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Substructure Search with Fingerprints
Can I do Substructure Search with fingerprints using Open Babel?
✍: FYIcenter.com
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
2020-12-02, 629👍, 0💬
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