Performing an Overlap Analysis

Instant JChem provides a simple way to look for identical or similar structures in two database tables. This allows you to answer questions like:

Which structures in this vendor library are already contained in my own database?
What proportion of structures in one database are more than 85% similar to a structure in another database?

Create a JChem table for each of the sets of structures you wish to analyse. These do not have to be in the same database, but typically are. Here we will assume that you have created two JChem tables, one with the query structures and one with the target structures.
Choose Tools -> Chemistry -> Overlap Analysis. The Overlap Analysis wizard opens.

Step 1: Query and Target selection

Select the query and target tables (these can be the same tables if you want to do a self-comparison), by selecting them from the mini Project Explorer and clicking on the appropriate 'Set as...' button:

Step 2: Search options

Specify the maximum number of hits to report for each query structure (this is most useful when running a similarity search).
Specify the type of search (perfect, exact, similarity).
Specify search options. These are the same as the structure search options when running a query.
Click Next to move to the next step

Step 3: Output options

Specify a name to use as a prefix for the resulting Fields. When running multiple sets of overlap analysis on the same query table, each one must be provided with a unique name to use as the field prefix.
Click 'Finish' to start the analysis. For large numbers of structures this can take some time to complete.
A report is written to the Output window, and progress can be followed by looking at the progress monitor in the bottom right corner of the main window:

Fields are added to the query table displaying the results of the search for each structure. The following fields may be added:

A field with a count of the number of hits found
A field with the highest similarity score (only present when a similarity search is run)
A field visiting the cd_id values of the hits (and the similarity score for each hit if a similarity search was run)

These fields can be sorted and queried like any normal field. This can be very helpful when performing an analysis of the results.