Unsupervised attention-guided atom-mapping
Installation instructions
From Conda
From Pip
Unfortunately, rdkit is not supported on pip, which makes this a slightly more involved process.
From github
conda create -n rxnmapper python=3.6 -y
conda activate rxnmapper
conda install -c rdkit rdkit
pip install git+https://github.ibm.com/PHS/rxnmapper.git
For development
You can install the environment for local development using the following:
conda env create -f environment.yml
conda activate rxnmapper
pip install -e .
pip install -r requirements.txt
Usage
Basic usage
from rxnmapper import RXNMapper
rxn_mapper = RXNMapper()
rxns = ['CC(C)S.CN(C)C=O.Fc1cccnc1F.O=C([O-])[O-].[K+].[K+]>>CC(C)Sc1ncccc1F', 'C1COCCO1.CC(C)(C)OC(=O)CONC(=O)NCc1cccc2ccccc12.Cl>>O=C(O)CONC(=O)NCc1cccc2ccccc12']
results = rxn_mapper.get_attention_guided_atom_maps(rxns)
The results contain the mapped reactions and confidence scores:
[{'mapped_rxn': 'CN(C)C=O.F[c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11].O=C([O-])[O-].[CH3:1][CH:2]([CH3:3])[SH:4].[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]',
'confidence': 0.9565619900376546},
{'mapped_rxn': 'C1COCCO1.CC(C)(C)[O:3][C:2](=[O:1])[CH2:4][O:5][NH:6][C:7](=[O:8])[NH:9][CH2:10][c:11]1[cH:12][cH:13][cH:14][c:15]2[cH:16][cH:17][cH:18][cH:19][c:20]12.Cl>>[O:1]=[C:2]([OH:3])[CH2:4][O:5][NH:6][C:7](=[O:8])[NH:9][CH2:10][c:11]1[cH:12][cH:13][cH:14][c:15]2[cH:16][cH:17][cH:18][cH:19][c:20]12',
'confidence': 0.9704424331552834}]
Testing
You can run the examples above with the test suite as well:
pip install -r dev_requirements.txtpytest testsfrom the root
Examples
To learn more see the examples.
Data
Data can be found at: https://ibm.box.com/v/RXNMapperData
5 maintainers
Release files for rxnmapper 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| rxnmapper-0.1.1.tar.gz | 3.0 MB | Details |
Release files / rxnmapper-0.1.1.tar.gz
| Download URL | rxnmapper-0.1.1.tar.gz |
|---|---|
| Size | 3.0 MB |
| Tags | Source |
|
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