # ... more reactants 
        ],
        'conditions': [
            {
                'category': '[Txt]', 'category_id': 2, 'bbox': (0.2941, 0.0641, 0.3811, 0.1450),
                'text': ['CIBcat', '(1.4 equiv)']
            }, 
            # ... more conditions
        ],
        'products': [ 
            # ...
        ]
    },
    # More reactions
]

We provide a function to visualize the prediction:

visualize_images = model.draw_predictions(predictions, image_file=image_file)

Each predicted reaction will be visualized in a separate image, where red boxes are reactants, green boxes are reaction conditions, blue boxes are products.

This notebook shows how to run RxnScribe and visualize the prediction.

For development or reproducing the experiments, follow the instructions below.

Requirements

Install the required packages

pip install -r requirements.txt

Data

Download the reaction diagrams from this link, and save them to data/parse/images/.

The ground truth files can be found at data/parse/splits/.

We perform five-fold cross validation in our experiments. The train/dev/test split for each fold is available.

This notebook shows how to visualize the diagram and the ground truth.

Train and Evaluate RxnScribe

Run this script to train and evaluate RxnScribe with five-fold cross validation.

bash scripts/train_pix2seq_cv.sh

Finally, we train RxnScribe with 90% of the dataset, and use the remaining 10% as the dev set. We have released the model checkpoint.

bash scripts/train_pix2seq_full.sh