NEWS: April 21st, 2008 - JChem 5.0.3 released • Includes Marvin 5.0.3 • Support for coordination compound representation • New table types: Query structures, Markush libraries • Improved API support for hit coloring and alignment • Progressive return of database search results • Structural search supports new generic query atom types • API: Unified search options for database and in-memory search • API support for custom atom & bond comparators • Substructure and exact structure searching in combinatorial Markush structures, Markush structure reduction to hit. See details • Performance enhancements of structure searching in database with queries containing atom lists, query bonds and higher vague bond options • JSP database example improvements • Duplicate filtering option to consider tautomers • Simplified installation, Oracle Optimizer support, hit coloring and alignment support for JChem Cartridge. • Improved reaction mapping and abbreviated group support in Reactor • New Standardizer tasks: ClearIsotopes, Neutralize, WedgeClean and ConvertWedgeInterpretation • New Chemical Terms functions, easier integration of custom calculations
History of changes

Introduction to the JChem suite

Short Description
Modules of the JChem suite
Documentation
Papers

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.

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 physico-chemical 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.
Reactor	generates reaction products from reaction equations and reactants.
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.
Screen	performs similarity screening based on different descriptors, like pharmacophore or chemical fingerprints, BCUT, etc.
Fragmenter	decomposes structures based on a scaffold (R-group decomposition) or generates building blocks based on cleavage rules from molecule libraries.
Chemical Terms Evaluator	evaluates chemical expressions and conditions. Integrated with the calculators and JChem Base (through calculated columns and Chemical Terms search filter).
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.
Calculator plugins	are ChemAxons range of structure based prediction tools. They are integrated with MarvinSketch and MarvinView, JChem Base (calculated columns and Chemical Terms filter search) and Reactor (reaction rules).
Molconvert application	is a command line program that converts between various chemical file types.

Notes

Although the modules are shipped together and are tightly integrated, they are licensed separately. See more details here.
Instant JChem, our desktop chemical database application, is not part of the JChem suite, although it relies on many JChem components.

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

model