Fastsearch format (fs) — Open Babel v2.3.0 documentation

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# Fastsearch format (fs)

Fingerprint-aided substructure and similarity searching

Writing to the fs format makes an index of a multi-molecule datafile:

    babel dataset.sdf -ofs

This prepares an index `dataset.fs` with default parameters, and is slow (~30 minutes for a 250,000 molecule file).

However, when reading from the fs format searches are much faster, a few seconds, and so can be done interactively.

The search target is the parameter of the `-s` option and can be slightly extended SMILES (with `[#n]` atoms and `~` bonds) or the name of a file containing a molecule.

Several types of searches are possible:

- Identical molecule:

      babel index.fs outfile.yyy -s SMILES exact

- Substructure:

      babel index.fs outfile.yyy  -s SMILES   or
      babel index.fs outfile.yyy  -s filename.xxx

  where `xxx` is a format id known to OpenBabel, e.g. sdf

- Molecular similarity based on Tanimoto coefficient:

      babel index.fs outfile.yyy -at15  -sSMILES  # best 15 molecules
      babel index.fs outfile.yyy -at0.7 -sSMILES  # Tanimoto >0.7
      babel index.fs outfile.yyy -at0.7,0.9 -sSMILES
      #     Tanimoto >0.7 && Tanimoto < 0.9

The datafile plus the `-ifs` option can be used instead of the index file.

See also

Molecular fingerprints and similarity searching

## Read Options

`t <num>` | Do similarity search: <num>mols or <num> as min Tanimoto
`a` | Add Tanimoto coeff to title in similarity search
`l <num>` | Maximum number of candidates. Default<4000>
`e` | Exact match Alternative to using exact in `-s` parameter, see above
`n` | No further SMARTS filtering after fingerprint phase

## Write Options

`f <num>` | Fingerprint type If not specified, the default fingerprint (currently FP2) is used
`N <num>` | Fold fingerprint to <num> bits
`u` | Update an existing index

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