localmapper 0.1.2

LocalMapper for precise reaction atom-mapping

LocalMapper

Implementation of LocalMapper developed by Prof. Yousung Jung group at Seoul National University (contact: [e-mail]).

Contents

• Developer
• OS Requirements
• Python Dependencies
• Installation Guide
• Usage
• Data
• Reproduce the results
• Publication
• License

Developer

Shuan Chen ([e-mail])

OS Requirements

This repository has been tested on both Linux and Windows operating systems.

Python Dependencies

• Python (version >= 3.6)
• Numpy (version >= 1.16.4)
• Matplotlib (version >=3.3.4)
• PyTorch (version >= 1.0.0)
• RDKit (version >= 2019)
• DGL (version >= 0.5.2)
• DGLLife (version >= 0.2.6)

Installation Guide

From pip

conda create -n localmapper python=3.6 -y
conda activate localmapper
pip install localmapper

From Github

git clone https://github.com/snu-micc/LocalMapper.git
cd LocalMapper
conda create -n localmapper python=3.6 -y
conda activate localmapper
pip install -e .

Usage

Single rxn input

from localmapper import localmapper
mapper = localmapper()
rxn = 'CC(C)S.CN(C)C=O.Fc1cccnc1F.O=C([O-])[O-].[K+].[K+]>>CC(C)Sc1ncccc1F'
result = mapper.get_atom_map(rxn)

The expected output of result should be

'[CH3:1][CH:2]([CH3:3])[SH:4].CN(C)C=O.[F:11][c:10]1[cH:9][cH:8][cH:7][n:6][c:5]1F.O=C([O-])[O-].[K+].[K+]>>[CH3:1][CH:2]([CH3:3])[S:4][c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11]'

Multiple rxns input

rxns = ['CC(C)S.CN(C)C=O.Fc1cccnc1F.O=C([O-])[O-].[K+].[K+]>>CC(C)Sc1ncccc1F', CCOCC.C[Mg+].O=Cc1ccc(F)cc1Cl.[Br-]>>CC(O)c1ccc(F)cc1Cl]
results = mapper.get_atom_map(rxns)

The expected output of results should be

['[CH3:1][CH:2]([CH3:3])[SH:4].CN(C)C=O.[F:11][c:10]1[cH:9][cH:8][cH:7][n:6][c:5]1F.O=C([O-])[O-].[K+].[K+]>>[CH3:1][CH:2]([CH3:3])[S:4][c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11]',
 'CCOCC.[CH3:1][Mg+].[O:3]=[CH:2][c:4]1[cH:5][cH:6][c:7]([F:8])[cH:9][c:10]1[Cl:11].[Br-]>>[CH3:1][CH:2]([OH:3])[c:4]1[cH:5][cH:6][c:7]([F:8])[cH:9][c:10]1[Cl:11]']

Return results as dictionary

rxns = ['CC(C)S.CN(C)C=O.Fc1cccnc1F.O=C([O-])[O-].[K+].[K+]>>CC(C)Sc1ncccc1F', CCOCC.C[Mg+].O=Cc1ccc(F)cc1Cl.[Br-]>>CC(O)c1ccc(F)cc1Cl]
results = mapper.get_atom_map(rxns, return_dict=True)

The expected output of results should be

[{'rxn': 'CC(C)S.CN(C)C=O.Fc1cccnc1F.O=C([O-])[O-].[K+].[K+]>>CC(C)Sc1ncccc1F',
  'mapped_rxn': '[CH3:1][CH:2]([CH3:3])[SH:4].CN(C)C=O.[F:11][c:10]1[cH:9][cH:8][cH:7][n:6][c:5]1F.O=C([O-])[O-].[K+].[K+]>>[CH3:1][CH:2]([CH3:3])[S:4][c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11]',
  'template': '[S:1].F-[c:2]>>[S:1]-[c:2]',
  'confident': True},
 {'rxn': 'CCOCC.C[Mg+].O=Cc1ccc(F)cc1Cl.[Br-]>>CC(O)c1ccc(F)cc1Cl',
  'mapped_rxn': 'CCOCC.[CH3:1][Mg+].[O:3]=[CH:2][c:4]1[cH:5][cH:6][c:7]([F:8])[cH:9][c:10]1[Cl:11].[Br-]>>[CH3:1][CH:2]([OH:3])[c:4]1[cH:5][cH:6][c:7]([F:8])[cH:9][c:10]1[Cl:11]',
  'template': '[C:1]-[Mg+].[C:2]=[O:3]>>[C:1]-[C:2]-[O:3]',
  'confident': True}]

See Demo.ipynb for more running instructions and plotting the results.

Data

USPTO dataset

The raw reactions of USPTO 50K and USPTO FULL are downloaded from the github repo of RXNMapper.

The mapped reactions of USPTO 50K and USPTO FULL are available at Figshare.

Reference dataset

AAM predictions on reactions sampled from USPTO 50K, Golden dataset, and Jaworski et al. generated by LocalMapper, RXNMapper, and GraphormerMapper are provided here.

Reproduce the results

[0] Change the chemist name

Go to LocalMapper/manual/ folder and change name of file User.user to [your-name].user.

[1] Sample the reaction from raw_data

Downlaod raw data of USPTO_50K from Go to LocalMapper/scripts/ folder and run Sample.py with -i (iteration) = 1

python Sample.py -i 1

[2] Manual map the sampled reaction

Back to LocalMapper/manual/ folder and use Check_atom_mapping.ipynb to correct the sampled reactions (0: reject and remap, 1: accept, 2: reject and skip). Make sure the templates you generate are chemically correct. The model is very sensitive to these templates.

[3] Train LocalMapper model

Go to the LocalMapper/scripts/ folder, and run following training code

python Train.py -i 1

This training process usually takes 3~6 hours to complete using cuda-supporting GPU depending on the number of training reactions.

[4] Predict the atom-mapping for raw data

To use the model to predict the atom-mapping on raw reactions, simply run

python Test.py -i 1

[5] Repeat step [1]~[4]

To sample more data for training, sample the data again and train-test the LocalMapper model by changing the arguement -i To start, you should run

python Sample.py -i 2

Publication

@article{chen2024precise,
  title={Precise atom-to-atom mapping for organic reactions via human-in-the-loop machine learning},
  author={Chen, Shuan and An, Sunggi and Babazade, Ramil and Jung, Yousung},
  journal={Nature Communications},
  volume={15},
  number={1},
  pages={2250},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

License

This project is covered under the The GNU General Public License v3.0.