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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 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

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:

pip3 install numpy
brew install rdkit --with-python3

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