It's a suite of tools, some of which are open source. To say that Anaconda is confusing to the beginner would be an understatement. To understand what this base business is all about, we need to dive deeper into Anaconda. The explanation can be found in this question. Should you want to query this flag in the future, use: conda config -show | grep auto_activate_base All Your BaseĪfter installing Anaconda I was greeted by a most unwelcome, persistent, foreign terminal prompt: (base) $įortunately, the fix was easy: conda config -set auto_activate_base False With these preliminaries out of the way, I launched the installer and clicked through the screens.
INSTALL JUPYTER NOTEBOOK CONDA INSTALL
Install AnacondaĪfter downloading the graphical installer, I verified its SHA-256 hash (note the two spaces between the hash value and filename): $ echo "e095c487d2837e4c984d0fcd2217be42c615504a2d7d6651095d34c2fa9807a0 Anaconda3-2020.07-MacOSX-x86_64.pkg" | shasum -a 256 -c -Įxpected hashes for all Anaconda installers are available here. Many of the points addressed here should apply to other operating systems.
What follows are some notes on my process for setting up RDKit together with Jupyter on a macOS system running Mojave. It does however link to an Installation document that leads with Anaconda, noting that this is the "fastest install." Moreover, the README never specifically recommends Anaconda as the preferred installation method. I was trying to avoid this option because Anaconda seems like a sledgehammer when the situation calls for little more than a screwdriver. I don't like it and I don't use it but it is the officially supported way to install rdkit… Ultimately, the maintainer offered the following advice: Although your results may vary, my experience with the macOS Homebrew formula resulted in an error that neither the maintainer nor I could resolve. Under the "Installation" heading the RDKit README lists several installers built to work with platform-specific package managers. For more, see the post by project lead Greg Landrum. A pull request is in the works, but with unclear status. A two-year old issue explains some of the reasons. Unfortunately, no PyPI package for RDKit exists, precluding pip install rdkit. The Python Package Index (aka PyPI, aka pip) is Python's standard package manager.
This article discusses the problem and a method for using RDKit within Jupyter notebooks. It's packed with functionality, deployed within multiple open source projects, and is widely-used in machine learning applications. RDKit is a cheminformatics toolkit with bindings for Python.
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