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Fingerprint format (fpt)

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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 index.fs

Reading from the fs format does a fast search for:

  • Identical molecule:

    babel index.fs -sSMILES outfile.yyy -ae  or
    babel -ifs -sSMILES outfile.yyy -ae
  • Substructure:

    babel index.fs -sSMILES outfile.yyy   or
    babel -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