Installing chemfp

Chemfp 4.1 is available as a pre-compiled package or a source distribution.

Installing a pre-compiled package

Pre-compiled chemfp distributions available for Python 3.8, Python 3.9, and Python 3.10. They were compiled under the”manylinux2014” Docker build environment, which means they should work for most Linux-based operating systems. While chemfp supports macOS, pre-compiled macOS distributions are not available.

These binary packages are NOT open source. By default they are distributed under the Chemfp Base License Agreement v1.1, which lets you use some of the chemfp functionality for internal purposes, including the ability to create FPS files and use the “toolkit” APIs.

However, the following features require a time-limited license key:

  • generate FPB files
  • create or search in-memory fingerprint arenas with more than 50,000 fingerprints
  • perform Tversky searches
  • perform Tanimoto searches of FPS files with more than 20 queries at a time.

These features can be enabled with a valid license key, set via the environment variable CHEMFP_LICENSE. Email to request a evaluation license or to purchase a license.

Use the following command to install a pre-compiled version of chemfp:

python -m pip install chemfp -i

If you get the message:

ERROR: Could not find a version that satisfies the requirement chemfp (from versions: none)
ERROR: No matching distribution found for chemfp

then you are likely installing from a non-Linux-based operating system like macOS or Microsoft Windows. Pre-compiled installers are not yet available for those OSes. Currently macOS is supported in the source distribution and Windows is not yet supported.

Installing from source

The chemfp source distribution requires that Python and a C compiler be installed in your machines. Since chemfp doesn’t yet run on Microsoft Windows (for tedious technical reasons), then your machine likely already has both Python and a C compiler installed. In case you don’t have Python, or you want to install a newer version, you can download a copy of Python from . If you don’t have a C compiler, .. well, do I really need to give you a pointer for that?

chemfp 4.1 supports Python 3.8 or newer.

The core chemfp functionality does not depend on a third-party library but you will need a chemistry toolkit in order to generate new fingerprints from structure files. chemfp supports the free Open Babel, RDKit, and CDK toolkits and the proprietary OEChem/OEGraphSim toolkits. Make sure you install the Python libraries for the toolkit(s) you select.

The easiest way to install chemfp is with the pip installer. This comes with all supported versions of Python. To install the source distribution tar.gz file with pip:

python -m pip install chemfp-4.1.tar.gz

The last step may need the --user option for a user installation instead of installing to Python’s own site-package. A likely better option is to use a virtual environment.

If you are making in-house modifications, you likely want to use the --editable option.

Configuration options

Chemfp uses the legacy file, which implements several configuration options. These can be used either from the python build command-line or through environment variables. The environment variable solution is the easiest way to change the settings under pip.

--with-openmp, --without-openmp

Chemfp uses OpenMP to parallelize multi-query searches. The default is --with-openmp. If your C compiler does not support OpenMP, then you will need to use --without-openmp to tell to compile without OpenMP:

python build --without-openmp

The system “gcc” on macOS is not GNU gcc but is instead a front-end to Apple’s clang-based compiler, which does not support OpenMP. You will need to configure chemfp to build without OpenMP support if you want to use that compiler. Otherwise, install GNU gcc with OpenMP support (eg, using Homebrew <> or “conda”) and use that alternative compiler.

You can also set the environment variable CHEMFP_OPENMP to “1” to compile with OpenMP support, or to “0” to compile without OpenMP support:

CHEMFP_OPENMP=0 python -m pip install chemfp-4.1.tar.gz

Use the environment variable CC to change the C compiler. On macOS I use the following to compile chemfp using GNU gcc 11:

CC=gcc-11 python -m pip install chemfp-4.1.tar.gz


If you are benchmarking then use the CC or CFLAGS environment variables to ensure you are passing the appropriate architecture flags to the compiler, eg, CC -march=native.

There are additional legacy configuration options which are no longer documented and will likely be removed in the future.

Installing CDK and JPype

CDK is a Java package. Chemfp is written for Python. Chemfp supports CDK. How can chemfp call into CDK?

There are several ways for Python programs to call into Java. I tried two of them and ended up using JPype, following Noel O’Boyle’s suggestion.

There are a few ways to install JPype. The easiest is likely to use conda (see the documentation for details) or, if you have the the Java run-time, you can pip install it with:

python -m pip install JPype1

This installs the jpype module for Python.

You’ll also need to put the CDK JAR on the CLASSPATH. For example, in the following I download the JAR file then set the CLASSPATH using bash syntax:

cd ~/ftps
curl -LO
export CLASSPATH=/Users/dalke/ftps/cdk-2.3.jar

(I put my manually downloaded packages in ~/ftps/ for historic reasons.)

Use cdk2fps --version to diagnose if things are working. If it’s a success it should look like:

% cdk2fps --version
cdk2fps 4.1

The following message occurs if jpype isn’t installed:

Cannot run cdk2fps: Cannot import jpype, which is required for
chemfp to access the CDK jar: No module named 'jpype'

The following message occurs if jpype is installed (eg, via pip) but either Java isn’t installed on your machine or jpype couldn’t find your installation:

Cannot run cdk2fps: No JVM shared library file (
found. Try setting up the JAVA_HOME environment variable properly.

The following message occurs if the CDK JAR file is not on the CLASSPATH:

Cannot run cdk2fps: It appears that CDK is not installed: Unable to
access the CDK jar via JPype. Is the jar on your CLASSPATH?: Failed
to import 'org.openscience'

The following message occurs if you are using Python 2 (jpype and therefore chemfp does not support Python 2):

Cannot run cdk2fps: Unable to use cdk2fps on Python 2