The IsotopeMappingToolKit enables the conversion of metabolic reactions summarized in SMBL format to an atomic transition networkbased on MetaNetX.
Download the MetaNetX database into the according subfolder.
The following python libraries need to be available:
- BeautifulSoup
- RXNMapper
- rdkit
- networkx
- pyvis (optional)
Run as
./01_bigg_to_smiles_reactions.py [SMBL Xml] [SMILES]
./02_atommap_smiles_reactions.py [SMILES] [Mapped SMILES]
./03_generate_ATN.py [Mapped SMILES] [ATN in GML format]