Building and searching fingerprint database

A program that builds a fingerprint database on-the-fly and then performs fingerprint search to identify molecules which are similar to a given query molecule

Command Line Interface

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

prompt> java SearchFP --help

will generate the following output:

Simple parameter list

 fingerprint database options
   -limit : Maximum number of similarity scores
   -simfunc : Similarity measure

 fingerprint options
   -atomtype : Fingerprint atom type
   -bondtype : Fingerprint bond type
   -fptype : Fingerprint type
   -maxdistance : Maximum number of bonds/radius in path/circular/tree
   -mindistance : Minimum number of bonds/radius in path/circular/tree
   -numbits : Size of bitvector

 input/output options
   -molfname : Input molecule filename
   -out : Output molecule filename
   -query : Input query filename

Code

Download code

SearchFP.java and SearchFP.txt interface file