RXN Files
RXN Files are part of the MDL Information Systems 🔗 Chemical Table Files which also include Molfiles. Each RXN File contains a RXN specific comment block at the beginning and following that multiple MOL blocks depending on the number of metabolites.
- Comment Block
- MOL Block
- Full RXN
Each Comment Block starts with $RXN marking the beginning of a RXN File. The following line contains a comment that is specific to the program generating the RXN File. The last line indicates the number of substrates and products respectively.
Each MOL Block starts with an indicator $MOL, which is followed by a comment block containing name, MetAMDB identifier, reactant and position, as well as a comment by the program used for atom mapping generation.
Indicated in orange is the counts lines, showing the number of atoms, the number of bonds and the MOL file format V2000.
Followed by the counts line is the atom block, containing x, y, and z coordinates used for the Reaction Image generation (blue), the element (green), and finally the atom mapping (yellow).
After the atom block comes the bond block, which shows the atoms which are participating in the bond and the bond type (1=single bond, 2=double bond). So for example atom 5 and 7 are bound by a double bond.
Warning!
Atom numbers are row numbers of the atom block, not the atom mapping number. This is only essential if the row number is unequal to the atom mapping number.
