This repo contains the molecular structures of metabolites present in different genome-scale models and its metabolic reactions atom mapped obtained with the function generateChemicalDatabase. The data is divided into three main directories:
Contains a metabolite and reaction databases from different genome-scale models including:
- ecoliCore
- iDopaNeuro1
- AGORA2
- ReconX
Contains a set of metabolite structures from genome-scale models. The metabolite structures are saved in different formats: images, MDL MOL, SMILES, and InChI and InChIkey for molecules without an R group (see Formats) and sorted as follows:
- molFiles: A directory with standardised MDL MOL files.
- images: A directory with graphical representation of the molecular structures.
- metaboliteStructures: Table containing the SMILES, InChIs and InChIkeys for each metabolite structure in the database.
Contains a set of metabolic reactions with their corresponding atom mapping in different formats:
- atomMapped: A directory with atom mapped MDL RXN files.
- inconsistent: A directory with atom mapped MDL RXN files modified by the atom mapping algorithm making the reaction inconsistent.
- unbalanced: A directory with atom mapped MDL RXN files with different number of atoms in the reactions and in the substrates.
- images: A directory with images of the atom mapped reactions.
- unMapped: A directory with unmapped metabolic reactions in MDL RXN file format.
- txtData: A directory with atom mapped in SMILES and additional atom mapped data.
This is an example of how you may give instructions on setting up your project locally.
git clone [email protected]:opencobra/ctf.gitRonan Fleming - [email protected]