chemfp 3.5b1 is available

I've just released chemfp 3.5b1, which is the latest version of the commercial chemfp development track. This is a beta version meant primarily as a way to get feedback about the new CDK support. See the previous posting for examples of the new features.

Because it is a beta release, you will need to specify the exact version to install it, using the following:

python -m pip install chemfp==3.5b1 -i

These are available at no cost under the Chemfp Base License Agreement. This license lets you use most chemfp features in-house, and generate FPS files for any purpose.

Some features are either limited or disabled. See the chemfp licensing page to learn how to request an evaluation key and to learn about the different licensing options.

CDK preview release

This beta release adds the command-line toolkit cdk2fps which uses the CDK cheminformatics toolkit to parse structures and generate fingerprints.

The CDK is written in Java. To use it, you will need to do the following:

  1. Download the JAR (tested with both cdk-2.3.tar and the latest CDK version from source control);

  2. Place the CDK JAR file on your CLASSPATH.

  3. Install JPype, which is an adapter so Python programs can uses Java JAR files.

  4. (optional) For Zstandard support, install Zstd-jni for Java and zstandard for Python.

Additionally, the Python module chemfp.cdk_toolkit implements the chemfp toolkit API for CDK, which lets you use the same Python API for file I/O and fingerprinting across all four supported toolkits (Open Babel, OEChem/OEGraphSim, RDKit, and CDK).

Use cdk2fps --help for command-line usage information. The Python API is not yet documented, but is consistent with the other three toolkits.

Feedback appreciated

The goal of this beta release is to get feedback from CDK users about chemfp's support of the toolkit. Let me know what you think!