Introduction to the JChem suite
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 6.1?
|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.
||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:
- 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 here.
The following diagram shows which ChemAxon products are included in the JChem
suite from the ChemAxon product line.
- Users guide
- Developers guide
- API documentation
- Administration guide
- History of changes
- Code examples
- Technical support forums
See our recent papers, which discuss the features and applications of our products.