JChem Engines

Boosting object-relational database management systems with chemical intelligence

Search, storage, structural and non-structural data management. JChem Engines are composed of backend technologies providing three different interface languages on various database engines.

Choral CartridgeMicroservicesPostgreSQL Cartridge
InterfaceOracle SQLRest APIPostgres SQL
Hit as you draw
Handling large datasets
Hit count estimation
Fast joined conditionsmanualintegrated
Low-memory setup
High availabilitysoon
Data in Amazon RDS
Data distributionsoonsoonsoon
2nd generation engine
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.
2nd generation engine
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.
2nd generation engine
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.

Pair performance with intelligence

A ‘workhorse’ for research informatics systems, they are fast and invisible in handling data stored in various database engines (e. g.: Oracle, PostgreSQL, MySQL, MSSQL), offering intricate search technologies, wide optional space, and advanced features to deal with chemical structures. The nearly immediate response to a structure query brings up new opportunities for developing chemistry-aware web applications that can benefit from the hit-as-you-draw feature.

Developer Guide

Integrates easily with your database

JChem provides a fast and invisible backbone for research informatics systems to rely on. It works with data stored in various database engines, such as Oracle, PostgreSQL, MySQL and MSSQL.

JChem database structure

Chemical intelligence

Not just fast (nearly instant) in returning the top best hits, results of a structural query are presented relevance sorted, according to their decreasing structural similarity to the original query.
Sophisticated tautomer handling.
Supporting wide range of stereochemical representation and searches.
Different query features including MDL type and Daylight type queries (like recursive SMARTS).
Wide range of chemical property calculations.
Structure standardization according to predefined business rules.
Structure checker functionality with suggestions or automatic fixing.

Combine search conditions flexibly

Our engines’ API enables the combination of chemical search with other search conditions (Choral, JPC, JOC). Our cartridges excel at combined search processes. Our engines store chemically relevant information of structures (molecules, reactions, etc.) that can be exported from/imported to various popular chemical and image formats.

Go to the cloud

Our Microservices are cloud-agnostic, ensuring smooth operation of the service on all cloud providers. Our Choral cartridge works on Amazon Web Services Relational Data Store (AWS-RDS), taking advantage Generally, all recent JChem Engines can run in a cloud environment (cloud-hosted) and enjoy of the benefits of an outsourced IT infrastructure (security and hardware maintenance is being taken care of by cloud and security experts at AWS). In addition, JChem Microservices is fully compatible with cloud infrastructures (cloud-ready), and provides a scalable and high availability service. Thanks to the low-memory-setup option, all recent JChem Engines offer an economical choice for the less performance-sensitive applications.

Resources