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