Third International Electronic Conference on Synthetic Organic Chemistry (ECSOC-3), www.reprints.net/ecsoc-3.htm, September 1-30, 1999

[E0003]

Received: 15 August 1999 / Uploaded: 21 August 1999

Introduction

JChem is a development tool written in Java for accessing chemical data over the Internet or in Intranets by web browsers. It stores structures in a relational database system on a server. JChem was designed to be portable on both the client and the server side. It supports most operating systems, web browsers, database management systems, and web servers.

JChem Components and Operation

JChem has the following components:

• Marvin Java Applets are tools for entering and displaying chemical structures using web browsers.
• JChem Class Library is a collection of Java classes that can be applied to search retrieve and store structures. It supports substructure and similarity searching, structure insertion, update and retrieval. Developers of chemical Inter- or Intranet sites can apply these classes to build custom web pages. JChem's modules can also be used in any Java software.
• JChem Manager is a Java application for creating chemical tables in relational databases, importing and exporting structure files in standard SDF format.

The architecture of a typical system built with JChem:

	Using a Java capable web browser (like Netscape Navigator or Internet Explorer), the client enters a query structure applying MarvinSketch as the graphical interface and other data for a combined substructure/similarity and SQL search .
	The previously prepared data are transmitted to the server-side script or Java servlet through the Internet or Intranet. Any user can connect to the server without installing additional packages or programs on the client's machine because, when necessary, the Marvin applets are downloaded automatically from the Internet site. The only requirement of the query is the Internet or Intranet connection and a web browser. Web technology provides easy access for potential users of the system.
	The servlet or the script processes the incoming data. Connects to a database through JDBC. Searches in a database table containing structures and other data. Creates a list containing the ID numbers of found structures. Redirects the result to the used custom script.
	The JDBC driver attaches Java code (servlet or script) with the database server.
	The database server processes SQL statements and retrieves structural and non-structural data from a database.

Features

Designing JChem, we wished to avoid several shortcomings of most commonly used chemical database management systems. As a result it has several unique features that are listed in the following table:

Technical details	Resulting features
JChem is built in Java	Portable code that runs in all common operation systems.
It uses JDBC technology to store and retrieve structures in widely used relational databases.	Most database engines (like Oracle, MySQL, MSSQL Server, etc...) can be used to store structures. Structural and other chemical or non-chemical corporate data can be handled together. SQL statements can access structural data.
Proprietary Java modules are supplied for substructure and similarity searching.	Fast and reliable search that can be built into custom systems. Web access to structure querying. Structure search can be accessed from Java servlets, JSP (Java Server Pages), CGI (e.g. Perl), PHP3, ASP scripts, etc. Structure search can be built into legacy databases.
Structure input/update/display by the Marvin Java Applets.	Convenient and interactive user interface that can be manipulated by Java capable web browsers, like Netscape or Internet Explorer.
Java application for table creation and SDF import/export.	Communication with traditional chemical databases is ensured.

Example

A simple application of JChem is shown below, which allows searching the MeDiverse database of ComGenex. At the time of writing this paper, the database consists 10,000 diverse structures from the compound library of ComGenex. To try substructure or similarity searching, draw a structure, select the options you prefer and then choose the Search button.

Search type: Substructure Similarity Similarity threshold: 0.4 0.5 0.6 0.7 0.8 0.9 0.95 Max. hits: 1 2 3 4 5 10 50 100 200 500 1000 2000 5000 unlimited Max. time: 1 min. 2 min. 3 min. 4 min. 5 min. 10 min. 20 min. unlimited Lines: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Columns: 1 2 3 4 5 6 7 8 9 10 11 12 13 14

(YOU SHOULD SEE A JAVA APPLET HERE) Conditions:

Acknowledgements

The authors wish to thank László Balázs-Csiki, Péter Csizmadia, Tamás Kárpáti and László Kovács for their participation in the JChem project.

References

1. ChemAxon Ltd.: http://www.chemaxon.com
2. Marvin site: http://www.chemaxon.com/marvin
3. JChem site: http://www.jchem.com