OraRdkitCart: Rdkit chemical structure data cartridge for Oracle

OraRdkitCart is an Oracle data cartridge/extensible index to allow substructure and similarity searching using SQL queries on tables which contain indexed chemical structures.

It uses a Java RMI server and RDKit wrappers for chemical structure handling.

This software was developed with funding from Beacon Discovery and Glysade LLC.

Quick-start

1. Satisfy Prerequisites
2. Build Java code
3. Install cartridge
4. Test installation
5. Run example SQL from the User Manual

All shell commands in the documentation should be run from project root.

Contents

• Background
• Prerequisites
  • Summary
  • Code Base
  • Oracle 12C or 18C
  • Java 11 JDK
  • RDKit Java library
  • Oracle JDBC driver
  • Maven 3.3.9 or later
  • Correct network configuration
  • RDBASE Environment Variable
• Building the code
• Installation
  • Automated Install
    • Choose Install Type
    • Specify JDBC Connection Options
    • Install Cartridge
    • Grant Permissions
    • Configure RMI Server
    • Load Test Data and Build Index
  • Post Installation
    • Configuration File
    • Grant Permissions
• Testing
• User Manual
  • Creating and Manipulating Domain Indexes
  • Using Domain Index Operators
  • When not to use the Domain Index Operators
  • Functional Operators
  • CHEM_STRUCTURE Functions and Procedures
    • Utility functions
    • Index Procedures
  • De Morgan/Extended Fingerprints
  • CLOB structure columns
• Implementation Notes
  • Reactions
  • Row level functions
  • Transactions
  • Logging
  • RMI Networking
  • PL/SQL Data Structures
  • Trouble Shooting
    • Cartridge is not responsive
    • Oracle internal errors
  • Reinstalling and Uninstalling the Cartridge
• Open Source Software
  • Cartridge License
  • Maven Libraries
  • RDKit Binary

• Index
• Search Page