FastSearch
From Open Babel
Filename Extensions | fs |
---|---|
Chemical MIME Type | Undefined |
Specification URL | http://openbabel.sourceforge.net/wiki/FastSearch |
Import | Yes, One record per input file |
Export | Yes, Output is a binary file |
Open Babel Version | 2.0.0 and later |
Options
Uses molecular fingerprints in an index file. 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: 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 -at15 (best 15 molecules) The structure spec can be a molecule from a file: -Spatternfile.zzz Write Options (when making index) e.g. -xfFP3 f# Fingerprint type 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 l# Maximum number of candidates. Default<4000>
Additional Comments
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.
For more information on using the FastSearch index format, see the user's tutorial.