This script gives an example of searching the database with every conformer of every query. The number of results depends on nHits and has a default value of 100 per search. A cutoff can also be specified and the similarity scoring function can be set to Tversky by adding the --tversky flag to the command line (default=Tanimoto). Results are written to one file per query molecule, with each conformer of the query molecule’s results listed sequentially. The query conformer id is saved as an SD tag for ease of identification.


Running this script with large numbers of queries and high numbers of conformers will
deplete system memory rapidly.


prompt> BestShapeOverlayMultiConfQuery <database> <queries> [--nHits 100] [--cutoff N] [--tversky]