FastSearch

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Filename Extensions fs
Chemical MIME Type Undefined
Specification URL Unknown
Import {{{import}}}
Export {{{export}}}
Open Babel Version {{{version}}}

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.