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

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

brew install --HEAD rdkit

• --with-python3 will install RDkit under the Python3 (By default, the RDkit is installed under Python2)
• --with-java will install the Java wrapper.
• --with-inchi will install the InChI support. This will download InChI from http://inchitrust.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.

• 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. However, when installing rdkit with python 3, a pip-installed numpy for python 2 can prevent homebrew properly installing numpy for python 3. To solve this, make sure you use pip in both python 2 and 3:

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

Or use homebrew in both python 2 and 3:

pip uninstall numpy
pip3 uninstall numpy
brew install rdkit --with-python3

• 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