Reaction File - Reaction Equation

Reactor processes reagent(s) according to a given reaction equation. Reactor will search the reaction equation specified substructure in reactant molecules, and combine them according to the specified product structure. Reaction equation can be specified:

  • in a reaction file (RXN, RDF, and MRV); or,

  • as SMIRKS/SMARTS strings.

If the reaction is given in RDF or MRV format, it is possible to set reaction rules, reactant standardization, and some additional properties in RDF/MRV tags. See epoxide+nucleophile.rdf and epoxide+nucleophile.mrv for an example:

Reaction rules defined in the SELECTIVITY and TOLERANCE RDF tags

images/www.chemaxon.com/jchem/doc/user/Reactor_files/epoxide_nucleophile.png

Reaction string

It is also possible to specify the reaction along with reaction rules in the reaction string in which case the above reaction is written in the following form: 

[C:1]1C[O:2]1.[H:4][N,S:3][#6]>>[#6][N,S:3][C:1]C[#8:2]..s:hcount(ratom(1))..t:1.5

The reaction string is a reaction SMARTS, optionally followed by reaction rules separated by "..", with the following prefixes:

  • "r:" - reactivity rule (including exlude rule AND-ed in negated form)

  • "s:" - selectivity rule(s)

  • "t:" - selectivity tolerance(s)