Reactor

Version 5.9.4

Contents

• Introduction
• Input
• Output
• Reaction file
• Reaction mapping
• Orphan atoms
• Isotopes
• Reaction stereo
• Reaction rules
• Usage examples
• ChemAxon's Reaction Library
• References
• Links

 

Introduction

Reactor is a virtual reaction processing tool which transforms starting compounds to products according to a given chemical reaction definition. The reaction scheme defines the way that the reactants are converted to products, and additional rules can encode the related knowledge to produce synthetically feasible molecules.

Atoms having changing bonds are marked by so called map numbers on both sides of the reaction arrow. The corresponding atoms on the two sides of the reaction arrow are identified by the same map number, but the atom maps cannot be duplicated on one side. When a map number appears only on one side of the reaction scheme, it marks an orphan atom. An orphan atom on the reactant side is removed, an orphan atom on the product side is added during the reaction. Note, that Reactor supports other mapping styles having different mapping logic.

Additional reaction rules can be specified in the reaction file that refine the reactive functional groups, define the corresponding regioselectivity rules, and exclude molecules possibly causing side reactions. These rules are formulated in Chemical Terms, which is a language containing logic and arithmetic operators, and lots of chemical structure related functions including many physicochemical predictions.

Reactor supports RXN, RDF and SMIRKS (all features of reaction SMARTS are available). The format of input and output molecules can be MRV, MOL, SDF, SMILES, CML and many others.

Example

The reaction

with reactants

will produce the following products:

A set of working examples are also provided.

ChemAxon's Reaction Library

Reactor users can enjoy a library of important synthetic organic reactions predesigned by experts (download reaction library). Though, many of these reactions produce feasible products in most cases, the predictions can be improved if needed in the reaction editor. ChemAxon does not consider the reaction library as a completed product. New reactions are added continuously and the existing ones are refined according to the tests and the feedback received via the forum.

ChemAxon's Reaction library is available in the JChem package in zip file, or can be downloaded separately.

 

References

Bode, J. W. Computer Software Reviews. J. Am. Chem. Soc. 2004 , 126(46) , 15317-15317.

Links

Reactor GUI Application Page
Reactor commandline help
ChemAxon's reaction library
Working examples
A simple JSP example
Reactor Frequently Asked Questions (FAQ)
Chemical Terms
Chemical Terms functions
Developers guide