https://github.com/rdkit/homebrew-rdkit

Homebrew formula for rdkit
https://github.com/rdkit/homebrew-rdkit

Last synced: about 2 months ago
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Homebrew formula for rdkit

• Host: GitHub
• URL: https://github.com/rdkit/homebrew-rdkit
• Owner: rdkit
• Created: 2012-04-16T21:25:56.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2022-06-22T08:12:35.000Z (over 2 years ago)
• Last Synced: 2024-09-26T02:01:34.415Z (3 months ago)
• Language: Ruby
• Size: 92.8 KB
• Stars: 44
• Watchers: 11
• Forks: 19
• Open Issues: 5
• Metadata Files:
  • Readme: README.md

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README

        
```

WARNING: this repository is outdated. Please consider using the more recent brew formula

WARNING: to install rdkit. The new formula does not require you to use the rdkit/rdkit tap

WARNING: and installs python bindings.

WARNING: pip might be able to install rdkit also: pip3 install rdkit

WARNING: Cf. https://formulae.brew.sh/formula/rdkit#default (brew install rdkit).

```

[![Build status](https://travis-ci.org/rdkit/homebrew-rdkit.svg)](https://travis-ci.org/rdkit/homebrew-rdkit)

# 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](http://rdkit.org) with just one line of command:

    brew install rdkit --with-python3

If you want to stay on the edge and use the latest and greatest from GitHub:

    brew install --HEAD rdkit --with-python3

### Optional installs

- `--with-python3` will install the Python 3 wrapper.

- `--with-java` will install the Java wrapper.

- `--with-inchi` will install the InChI support. This will download InChI from https://inchi-trust.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.

- `--with-pycairo` if you want to draw molecules with Cairo.

### Forcing brew to install rdkit and all its dependencies from scratch

Brew is not a very smart or reliable package manager.

If you encounter any error, you might try the following to force installing

rdkit:

    # backup your brew installed packages list

    brew list --formula > my_brew_packages.txt

    # uninstall all of them

    brew uninstall --force $(cat my_brew_packages.txt)

    # install rdkit from scratch

    brew install rdkit --with-python3

### 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`:

    pip3 install numpy

    brew install rdkit --with-python3 --without-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_ptr*

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