"babel -i fs ..." - Fingerprint Index Based Search
How to perform a Fingerprint Index Based Search with the "babel" command?
You can perform a Fingerprint Index Based Search with the "babel" command using the "-i fs" option to specify the fingerprint index file as the input.
For more information, read the help document on fastsearch index file format "fs":
fyicenter$ babel -H fs fs Fastsearch format 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 :file:`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 and Tanimoto < 0.9 The datafile plus the ``-ifs`` option can be used instead of the index file. NOTE that the datafile MUST NOT be larger than 4GB. (A 32 pointer is used.) .. seealso:: :ref:`fingerprints` Write Options (when making index) e.g. -xfFP3 f# Fingerprint type If not specified, the default fingerprint (currently FP2) is used 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 in similarity search l# Maximum number of candidates. Default is 4000 e Exact match Alternative to using exact in ``-s`` parameter, see above n No further SMARTS filtering after fingerprint phase
⇒ "babel -i fs ... -s ... -at n" - Top n Similarity Search
⇐ "babel ... -o fs" - Generate Fastsearch Index
⇑ Using Fastsearch Fingerprint Index
2020-08-25, 595👍, 0💬
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