Substructure Search with Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Substructure Search with Open Babel

This chapter provides introductions and tutorial examples on Open Babel 'obabel -s ...' command to do molecule substructure search. Topics include substructure search using SMARTS expressions with wildcard atoms/bonds and logical operators.

"obabel -s ..." Command - Substructure Search

Substructure Search with Wildcard Atom "*"

Substructure Search with Wildcard Bond "~"

Substructure Search with SMARTS Expressions

Takeaways:

Open Babel "obabel ... -s ..." command performs a molecule substructure search with a SMARTS string to represent the substructure pattern.
Open Babel supports "*" as the wildcard atom in SMARTS expressions for substructure search.
Open Babel supports "~" as the wildcard bind in SMARTS expressions for substructure search.
Open Babel supports logical operators in SMARTS expressions for substructure search.