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. Jupyter is just a Python library, which is pre-installed with Anaconda, but can also be installed via pip, apt and other package managers.RDKit is a cheminformatics toolkit with bindings for Python. you describe is the program "Anaconda Navigator", which is installed with Anaconda. That graphical menu with Jupyter, RStudio etc. Jupyter Notebook is a programming environment, where you can execute shell commands with !command, so depending on the system where the Jupyter server is running, you can use !pip install numpy, !conda install numpy or other commands as cells in the Jupyter Notebook you are working in. All these package managers download packages from their own repositories, so conda install numpy, pip install numpy and apt install python3-numpy all install a package numpy, but from different sources and in possibly different versions. Some Linux distributions also offer python packages via their package manager (e.g.
Instead, an external package manager usually is used to install and possibly compile the package files to a directory where python can import it from.Īnaconda offers (among others) the package manager conda. Python packages are not installed with python functions, like it would be the case in R with install.packages("package name").
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