Fingerprint Index for Fastsearch with Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Fingerprint Index for Fastsearch with Open Babel

This chapter provides introductions and tutorial examples on using Fastsearch Index file with Open Babel. Topics include generating Fastsearch (or Fingerprint) Index file; similarity search and substructure search with fingerprint index files.

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"obabel ... -o fs" - Generate Fingerprint Index

"obabel -i fs ..." - Fingerprint Index Based Search

"obabel -i fs ... -s ... -at n" - Top n Similarity Search

"obabel -i fs ... -s ... -at range" - Similarity Range Search

"Difficulty opening ..." Error Using Fastsearch Index

"obabel -i fs ... -s ..." Substructure Search with Index

"obabel -i fs ... -s file" - Index Search with File

Takeaways:

Open Babel "obabel ... -o fs" command generates Fastsearch Index file which contains fingerprint indeces of original molecules.
Open Babel "obabel -i fs ... -s ... -at n " command performs top n similarity search on fingerprint index files.
Open Babel "obabel -i fs ... -s ... -at range " command performs similarity score range search on fingerprint index files.
Open Babel "obabel -i fs ... -s ..." command performs substructure search on fingerprint index files.