The chemfp project is meant to address the following use cases.

Use case #1: Web service for 3-nearest similarity searches

A research group has a set of structures with associated experimental values. The information is updated every month. They want to provide a web service which takes an input structure and finds the 3 nearest compounds with better than 70% Tanimoto similarity, and reports the similarity score and structure information.

There are no ready-made tools for this, excepting groups which have a chemistry-aware database. The pieces to build it are available from several projects, but large parts need to be filled in. Ideally there should be a set of command-line and library functions for working with chemfp files.

Use case #2: Data provenance

It's time to write the paper. Where did this data set come from? Which program generated it and with which options? Was it the one which used the buggy SMARTS definitions?

Most formats don't track this information. While it's impossible to be perfect, some information would help.

Use case #3: New fingerprint types

A researcher develops a new fingerprint scheme and wants to compare the applicability to existing fingerprints, including the linear hash in OpenBabel and the topological hash in RDKit.

Currently that requires quite a bit of work to figure out how to use each program to read the input files and generate the fingerprints which can be used for the analysis.

Separating fingerprint generation from fingerprint use also makes it easier to implement things like N*N similarity clustering on a cluster without needing to install the chemistry tools on all the machines.

Use case #4: Comparison of search algorithms

An algorithms developer comes up with a new scheme for fast similarity wants to compare the effectiveness of the algorithm against other implementations.

While there are many published papers on this topic, few of the algorithms and data sets are available for direct comparison. I don't think the problem is the lack of a common format, but I suggest it might help.