Fastsearch format (fs)

Fingerprint-aided substructure and similarity searching

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

obabel 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:

  obabel index.fs -O outfile.yyy -s SMILES exact
  

• Substructure:

  obabel index.fs -O outfile.yyy  -s SMILES   or
  obabel index.fs -O outfile.yyy  -s filename.xxx
  

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

• Molecular similarity based on Tanimoto coefficient:

  obabel index.fs -O outfile.yyy -at15  -sSMILES  # best 15 molecules
  obabel index.fs -O outfile.yyy -at0.7 -sSMILES  # Tanimoto >0.7
  obabel index.fs -O 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.

NOTE on 32-bit systems the datafile MUST NOT be larger than 4GB.

Dative bonds like -[N+][O-](=O) are indexed as -N(=O)(=O), and when searching the target molecule should be in the second form.

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