RXN File

RXN File

The RXN file (*.rxn) format was developed by MDL. It is an important source of reaction input for ADMET Predictor.

The first four lines of an RXN file form a header that describes the reaction. The header is followed by a line with two three-digit integers indicating the number of reactants and products, respectively. That is followed by MOL file blocks, each containing the chemical structure of a reactant or product. The format of RXN files is shown below.

where:

*r is repeated for each reactant

*p is repeated for each product

RXN files are usually exported from drawing packages such as ChemDraw or MedChem Designer.

Note that even though reactions are not required to be fully balanced when sketched (e.g., the water produced can be omitted in condensation reactions), ADMET Predictor does impose a requirement that every atom that is present must be mapped, except those whose counterparts on the other side of the reaction are omitted. In the amide formation reaction below, for example, the hydroxyl oxygen should not be mapped if it is to form an omitted water molecule on the product side, whereas the carbonyl carbon and oxygen and the amino nitrogen must be mapped.

Unlike the standard REACCS RXN file format, ADMET Predictor allows multiple reactions in a single RXN file. The reactions are concatenated and delimited by a "$$$$" separator. The RXN file format is useful for packaging a series of reactions so they can be executed in succession in applications such as Combinatorial Transform.