Introduction to the JChem suite

Short Description

JChem is a suite of integrated programs and toolkits for many cheminformatics tasks. Its components include chemical database engines, chemical structure editor and visualization tools, physicochemical property predictors, and other tools for chemical structure manipulation. Most components come with intuitive graphical user interface and all are accessible through Java and .NET API (Application Programming Interface) and command-line(batch) tools.

As the JChem suite was developed in Java, it is available on major platforms and the components are ideal for intra- and internet applications and web-based delivery. (Through the use of Java applets or Java Web Start.) The distribution contains numerous web and standalone application examples.

What is new in version 6.2?

  • Nested defined R-group queries are also supported in R-group search
  • Default value of occurrence condition in R-logic has been changed from ">0" to "all"
  • Performance of Markush search has been substantially improved

Detailed release notes

Modules of the JChem suite

JChem comprises the following modules:
JChem Base adds a chemical interface to relational database engines, which can be applied for combined SQL and chemical structure queries;
imports/exports molecules, reactions, query and Markush structures in standard formats (Molfile, SD file, RD file, SMILES, SMARTS, CML, etc.). It is integrated with physicochemical calculations(calculated columns) and Standardizer for structure canonicalization. Many different RDBMS engines are supported.
JChem Cartridge
adds chemical operators and JChem indexes to the Oracle SQL language. Can handle structure tables of JChem Base and other free-form tables containing chemical structure data. Also provides interface to other JChem modules (calculations, standardization, molecule enumeration, format conversions, etc).
Standardizer transforms chemical structures based on a configuration. It is useful for canonicalization of molecules from different formats into standard representation.
Structure Checker runs a check on the molecule to filter drawing mistakes or special structural elements. The new Structure Checker GUI is accessible from MarvinBeans.
Screen performs similarity screening based on different descriptors, like pharmacophore or chemical fingerprints, BCUT, etc.
JKlustor clusters molecular libraries by a novel maximum common substructure(MCS) based algorithm or by using molecular descriptors with Jarvis-Patrick or Ward algorithms. Also suitable for diversity calculations. Library MCS is the desktop application of JKlustor and provides structure based hierarchical clustering.
Reactor is the virtual reaction engine of Chemaxon's JChem technology. It supports "smart" reactions and generates chemically feasible products even in batch mode.
Metabolizer preview enumerates all feasible metabolites, concludes the metabolic pathways of a given compound, predicts major metabolites, the likelihood of formation, calculates production and accumulation indicators.
Fragmenter decomposes structures based on a scaffold (R-group decomposition) or generates building blocks based on cleavage rules from molecule libraries.
Name to Structure is a powerful naming engine that consistently derive accurate chemical names for chemical structures or generate chemical structures from various sources.
Markush Search is an add-on to JChem Base and Instant JChem, and allows the registration of generic structures into the database as well as substructure and full structure searching in their enumerated libraries.
Markush Viewer is a viewer for the various R-group definitions of Markush structures.
The JChem suite also contains the full Marvin suite:
MarvinSketch is a 2D/3D chemical structure editor for drawing molecules, queries, reactions, and Markush structures. It is integrated with the calculator plugins, MarvinView, and MarvinSpace.
MarvinView is a 2D/3D chemical viewer for single and multiple chemical structures, queries, and reactions. It is integrated with the calculator plugins, MarvinSketch, and MarvinSpace.
MarvinSpace is a high performance 3D molecule visualization tool.
Molconverter is a command line program in Marvin Beans and JChem that enables conversions between various chemical file types.
Calculator Plugins calculate chemical properties descriptors from chemical structures.

Further ChemAxon products that are not included in the JChem suite:
  1. Instant JChem, our desktop chemical database application, is not part of the JChem suite, although it relies on many JChem components.
  2. JChem for Excel integrates structure handling and visualizing capabilities within a Microsoft Excel� environment.
  3. JChem Web Services is available as a separate download.


  • Although the JChem modules are shipped together and are tightly integrated, they are licensed separately. See more details here.

The following diagram shows which ChemAxon products are included in the JChem suite from the ChemAxon product line.



The following links provide the starting points to documentation:


See our recent papers, which discuss the features and applications of our products.

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