JChem Developer's Guide

The Developer's Guide of JChem explains how to develop applications that can

• search structures
• retrieve and display hits
• modify structure tables
• write custom applications for virtual high throughput screening

Contents

1. Introduction
   • Software Requirements
   • Initializing the Database for Structure Handling
   • What is Useful to Be Familiar With Before Starting the Development
   • Development of Graphic User Interfaces for JChem Applications
   • Accessing Structure Tables
   • Demo applications
   • Connecting to Databases
2. Structure Searching
   • Defining Queries in Web Applications
   • Initializing Search
   • Exact Structure Search
   • Substructure Search
     • Starting a Search
     • Running Search in a Separate Thread
     • Retrieving Results
     • Caching Structures
     • Combining SQL queries with Structure Searches
     • Setting More Parameters
   • Similarity search
   • Searching by Stored Procedures in Oracle8i
   • Search Access Level
   • Stereo Notes
3. Modifying Structure Tables
   • Inserting or Modifying Rows
   • Deleting Rows
   • Other Methods
4. File Import/Export Tools
   • Importer
   • Exporter
5. Utilities
   • Handling Molecules
   • Methods for Servlets and JSP
   • Comments for Using JChem in ASP or Other ActiveX Environments
6. JChem Cartridge for Oracle
   • Using JChem Cartridge for Oracle
   • API
7. Virtual screening
   • Examples on basic API usage
   • Generating fingerprint
   • Dissimilarity calculation
   • Custom descriptor implementaion