This chapter contains the docstrings for the public portion of the chemfp API. Chemfp also has internal modules and functions that should not be imported or used directly. If you use parts of the undocumented API then your code is more likely to break with newer chemfp releases.
See “Getting started with the API” for some introductory examples.
- chemfp top-level
The top-level chemfp module is the starting point for using chemfp. It contains functions to read and write fingerprint files, “high-level” commands for working with chemfp, and more.
The fingerprint arena class is defined in
chemfp.search module contains similarity search functions
for searching fingerprint arenas, and the
SearchResults result class definitions. This is lower-level
API than using
chemfp.fps_search module contains similarity search
functions for searching FPS files, and the search result class
definitions. This is only needed when working in a streaming
environment where fingerprint arena creation overhead is too large.
chemfp.diversity module contains chemfp’s diversity
pickers, all of which require a fingerprint arena. This is a
lower-level API than using
contain the public-facing API for chemfp’s cheminformatics toolkit
wrapper implementations. The
objects will automatically import the underlying toolkit and forward
Sometimes you need to work with SMILES or SD files as text records,
not molecules. For that, use the
Sometimes you need to work with CVS files containing structure records
or fingerprint. For that, use the
chemfp.csv_readers module or
read_csv_ids_and_molecules function in the toolkit wrapper
chemfp.bitops module has functions to work with
fingerprints represented as byte strings or hex-encoded strings, as
well as configuration functions for configuring chemfp’s bit
operations. Use the
chemfp.encodings to decode from various
fingerprint string representations to a byte string.
chemfp.types module contains a few public
exceptions which derived from ValueError but which don’t yet also
derive from ChemFPError.