Chemfp 3.4 is available as a pre-compiled package or a source distribution.

Installing a pre-compiled package

Pre-compiled packages for chemfp are available for Python 2.7, Python 3.6, Python 3.7, and Python 3.8. They were compiled under the “manylinux1” and “manylinux2014” Docker build environment, which means they should work for most Linux-based operating systems.

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

Installing from source

The chemfp source distribution requires that Python and a C compiler be installed in your machines. Since chemfp doesn’t 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?

You may use chemfp 3.4 with either Python 2.7, or Python 3.6 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 and RDKit toolkits and the proprietary OEChem toolkit. 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 Python 2.7.9 or later, and with Python 3.4 and later so is almost certainly installed if you have Python. To install the source distribution tar.gz file with pip:

python -m pip install chemfp-3.4.tar.gz

Otherwise you can use Python’s standard “”. Read for details of how to use it. The short version is to do the following:

tar xf chemfp-3.4.tar.gz
cd chemfp-3.4
python build
python install

The last step may need a sudo if you otherwise cannot write to your Python site-package. Another option is to use a virtual environment.

Configuration options

The file has several compile-time options which can be set 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 you have a very old version of gcc, or an older version of clang, or are on a Mac where the clang version doesn’t support OpenMP, then you will need to use --without-openmp to tell to compile without OpenMP:

python build --without-openmp

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-3.4.tar.gz

Note: you can use the environment variable CC to change the C compiler. For example, the clang compiler on Mac doesn’t support OpenMP so I installed gcc-6 and compile using:

CC=gcc-6 LDFLAGS="-L/usr/local/lib -lomp" \
    python -m pip install chemfp-3.4.tar.gz

(Hmm. Perhaps I should upgrade my copy of gcc.)

--with-ssse3, --without-ssse3

Chemfp by default compiles with SSSE3 support, which was first available in 2006 so almost certainly available on your Intel-like processor. In case I’m wrong (are you compiling for ARM? If so, send me any compiler patches), you can disable SSSE3 support using the --without-ssse3, or set the environment variable CHEMFP_SSSE3 to “0”.

Compiling with SSSE3 support has a very odd failure case. If you compile with the SSSE3 flag enabled, then take the binary to a machine without SSSE3 support, then it will crash because all of the code will be compiled to expect the SSSE3 instruction set even though only one file, popcount_SSSE3.c, should be compiledthat way.

--with-avx2, --without-avx2

Chemfp 3.0 added support for the AVX2 instruction set. This can be 30% faster than the POPCNT instruction for 1024 or 2048 bit fingerprints. By default it is enabled, and chemfp checks that the chip implements AVX2 before calling the functions which are explicitly written with AVX2.

Use --without-avx2 or set the environment variable CHEMFP_AVX2 to “0” to disable it.