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!!!