Introduction

The LICSS System (Excel-CDK) constructs a bridge between MS Excel for Windows and the Chemistry Development Kit (CDK) Java code tools enabling users to chemically enable existing spreadsheets which contain representations of chemical structures as SMILES strings.

Once enabled, Excel spreadsheets have easy access to CDK functionality currently (v2.1) including Structure Display, Substructure/Similarity searching, R Group Table creation, Clustering, Diverse Compound Picking, Sammon Projections, Molecular Property calculation and Name to Smiles conversion. Structure display is activated by directly selecting cells containing SMILES strings but also by mouse hover over chart points charting data from an enabled spreadsheet. Structures are displayed in a pop-up Java window using CDK/J Chem Paint rendering capabilities. In version 2.0 onwards, this window may be resized/repositioned by the user and its new setting will be remembered for the current Excel session. Display of all structures on enabled worksheets is available as a toggle.

Substructure searching of very large spreadsheets may be speeded up by pre-calculation of CDK fingerprints (which are stored compactly in the sheets as hex strings). In this way, substructure searching of sheets containing many tens of thousands of structures is eminently feasible (tested with 250k structures).

The system requires no installation beyond file copying and, if a shared network location is provided with the necessary LICSS JAR/CPP and CDK/J Chem Paint/Opsin JAR files, enabled spreadsheets may be shared between users, downloading the necessary support files automatically. The latest version also offers users the chance to download necessary files automatically from this project site if unavailable locally.

Latest News

New: Take a look at a 'taster' video for LICSS 2.1: http://www.screencast.com/t/Oy1cwtO0ht

Version 2.1 of LICSS was released 10 October 2011. This adds Similarity searching and new Diverse Compound Picking functionality to that of version 2.0. There are several bug fixes also including more robust structure display toggling and eliminating Excel crashes caused by attempted multiple initialisation.

Version 2.0 of LICSS was released 1 August 2011. This uses a new method for calls to Java where Java Classes are proxied in a CPP Dll. This allows very fast access to CDK/J Chem Paint functionality and has made possible on-the-fly visualisation of structures for all visible Smiles strings on a worksheet. Excel functions to calculate molecular properties (using the new technology) have also been introduced. Other new features include conversion of IUPAC names to Smiles and automatic LICSS installation for shared workbooks via download from this project site.

Limitations

LICSS only currently works with MS Excel for Windows (although there is no reason why the code could not be adapted for other operating systems). See also section on compatibility within GettingStarted.

Contact

You are welcome to contact the developer with issues, suggestions and comments: kevin.lawson@syngenta.com. Better still, join and post to the new Google Group for the project: http://groups.google.com/group/licss-users.

New code created by Syngenta Ltd and licensed under GPL v2