FastSearch

From Open Babel

Filename Extensions	fs
Chemical MIME Type	Undefined
Specification URL	http://openbabel.sourceforge.net/wiki/FastSearch
Import	Yes, One record per input file
Export	Yes, Output is a binary file
Open Babel Version	2.0.0 and later

Options

 Uses molecular fingerprints in an index file.
 Writing to the fs format makes an index (a very slow process)
   babel datafile.xxx index.fs
 Reading from the fs format does a fast search for:
   Substructure
     babel index.fs -sSMILES outfile.yyy   or
     babel datafile.xxx -ifs -sSMILES outfile.yyy
   Molecular similarity based on Tanimoto coefficient
     babel index.fs -sSMILES outfile.yyy -t0.7  (Tanimoto >0.7)
     babel index.fs -sSMILES outfile.yyy -t15   (best 15 molecules)
   The structure spec can be a molecule from a file: -Spatternfile.zzz
 
 Write Options (when making index) e.g. -xfFP3 
  f# Fingerprint type
  N# Fold fingerprint to # bits
  u  Update an existing index

 Read Options (when searching) e.g. -at0.7
  t# Do similarity search: #mols or # as min Tanimoto
  a  Add Tanimoto coeff to title
  l# Maximum number of candidates. Default<4000>
 

Additional Comments

This format uses molecular fingerprints to prepare and search an index of a multi-molecule datafile. It allows fast substructure and structural similarity searching. The indexing is a slow process (~30 minutes for a 250,000 molecule file). The subsequent seaching is much faster, a few seconds, and so can be done interactively.

For more information on using the FastSearch index format, see the user's tutorial.