STRUCTURE SEARCHABLE CHEMICAL INVENTORY

Most organic chemists probably know internet databases as Emolecules or Chemexper, that allow searching suppliers of molecules basing on the structure. Also Scifinder or Reaxys are famous for structure searching ability. I wanted to have such a tool for chemical inventory in my own chemical company. I was looking for a commercial solution but they were either expensive or did not fulfill my expectations. As I am a hobbyist programmer I decided to create the database myself.

My goals were:

• possibility to work over a network (local or internet)
• possibility for many users to be able to connect simultaneously
• possibility to edit structures in popular web browsers regardless the operating system
• possibility to substructure search
• possibility to connect analytical data or biological assays with the entry
• minimal level of security (automatic backup, history of changes)
• possibility to export as SDF (structure-data file) in order to exchange data with other databases (Emolecules, Chemexper)

The components I used:

• Operating system and the server - Linux and Apache as common in Linux system
• Database - SQLite - a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.
• Chemical structure analyser - Open Babel - a chemical toolbox designed to speak the many languages of chemical data that allows substructure search, interconversion of chemical formats such as SMILES, MOL, etc.
• Programming language - client side: JavaScript - a popular and portable language implemented in most web browsers. Server-side: Tcl as a Rivet module for Apache. This might seem not the best choice as Python or Ruby would deal better with Open Babel but I just used the tool I was familiar with.
• Structure editor - applet JSME or a Sketcher from ChemDoodle Web Components that works in a web browser. When license is purchased it has additional abilities, e.g. NMR spectra prediction

Assembling all the components was not an easy task but finally I did manage to meet the assumptions. The demo version of the inventory can be reached via this link:
http://95.175.17.4/demo/search.rvt?dbname=magazyn&lang=enTemporarily out of service
I need to mention that some component (editing, SDF export ) were disabled in this demo version. The database contains over 4 thousand entries. The inventory can be also searched via names, molecular mass and other fields. It allows also to find the substance in Emolecules and Chemexper (available in edition window).

I have used some components licensed with GNU GENERAL PUBLIC LICENSE. Thus I`m providing the source code of the full version of the database (with enabled editing, SDF export, analytical data and history of changes).

VISIT MY HOMEPAGE