JChem Engines

Boosting object-relational database management systems with chemical intelligence

JChem technology provides sophisticated implementations for chemical representation, search, storage, structural and non-structural data management functions. Data management functions are a widely embedded core engine across a wide variety of integrated systems in ChemAxon applications - And, provide a fast and invisible backbone for research informatics systems to rely on. As a 'workhorse', it's capable of handling: data stored in various database engines (e. g.: Oracle, PostgreSQL, MySQL, MSSQL), offers intricated search technologies, a wide optional space, and advanced features to deal with chemical structures.

JChem Suite

JChem suite is composed of four applications providing three different interface languages - on various database engines. JChem is a cheminformatics backend technology for diverse workflows and integration platforms:

  • JChem Base is the core engine for Java and .NET applications
  • JChem Web Services is a versatile interface that extends access to the JChem Base cheminformatics package for web-based usage
  • JChem Oracle Cartridge integrates chemical functions into Oracle
  • JChem PostgreSQL Cartridge is the next generation JChem engine available from PostgreSQL

JChem Engines Summary Table

JChem Base technology

JChem Base stores chemical structures and precalculated metadata in a dedicated database table that combines structural and non-structural information. The technology offers high speed and extensive query optional space, including fine-tuned stereo and tautomer search, reaction queries (even with reaction mapping), generic query atoms, R-group query expressions or SMARTS strings. Read more about queries in JChem. JChem Base is a straightforward toolkit for developers and integrators handling chemical information. In order to fit a large variety of related workflows, ChemAxon applications are natively supported e.g.:

  • Chemical Terms language for complex chemical queries, expressions, and rules
  • Standardizer component for canonicalization and normalization
  • Calculator Plugins for predictions and structure based descriptors
  • Markush search add-on, to register generic structures and exploit substructure, full structure and duplicate searching without enumeration
  • Reactor, for reaction-based virtual library enumeration
JChem Base architecture

JChem Web Services

JChem Web Services is a flexible interface that expands access to ChemAxon's cheminformatics solution package in a web or in a non-Java environment like Python, Perl or R. - Via a simple ergonomic route it can be easily integrated into pure HTML5, JavaScript, PHP, Django and other languages and frameworks. Selected workflows with web services:

  • Development of mobile applications
  • As a backend for Marvin JS and Plexus Suite
  • Adding JChem capabilities to existing Java Enterprise Service Bus
  • Rapid prototyping a Java application

Read more about the web services

jchem-web-services

JChem Oracle Cartridge

JChem Oracle Cartridge adds the chemical intelligence of JChem Base to the Oracle platform using Oracle’s native SQL language. This tool is an enterprise solution for companies in the life science industry, and corporations in the chemical industry. By having Marvin Services in JChem Oracle Cartridge, third-party structure manipulation is seamlessly integreated within the Cartridge framework.

Read more about JChem Oracle Cartridge

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JChem PostgreSQL Cartridge

ChemAxon has been developing a new, high-performance engine relying on cutting-edge technology. The second generation JChem engine was built with a PostgreSQL interface. JChem PostgreSQL Cartridge adds chemical database management and search capabilities to PostgreSQL databases via the JChem-psql service. A custom column type and named ‘Molecule’ appears for storing chemical structures. The Molecule column can be customized based on business rules regarding standardization and tautomer handling.

Read more about JChem PostgreSQL Cartridge

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