https://github.com/mcs07/homebrew-cheminformatics
Cheminformatics formulae for the Homebrew package manager
https://github.com/mcs07/homebrew-cheminformatics
cheminformatics formulae homebrew packages ruby science
Last synced: 3 months ago
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Cheminformatics formulae for the Homebrew package manager
- Host: GitHub
- URL: https://github.com/mcs07/homebrew-cheminformatics
- Owner: mcs07
- Created: 2013-08-09T13:17:33.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2018-03-30T21:23:13.000Z (over 7 years ago)
- Last Synced: 2025-04-13T05:40:38.188Z (6 months ago)
- Topics: cheminformatics, formulae, homebrew, packages, ruby, science
- Language: Ruby
- Size: 171 KB
- Stars: 20
- Watchers: 5
- Forks: 5
- Open Issues: 5
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# homebrew-cheminformatics [](https://travis-ci.org/mcs07/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](https://github.com/mcs07/homebrew-cheminformatics/tree/master/Formula) 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//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](https://github.com/mcs07/homebrew-cheminformatics/issues). Alternatively, email me at m.swain@me.com.