Version 6.2.2


User's Guide
Graphical User Interface
User's Guide
Command-line Interface
Reactor GUI Reactor CLI


The virtual enumeration of chemical reactions is a powerful tool in systematic compound library design or combinatorial chemistry. Reactor is the virtual reaction enumeration engine of ChemAxon's JChem technology that supports generic reaction equations combined with reaction rules; therefore, it is capable of generating chemically feasible products without pre-selection of reagents. Reactor is able to carry out highly automated reaction enumeration as well as the manual selection of main products for a given chemical reaction is supported.

Predicting products of chemical reactions

Reaction synthesis on your desktop

Reactor is a high performance, integratable reaction enumeration engine. It works with generic reaction equations that can be defined and imported in various formats, including among others SMIRKS/SMARTS strings, RDF, RXN and MRV files, or be drawn in MarvinSketch.
Reagent(s) are processed according to the given reaction schema; if the reaction is in RDF or MRV format, reaction rules, reactant standardization, and some additional properties are also possible to set in RDF/MRV tags.
The Reactor package includes a large and constantly increasing library of organic chemical reactions that can be used directly without any further configuration. See the list of available reactions of ChemAxon's reaction library. Download ChemAxon's reaction library.

Define your reactants

Using the generic reaction equations virtual synthetic compound libraries can be generated under full manual control. When doing so, users have the opportunity to draw and edit reactants directly and to select chemically meaningful products from the output of the enumeration process by using their chemical intuition on the fly. This approach is particularly advantageous for enumerating small, focused libraries.

Get synthesizable molecules by proper reaction rules

The reaction rules are defined in Chemical Terms, ChemAxon's scripting language that is designed to add chemical intelligence to cheminformatics applications. Through Chemical Terms a large number of calculated properties can be included in the reaction rules to produce valid compound libraries. Besides calculating physicochemical properties on the fly, Chemical Terms language also supports importing of arbitrary fields from the input reactant files to be used for the evaluation of the reaction rules.

Intelligent and flexible reaction enumeration

Stereochemically aware reactions

Reaction schemes can include stereochemical information. Reactor is capable of handling both tetrahedral and double bond stereochemistry flexibly; inversion and retention centers as well as cis-trans configuration changes can be determined within Reactor's smart reaction schemes. Prochiral reaction schemes are also supported since version 5.5, allowing the user to manage syn/anti additions.

Library design

Reactor can be set up to carry out simple sequential enumeration, in which case Reactor is also capable of combinatorial enumeration, generating combinatorial virtual synthetic libraries. Users also have the option to exclude unwanted products from the enumeration results manually, restricting the outcome of the reaction enumeration process to the desired main products only. Reactor supports the generation of product or reaction libraries in a large variety of different output formats.

Create rich molecular libraries

Reactor has the option to copy arbitrary property fields from the input reactant files to the results. These can include e.g. solubility or availability information of the reactants. Also, Reactor can generate synthesis codes for each reaction in the enumeration process containing selected information from the reaction scheme and the reactants.

Ease of access

A wizard-like user interface

The standalone version of Reactor has a clean and straightforward graphical user interface for configuring the reaction enumeration process. The Reactor GUI leads users step by step through the whole configuration process of the virtual chemical reaction.

Accessibility on various platforms

Reactor is available as a standalone application and has also been integrated into Instant JChem and JChem for Excel. It is also available in the workflow management tools KNIME and Pipeline Pilot. In its standalone version it can be used through the GUI, as a command line application and also through a full featured Java API. Reactor offers full platform independence, it is equally available for Microsoft Windows®, Mac OS, and Linux platforms.

Create and test your reactions

Reactor has an integrated reaction sketcher and editor tool. Users can create their own reaction schemes and add corresponding reaction rules to them using the Chemical Terms language. The prepared reaction schemes can be tested and the reaction rules can be validated using the integrated reaction testing tool of Reactor.



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


Reactor GUI User's Guide
Reactor CLI User's Guide
Reactor Glossary
ChemAxon's reaction library
Reactor FAQ
Working examples
Chemical Terms
Chemical Terms functions
Developers guide

Do you have a question? Would you like to learn more?

Please browse among the related topics on our support forum or search the website. If you want to suggest modifications or improvements to our documentation email our support directly!