"babel ... -o fs" - Generate Fastsearch Index

Q

What is Open Babel Fastsearch Index file? How to generate it with the "babel" command?

✍: FYIcenter.com

A

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 similarty 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

⇑⇑ Open Babel Tutorials

2020-08-25, 205👍, 0💬