Chemical table files for constraint-based modelling

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:

modelDatabases

Contains a metabolite and reaction databases from different genome-scale models including:

• ecoliCore
• iDopaNeuro1
• AGORA2
• ReconX

mets

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.

rxns -

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.

Getting Started

This is an example of how you may give instructions on setting up your project locally.

Installation

git clone [email protected]:opencobra/ctf.git

Contact

Ronan Fleming - [email protected]