This lesson is still being designed and assembled (Pre-Alpha version)

Lesson Title: 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.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine, 2.7 is not). Also, please set up your python environment at least a day in advance of the workshop. If you encounter problems with the installation procedure, the instructors will be available 30 minutes before the workshop begins to help you.

Windows - Video Tutorial

  1. Open the Anaconda Windows download page.
  2. Download the installer. Be sure you get the Python 3 version.
  3. Double-click the installer icon and follow the setup instructions on screen. You can use MOST of the default options. The only exception is to check the Make Anaconda the default Python option.

Mac OS X - Video Tutorial

  1. Open the Anaconda MacOS download page.
  2. Download the installer. Be sure you get the Python 3 version.
  3. Double click the installer icon and follow the setup instructions. You can use all of the default options.

Obtain lesson materials

We are utilizing two Molecular Dynamics packages to show examples of some of the design patterns. MDanalysis and MDTraj are both available through conda-forge.

To start, open an Anaconda prompt. Then enter

conda create --name design_patterns python=3.7

Enter Y to continue.

We now need to activate our new environment.

$ conda activate design_patterns

Then we will install MDAnalysis and MDTraj.

$ conda install -c conda-forge mdanalysis
$ conda install -c conda-forge mdtraj

We have included a sample trajectory file to use with the example design patterns. The trajectory was extracted from the MDAnalysisTests