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homebrew-cheminformatics

Cheminformatics formulae for the Homebrew package manager.

Instructions

Homebrew must be installed:

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
brew update
brew doctor

Add this cheminformatics tap:

brew tap mcs07/cheminformatics

Install what you want:

brew install cdk
brew install filter-it
brew install helium
brew install indigo
brew install inchi
brew install opsin
brew install osra
brew install rdkit
...

Look in the Formula directory for a full list of what is available.

Options

Use brew info to see information and all the available options for a formula:

brew info rdkit

Most options are to enable optional features that have extra dependencies or to include additional language bindings for Python and Java.

For many formulae, there is also a --HEAD option to install the latest cutting edge development master.

Open Babel

There is already an Open Babel formula in the main homebrew repository. To use the formula in this tap, you will need to specify the full path:

brew install mcs07/cheminformatics/open-babel

The formulae are very similar. The main difference is that the formula in this tap installs Open Babel in a way that won't clash with other tools that also depend on the InChI library.

RDKit and Python 3

RDKit can be built to work with either Python 2 or Python 3, but not both simultaneously. The default is Python 2. For Python 3 support, use the --with-python3 option.

RDKit can have trouble finding the correct boost-python3 libraries. If you get errors installing RDKit, consider installing boost-python without support for python 2:

brew install boost-python --without-python --with-python3
brew install rdkit --HEAD --with-python3

RDKit and virtualenvs

RDKit does not play nice with virtual environments. Running brew install rdkit while inside a virtualenv tends not to work properly. To install RDKit in a a virtual environment:

• Run brew install rdkit outside a virtualenv. This will install everything to /usr/local/Cellar/rdkit, and RDKit should work in your main python install outside a virtualenv.
• Copy the contents of /usr/local/Cellar/rdkit/20XX.XX.X/lib/python2.7/site-packages to ~/.virtualenvs/<env>/lib/python2.7/site-packages. RDKit should then work within that virtualenv.

Every time you update RDKit or python, you will probably have to repeat this process. Not great, but it works.

Feedback and requests

Please add any requests for a new formula or bug reports to the Github issue tracker. Alternatively, email me at [email protected].