MDF Simple Web Application

This is a small web application for demonstrating some functionality of Molecule Database Framework. It is a web application for managing a simple compound database that supports multi-component compounds (mixtures). You can search by substructure and / or CAS, compound name and compound description.

Screen-shot of Search Page: Full Size

Search Page


  • added Salt Handling

To add a Salt, create a new compound and then as the first composition just draw the complete salt into the chemical structure editor. The salt will be split automatically into individual ions and each of them will be neutralized.


In development. The web application is functional and can be used. However it's not a "production ready" application as there is no real exception handling done. What is also missing is stuff like success messages to the users when as example submitting changes to a compound.


  • Import SD-File (Structures and molfilename only)
  • Chemical Substructure Search with paged results display (using datatables)
  • highlighted substructures on search results page
  • downloading of search hits as SD-File
  • viewing individual compounds
  • adding, editing and deleting of compounds including managing of compositions


Search Results Page: Full Size

Search Result

Single Compound View: Full Size

Single Compound View

Single Composition View: Full Size

Single Composition View

Standalone Runnable Version

Please find in the download section the 7z archive for MDFSimpleWebAppStandalone with everything pre-installed including PostgreSQL, Bingo Cartridge, tomcat and this web application.


  • Windows 64-bit only
  • is not always in-sync with most current source code
  • don't be fooled by the download counter - I always just remove the old version setting the counter to 0 again


You need to unzip it using 7z (file is much smaller than with zip).


  1. Start PostgreSQL
  2. Start Web Application
  3. Open Application in Browser

The database contains 3 compounds with one of them being a mixture.

Evaluating the Web Application

It is suggested you import additional compounds to better understand the performance of the application.

Depending on your hardware, importing or exporting a big amount (several 1000) of compounds can take several minutes. Please be patient.

When importing large numbers of compounds (10'000+) you may drop the chemical structure search index, import the compounds and then reindex the table. This is a lot faster than importing with index enabled. To do that first execute drop structure index.cmd, then import the SD-File and after import run create structure index.cmd. Index creation can take several minutes depending of the amount of compounds in the database.

With index enabled importing 20'000 compounds takes 15-30 min. This process is mainly CPU dependant. With index disabled it takes about 2-3 min and about the same time for creating the index.

Basic Usage Hints

The application should be very intuitive to use. One point however needs to be explained. Namely when creating a new compound you first are asked to enter the compounds properties and there is no chemical structure drawing field. Just fill out the form and click on "Add Compound". You will then be transferred to a page were you can add a composition to the compound. That form contains a checkbox. If it is checked you may add another composition after saving one. If you leave it unchecked the creation of the compound will be completed.