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Homebrew formula for rdkit
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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

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

brew install --HEAD rdkit

Optional installs

  • --with-java will install the Java wrapper.
  • --with-inchi will install the InChI support. It will NOT use system InChI even it is present. Instead, it will always download InChI from

Errors you might encounter

  • Unsatisfied dependency: numpy

Homebrew does not manage Python package dependencies for you. You need to install numpy with sudo easy_install numpy.

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

This indicates that rdkit or one of its dependencies (eg. 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 -exec otool -L {} \;
find /usr/local/Cellar/boost -name libboost_python-mt.dylib -exec otool -L {} \;
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