JChem Developer's Guide

The Developer's Guide of JChem explains how to develop applications with the JChem suite of products. This includes:

• Handling chemical databases: search structures, retrieve and display hits, modify structure tables,
• Running similarity calculations
• Standardization of chemical structures,
• Reaction-based enumeration, etc.

Contents

1. JChem chemical database concepts
   • Software architecture
   • Table types
   • JChem table structure
   • Search types and options
   • The structure cache
   • Fingerprints, optimization of fingerprint parameters
   • Standardizer integration
   • Chemical Terms calculated columns
   • Handling of tautomers
2. Introduction to development with JChem Base
   • Software Requirements
   • .NET support
   • JChem Base features and architecture
   • 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
3. Structure Searching using JChem Base
   • Database Searching
   • Defining Queries in Web Applications
   • Initializing Search
   • Perfect 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
   • Exact Structure Search
   • Exact Fragment Search
   • Similarity search
   • Search Access Level
   • Structure Searching in memory and flat files
   • Stereo Notes
4. Modifying Structure Tables
   • Inserting or Modifying Rows
   • Deleting Rows
   • Other Methods
5. File Import/Export Tools
   • Importer
   • Exporter
6. Utilities
   • Handling Molecules
   • Hit coloring and alignment
   • Methods for Servlets and JSP
7. JChem Cartridge for Oracle
   • Using JChem Cartridge for Oracle
   • API
8. Virtual screening
   • Examples on basic API usage
   • Generating fingerprint
   • Dissimilarity calculation
   • Custom descriptor implementation
9. Pharmacophore Mapping
10. Standardization
11. Reaction Processing
12. Fragmentation
13. R-group Decomposition