WARNING: this repository is outdated. Please consider using the more recent brew formula
WARNING: to install rdkit. The new formula does not require you to use the rdkit/rdkit tap
WARNING: and installs python bindings.
WARNING: Cf. https://formulae.brew.sh/formula/rdkit#default (brew install rdkit).

Homebrew-rdkit: tap-ready formula for rdkit

First, make sure you Homebrew version is 0.9 or above (you can check your brew version with brew --version).

After tapping this repo with

brew tap rdkit/rdkit

You can install rdkit with just one line of command:

brew install rdkit --with-python3

If you want to stay on the edge and use the latest and greatest from GitHub:

brew install --HEAD rdkit --with-python3

Optional installs

• --with-python3 will install the Python 3 wrapper.
• --with-java will install the Java wrapper.
• --with-inchi will install the InChI support. This will download InChI from https://inchi-trust.org if necessary.
• --with-avalon will install the Avalon toolkit support. This will download the Avalon Toolkit source.
• --with-postgresql will install the PostgreSQL cartridge.
• --with-pycairo if you want to draw molecules with Cairo.

Forcing brew to install rdkit and all its dependencies from scratch

Brew is not a very smart or reliable package manager. If you encounter any error, you might try the following to force installing rdkit:

# backup your brew installed packages list
brew list --formula > my_brew_packages.txt
# uninstall all of them
brew uninstall --force $(cat my_brew_packages.txt)
# install rdkit from scratch
brew install rdkit --with-python3

Errors you might encounter

• Unsatisfied dependency: numpy

By default, Homebrew will attempt to install and manage numpy for you, like all other dependencies. You may alternatively install and manage numpy separately, via pip:

pip3 install numpy
brew install rdkit --with-python3 --without-numpy

• Fatal Python error: Interpreter not initialized (version mismatch?)

This indicates that rdkit or one of its dependencies (e.g. boost) was linked against a different version of Python than the one you are using it with. Try rebuilding boost from source:

brew uninstall boost
brew install boost --build-from-source

If that doesn't fix it, try comparing the output of these three commands:

python-config --prefix
find /usr/local/Cellar/rdkit -name rdBase.so -exec otool -L {} \;
find /usr/local/Cellar/boost -name libboost_python-mt.dylib -exec otool -L {} \;

• TypeError: No to_python (by-value) converter found for C++ type: boost::shared_ptrRDKit::ROMol

This is likely due to a bug in boost-python v1.60, which has now been patched in the boost homebrew formula. To get the patch, run:

brew reinstall boost
brew reinstall rdkit