Searching fast fingerprint database¶

A program that initializes a fast fingerprint database with the fingerprint file generated from the previous example and then performs a fingerprint search to identify molecules which are similar to a given query molecule.

Schematic representation of fast fingerprint search process¶

Command Line Interface¶

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> java SearchFastFP --help

will generate the following output:

Simple parameter list

 fingerprint database options
   -memorytype : Fingerprint database memory type

 fingerprint database search options
   -cutoff : Similarity cutoff value
   -descending : Order of similarity scores
   -limit : Maximum number of similarity scores
   -simfunc : Similarity measure

 input/output options
   -fpdbfname : Input fast fingerprint database filename
   -molfname : Input molecule filename
   -out : Output molecule filename
   -query : Input query filename

Code¶

Download code

SearchFastFP.java and SearchFastFP.txt interface file