2D structure visualization tool specification

From Chemical Informatics and Cyberinfrastructure Collaboratory

Chemical structure visualization applet proposal David Wild, djwild@indiana.edu, February 2006

Develop a client-side tool that can run in a web browser (preferably an applet) for displaying and manipulating tables where each row contains a chemical structure (specified in SMILES format) in the first column, an ID or name in the second column and an arbitrary number of columns of numeric or textual data. The SMILES column should be displayed as a 2D chemical structure diagram using one of the available structure drawing applets/beans such as Marvin (www.chemaxon.com/marvin).

The applet should read the input file from the web server (local server filename supplied). The input file will be in either a tab/space delimited file, or in VoTables XML format (see http://www.ivoa.net/Documents/latest/VOT.html and http://communitygrids.blogspot.com/2005/12/introduction-to-votable-11_27.html) . The tables will have a header row describing each column. An example space/tab delimited file would be:

SMILES Name Scn1 Scn2 Scn3
c1ccccc1 Benzene 3.2 6.7 5.8
c1cc(Cl)ccc1 Chlorobenzene 2.8 9.7 8.6
…

The applet should be robust enough to handle a few hundred structures, although most visualizations will be of <200 structures. It should display the column names, as well as the data for the compounds

Users should be permitted to sort the table by any column (ascending or descending order). At this point, it is not necessary to be able to sort on the 2D structure / smiles column.

Users should be able to select rows and copy the contents in selected rows to clipboard.

More links, etc can be found at: http://www.chembiogrid.org/wiki/index.php/Visualization_and_End_User_Tools (username cicc_grid, password cicc_grid)