Python Scripting for Computational Molecular Science: Setup

Installing Python through Anaconda

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, however, so we recommend the all-in-one installer Anaconda.

  1. Navigate to the download page for Anaconda.
  2. Download the appropriate installer for your operating system. Make sure you get the installer listed under Python 3 (not 2.7).
  3. Double click the installer icon and follow the set-up instructions, keeping most of the default options. If you are Windows, make sure to choose to choose the option Make Anaconda the default Python during installation.

Installing a Text Editor

You will need a text editor for this workshop. If you do not have a preferred text editor for writing code, we recommend Atom. Download Atom at the link and install on your computer.

Obtain lesson materials

  1. Download the files needed for these lessons here
  2. Create a folder called cms-workshop on your Desktop.
  3. Move the downloaded materials to the new folder.
  4. Unzip the file.

Start a Jupyter notebook

From Finder or Spotlight (Mac OS) or the Start Menu (Windows) find the Anaconda Navigator. The icon looks like a green circle. Click Launch under Jupyter Notebook. It may take a few seconds to load the page, especially if it is the first time you have ever used the jupyter notebook, so don’t panic if nothing loads for a few seconds. Then a new window should open in your default internet browser. Use the file navigation window to navigate to Desktop and then to the cms-workshop folder. In the upper right hand corner, click New, then choose Python 3 from the dropdown list (shown below)

This will start a new Jupyter notebook using Python 3. You’re ready to go!