Free SDF Viewer

Free SDF Viewer is a free and open-source desktop viewer for the chemical structure file format sdf. It has good performance and also works with very large SD-files. It is targeted at users that quickly want to look and scan through any type of sd-file.


SD-files is a widely used format for storing and sharing chemical structures and properties of these structures. These files are often use to exchange chemical structure databases. Such files can contain thousands to millions of chemical structures.


  • tabular display of records in the file including all properties
  • resizeable chemical structure image column
  • row index column
  • selected rows can be copy & pasted into Excel (Structure as SMILES)


Properties and row height

Below images shows all the properties in the SD-file and the last row is higher to better fit the larger molecule:

variable row height

Viewing large SD-Files

This screenshot is an example of a rather large file. See the row number on the left side of the table:

large file example

Scrolling remains smooth with very reasonable memory usage.


The application can create an .index file for each sd-file you load. This is set in the settings menu. By default the index is not saved. This file is created only once and loading the same file (must be unchanged!!!) again later will be much quicker. You may safely delete it.

For rendering the chemical structures the Indigo toolkit is used.


When opening very large sd-files (million+ molecules) the file might not load. In that case you need to close the application and start it from the command-line so that you can increase the memory available to FreeSDFViewer. On the command-line enter

javaw -Xmx512m -jar "C:\Program Files\FreeSDFViewer.jar"

You must add the full path. Above assumes Windows and that you put the jar file into the Program Files folder. If it still does not load increase the number in -Xmx512m further. It denotes amount of memory to use in megabytes.