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In enviPath, a rule object represents a biotransformation rule. Biotransformation rules are generalizations of reactions and used for the prediction of pathways. The left-hand side of a rule represents a pattern that matches functional groups in compounds. If the functional group is matched, a transformation described via a mapping to the right-hand side of the rule is carried out.


To represent the biotransformation rules, we use SMIRKS. enviPath can import or export transformation rules using this format. Additionally, the web interface offers the graphical molecule editor Ketcher, that can create transformation rules which can be stored directly from the editor.

Available rules

A list of all available rules is provided here: To view all rules of a particular package, select the package first, then the rules within his package (<id>/rule).

Additional fields

  • A rule can have additional SMARTS filter that exclude matching products or reactants when applying the rule.
  • In the core data provided in enviPath, the aerobic rule likelihood is stored as additional information. This information can be used to apply a truncation strategy when predicting a pathway, e.g. to suppress reactions that are unlikely under aerobic conditions.