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 is 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 five 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 Oracle Cartridge integrates chemical functions into Oracle
- JChem PostgreSQL Cartridge is the next generation JChem engine available from PostgreSQL
- JChem Choral is the newest JChem engine available for Oracle.
- JChem Microservices extends the JChem capabilities to the web via specialized modules
Watch the video for a guide to migrate to the new, second generation engines.
| Choral Cartridge | Microservices | PostgreSQL Cartridge | |
|---|---|---|---|
| Interface | Oracle SQL | Rest API | Postgres SQL |
| Hit as you draw | |||
| Handling large datasets | |||
| Hit count estimation | |||
| Fast joined conditions | manual | integrated | |
| Low-memory setup | |||
| High availability | soon | ||
| Data in Amazon RDS | |||
| Data distribution | soon | soon | soon |
Choral Cartridge
JChem Choral Cartridge was built with an Oracle interface. This engine adds chemical database management and search capabilities to Oracle databases via an external service. A custom index type is applied for handling the chemical structures in the database. The index type can be customized based on business rules regarding standardization and tautomer handling.
Microservices
Microservices extends the capabilities of our chemical intelligent platforms to the web via specialized modules using our second generation JChem engine. With common modules the technical framework is ensured for the chemical functional modules, such as the DB module, to work together as a system. The separate chemical functional modules range from I/O to Markush to Reactor web services, covering structure checker and structure manipulation tools.
PostgreSQL Cartridge
JChem PostgreSQL Cartridge adds chemical database management and search capabilities to PostgreSQL databases via an external service. A custom column type named ‘Molecule’ appears for storing chemical structures. The Molecule column can be customized based on business rules like standardization and tautomer handling. To comply with the latest expectations it is tested on a database of over having ~100M structures.
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 Microservices
We have recently started our microservices which provides small separate modules for different areas of ChemAxon functionalities. Since it is a rather new development, at the beginning we provide modules for the following services:
JChem Web Services Classic
NOTE: This product will be terminated. New orders and renewals are accepted in 2020, but maintenance of the product will close in March 2022.
JChem Web Services Classic 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
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 integrated within the Cartridge framework.
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.
JChem Choral
ChemAxon has been developing a new, high-performance engine relying on cutting-edge technology. The second generation JChem engine was built with an Oracle interface. JChem Choral adds chemical database management and search capabilities to Oracle databases via the choral service. A custom index type is applied for handling the chemical structures in the database. The index type can be customized based on business rules regarding standardization and tautomer handling.
JChem Neo4j Cartridge
JChem Neo4j Cartridge combines the advantages of the graph database, Neo4j, and the high performance and chemical intelligence of ChemAxon's second generation chemical search engine. JChem Neo4j Cartridge extends the graph database functionality such a way that
- chemical structures and their properties stored on the graph database nodes
- and the defined relationships between them
are quickly searchable.
Resources
Documentation
- JChem Base User's Guide
- JChem Base Developer's Guide
- JChem Oracle Cartridge Developer's Guide
- JChem Base Admin Guide
- JChem Oracle Cartridge Admin Guide
- JChem PostgreSQL Cartridge Guide
- JChem Web Services Classic Admin Guide
- JChem Microservices Docs
- JChem Base Query Guide
- File Formats Guide
- JChem Choral Docs