An introduction to Structural Bioinformatics Algorithms and scientific computing using Python/PyMOL.

The best way to take advantage of this material is to download a copy of the repository and run it into your computer (see below for installation details)

Alternatively, you can see the static versions of the notebooks by following the below links:

• Chapter 0 Introduction
• Chapter 1 NumPy introduction
• Chapter 2 Primer on Linear Algebra
• Chapter 3 Distances, angles and geometry
• Chapter 4 Comparing structures
• Chapter 5 Sequence alignment and clustering
• Chapter 6 Protein and RNA structure from sequence
• Chapter 7 Primer on molecular mechanics

You will need to install the following packages

• Python 2.7
• PyMOL
• NumPy
• SciPy
• Matplotlib
• IPython
• Seaborn (optional)
• Numba (optional)

All the above packages are available with most Linux distributions (except probably seaborn and numba)

If you are using Ubuntu (or a similar Linux-distribution) you can do:

sudo apt-get install pymol python-numpy python-scipy python-matplotlib ipython ipython-notebook

A good idea will be to install all the above packages using a Python distribution like Anaconda.

The first version of the material will be available in english, although a translation to Spanish is planned in the short time. (El material estará disponible primero en ingles y más adelante en español)

Please let me know of any error, suggestion, doubt, etc. E-mails and commits are welcome!!!