====== Rules ======

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.


 ===== Available Rules =====
 


A list of all available rules in enviPath can be found [[https://envipath.org/rule|here]]. To view all rules of a particular [[package|package]], select the package start page and click on the rules tab.



 ===== Description =====
 


The description explains the general biochemical reaction represented by a given rule and also explains any exceptions (e.g., substructures that prevent application of the rule).

 ===== Reaction Patterns - SMIRKS =====
 


A rule consists of one (simple rule) or several (composite rule) reaction patterns. Each pattern is represented by a [[https://www.daylight.com/dayhtml/doc/theory/theory.smirks.html|SMIRKS]] string. enviPath can import or export transformation rules using this format. Additionally, the web interface offers the [[https://lifescience.opensource.epam.com/ketcher/|graphical molecule editor Ketcher]], which can create transformation rules that can be stored directly from the editor.

===== EC numbers =====


Here, 4th level EC (Enzyme Commission) numbers (see [[http://en.wikipedia.org/wiki/Enzyme_Commission_number|numerical classification scheme for enzymes]] recommended by [[https://iubmb.org/|IUBMB]]) are listed for enzymes known to catalyze reactions that are consistent with the respective rule. Details on how these rule-enzymes linkages were generated are described in [[https://www.biorxiv.org/content/10.1101/2021.05.20.442588v1|Schmid, Fenner, enviLink: A database linking contaminant biotransformation rules to enzyme classes in support of functional association mining, submitted to Biofinformatics, 2020]].

===== Additional fields =====


  * A rule can have additional [[https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html|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 [[settings|truncation strategy]] when predicting a [[pathways|pathway]], e.g. to suppress reactions that are unlikely under aerobic conditions.