/homebrew-rdkit

Homebrew formula for rdkit

Primary LanguageRuby

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 GitHub:

brew install --HEAD rdkit

Optional installs

  • --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.

Errors you might encounter

  • Unsatisfied dependency: numpy

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