FastSearching (fs) — Open Babel v2.3.0 documentation

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# FastSearching (fs)

Uses molecular fingerprints in an index file.

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.

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:

- Identical molecule:

      babel index.fs -sSMILES outfile.yyy -ae  or
      babel datafile.xxx -ifs -sSMILES outfile.yyy -ae

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

  The structure spec can be a molecule from a file: -Spatternfile.zzz

Note that the parameter of the -s option needs to be a valid SMILES molecule when using fastsearch. You can use the more versatile SMARTS in a normal substructure search.

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

## 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
`S <filename>` | Structure spec in a file
`n` | No further SMARTS filtering after fingerprint phase
`h` | SMARTS uses explicit H in pattern file

## Write Options

`f <num>` | Fingerprint type
`N <num>` | Fold fingerprint to <num> bits
`u` | Update an existing index

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