You will set the reaction definition with rules and optional example reactions and set the Reactor parameters. You can also save the reaction by pressing .

1. Set the reaction definition by any of the following:
   • select a predefined reaction from the reaction library
   • type and load the reaction SMARTS
   • select and load a reaction file
   • draw the reaction (invoke the sketcher by double clicking on the reaction viewer)
   
   
2. Set the Reaction rules:
   1. Reactivity: a rule that refines the reaction with additional description of the reactive functional groups
   2. Selectivity: a rule that selects the main product list when two or more reactive sites are present in a reactant - if this rules is specified, product lists are sorted by decreasing selectivity, the result with highest selectivity value is returned first
   3. Tolerance: a numerical value that determines the acceptance range of the selectivity rule - high tolerance for the selectivity rule allows more than one main product lists (the default is 0.0001 which essentially means that only the maximum selectivity value is accepted)
   4. Exclude: an additional rule to avoid the generation of synthetically non-feasible products - determines problematic reactants that should be skipped because they contain functional groups causing side reactions
   Edit the rules in the text areas, you can also add explanations describing the meaning of the rules (you can always reload the original rules by pressing ). These rules are chemical expressions composed of predefined functions and plugins, logical and arithmetical operators and are evaluated by the Chemical Terms Evaluator.
   
   
3. Set the example reactions in the example viewer by either of the following:
   • type the reaction SMILES (one example reaction in each line) and load the examples by pressing or - you can also get the example reactions from the viewer in SMILES format by pressing , then edit the SMILES strings and reload them by pressing
   • draw the example reactions in subsequent viewer cells (invoke the sketcher by double clicking on the cell)
   
   
4. Set the Reactor options:
   1. reverse: select this option if the reaction should be processed reversely (with reactant and product sides swapped)
   2. single: select this option if only unambiguous reactions should be processed, that is, if there are multiple functional groups in either of the reactants then no products should be generated

Finally, pressing will direct you to the next page to set the reactants.

Links:

• ChemAxon home
• ChemAxon forum
• Reactor documentation
• Evaluator documentation and short reference
• Standardizer documentation