"babel ... -o fs" - Generate Fastsearch Index
What is Open Babel Fastsearch Index file? How to generate it with the "babel" command?
Fastsearch index file is an Open Babel specific binary file that stores pre-calculated fingerprints and their indexes for multiple molecules. Fastsearch index file can improve similarity search significantly faster for large number of molecules.
You can use the "fs" output file format with the "babel" command to generate fastsearch index file using the following syntax:
babel input_section -o fs
Here is an example of generating fastsearch index file for a SDF file of 409 molecules:
fyicenter$ babel molecules.sdf -o fs molecules-index.fs This will prepare an index of molecules.sdf and may take some time... It contains 409 molecules It took 0 seconds 409 molecules converted 37 audit log messages fyicenter$ ls -l molecules*.* -rw-r--r-- 1 fyicenter staff 54272 May 25 09:49 molecules-index.fs -rw-r--r-- 1 fyicenter staff 3295245 May 25 09:48 molecules.sdf
Note that molecules-index.fs stores fingerprint indexes for molecules stored in molecules.sdf. So both files need to be maintained and used together.
⇒ "babel -i fs ..." - Fingerprint Index Based Search
⇐ Using Fastsearch Fingerprint Index
⇑ Using Fastsearch Fingerprint Index
2020-08-25, 608👍, 0💬
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