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Code Zone  

Here you find some of the codes that I have been using in Bioinformatics classes. Each code has a PDF file with a brief description of the program and also any related file(s) that you might need to run the code. You need to have Python 3 installed on your computer. In addition, you also need NumPy, Matplotlib, SciKit-Learn, and SciPy. You can make you installing processing easier installing pyzo2015a or latter, which has all these libraries. To download pyzo click here.        


- Docking Root Mean Square Deviation (RMSD) in Python   PDF    ZIP         

Crystallographic position and pose for docking simulation.


- B-factor Plot in Python   PDF   ZIP    

 

B-factor plot generated by bfactor_plot.py  .


- Dihedral Angle in Python   PDF   ZIP       

Orthogonal system for calculation of torsion angle.  


- Ramachandran Plot in Python   PDF   ZIP    

Ramachandran plot for 1KXY