Chemfp 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 3.1 with either Python 2.7, or Python 3.5 or newer. If you want to run on Python 2.6 then you’ll need to use chemfp 2.1.

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 it may already be installed. To install the tar.gz file with pip:

pip install chemfp-3.1.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-3.1.tar.gz
cd chemfp-3.1
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 pip install chemfp-3.1.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-7 and compile using:

CC=gcc-7 pip install chemfp-3.1.tar.gz
--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 my 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.

The solution is to compile popcount_SSSE3.c with the SSSE3 flag enabled and all of the other files without that flag. Unfortunately, Python’s doesn’t make that easy to do. If this is a problem for you, take a look at filter_gcc in the chemfp distribution. It’s used like this:

CC=$PWD/filter_gcc python build

It’s a bit of a hack so contact me if you have problems.

--with-avx2, --without-avx2

Chemfp 3.0 added support for the AVX2 instruction set. This can be 15% faster than the POPCNT instruction for large (ie, 2048 bit or greater) fingerprints. By default it is disabled. Use --with-avx2 or set the environment variable CHEMFP_AVX2 to “1” to enable it.

While 15% faster sounds great, I have only tested the AVX2 support in one machine environment. I expect that it will have similar portability problems as the SSSE3 code had, that is, if the code is compiled with the AVX2 compilation flag then it’s free to assume that some other instruction sets, like SSE4.2, are also available. Because of the way Python’s works, all of the code will be compiled to use these more advanced instructions. If chemfp is then run on a machine without those instructions, it will cause the program to crash with an illegal instruction.

Chemfp does check that the chip implements AVX2 before calling the functions which are explicitly written with AVX2. The problem is that other parts of the code may be affected, at the compiler’s disgression. I have no way of knowing.

A solution is to modify the filter_gcc option I mentioned earlier. Let me know if this is something you want me to work on with you.