Introduction to the JChem suite
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
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
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:
||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.
|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).
||transforms chemical structures based on a configuration. It is useful for canonicalization of molecules from
different formats into standard representation.
||runs a check on the molecule to filter drawing mistakes or special structural elements. The new Structure Checker GUI is accessible from MarvinBeans.
||performs similarity screening based on different descriptors, like pharmacophore or chemical fingerprints, BCUT, etc.
||clusters molecular libraries by a novel maximum common
substructure(MCS) based algorithm or by using molecular
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.
||is the virtual reaction engine of Chemaxon's JChem technology.
It supports "smart" reactions and generates chemically feasible products even in batch mode.
||enumerates all feasible metabolites, concludes the metabolic
pathways of a given compound, predicts major metabolites, the likelihood of formation, calculates
production and accumulation indicators.
||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.
||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.
||is a viewer for the various R-group definitions of Markush structures.
|The JChem suite also contains the full Marvin suite:
|| 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.
||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.
||is a high performance 3D molecule visualization tool.
||is a command line program in Marvin Beans and JChem that enables conversions between various chemical file types.
||calculate chemical properties descriptors from chemical structures.
Further ChemAxon products that are not included
in the JChem suite:
- Instant JChem,
our desktop chemical database application, is not part of the
JChem suite, although it relies on many JChem components.
- JChem for Excel integrates structure handling
and visualizing capabilities within a Microsoft Excel� environment.
- 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
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
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!