Can I do Substructure Search with fingerprints using Open Babel?

Yes, you can do Substructure Search with fingerprints using Open Babel. All you have to do is to take substructure as the query molecule and run a similarity search using the fingerprint output option "-o fpt ".

When Open Babel calculates the Tanimoto coefficient of query fingerprint and object fingerprint, it will check to see whether the query fingerprint is sub-set of the object fingerprint. If yes, it will output a message to say that the object molecule is a possible superstructure of the query. In other words, the object molecule is a substructure match.

For example, if you run a similarity search of the benzene ring against the tyrosine molecule, you will get:

fyicenter$ babel benzene.sdf tyrosine.sdf -o fpt 
>
>   Tanimoto from first mol = 0.125
Possible superstructure of first mol
2 molecules converted
38 audit log messages 

If "babel" command outputs "Possible superstructure of first mol" message for many object molecules, you can collect all of them as multiple substructure matches.

⇒ Generate Fingerprint of Single Molecule

⇐ Fingerprint Types Supported in Open Babel

⇑ Similarity Search with Open Babel

⇑⇑ Open Babel Tutorials