Plotting Ramachandran Plot from more than one PDB file

Question

I want to plot a Ramachandran Plot for around 5000 PDB files in python that is saved in a folder in my system. I am searching for a way to make it without accessing each file by hard-coding each file name. Please tell if there is a way around this.

Answer 1

You could probably use PyRAMA for that. The only problem is that by PyRAMA plots to display, while you probably would like to save to a file.

One way to get around this is to:

1. Patch PyRAMA to allow ramachandran function to accept output image filename.

   def ramachandran(file_name_list, output_image=None):
       ...
       plt.tight_layout()
       if output_image is not None:
           plt.savefig(output_file, dpi=300)
       else:
           plt.show()
   

   If this works as expected I would really encourage you to submit a pull-request (or at least open an issue) on github.

2. Now you can write your main script:

   from glob import iglob
   
   from rama_lib.ramachandran_calc import ramachandran
   
   
   for pdb_filename in iglob('/my/dir/with/pdb/', '*.pdb'):
       img_filename = pdb_filename.rsplit('.', 1)[0] + '.png'
       ramachandran((pdb_filename,), img_filename)
   

I did not test the code, but I hope you get an idea.

There are also other ways to make a ramachandran plot in python. Please check: 1, 2, 3.