Monday, December 22, 2014

Structural Superimposition of Local Sequence Alignment using BioPython

This task was given to me as a homework in one of my courses at the university and I wanted to share my solution as I saw there is no such entry on the Internet.

Objectives here are;
  • Download (two) PDB files automatically from the server
  • Do the pairwise alignment after getting their amino acid sequences
  • Superimpose them and report RMSD
Bio.PDB module from BioPython works very well in this case. It's what I used in this solution.

Wednesday, December 3, 2014

How to Install openpyxl on Windows

openpyxl is a Python library to read/write Excel 2007 xlsx/xlsm files. To download and install on Windows:

Download it from Python Packages

Then to install, extract the tar ball you downloaded, open up CMD, navigate to the folder that you extracted and run the following:

C:\Users\Gungor>cd Downloads\openpyxl-2.1.2.tar\dist\openpyxl-2.1.2\openpyxl-2.1.2
C:\Users\Gungor\Downloads\openpyxl-2.1.2.tar\dist\openpyxl-2.1.2\openpyxl-2.1.2>python setup.py install

It's going to install everything and will report any error. If there is nothing that seems like an error. You're good to go. Verify the installation by opening Python (command line) and running the following line in Python CMD:

>>> from openpyxl import Workbook
>>>

openpyxl documentation is a great place to start with it.