How to get secondary structure of multiple PDB files using DSSP in Python?
In this article, we will obtain the secondary structure of multiple PDB files present in a directory using DSSP . You need to have DSSP installed on your system.
If not, then you can install it using the following command:
$ sudo apt-get install dssp
Now, let’s obtain dssp files from PDBs.
Keep all your PDB files in a directory, here named pdb_files, and make a directory for your output dssp files, here named dssp_files.
Save the following Python script and run it in the terminal as
$ python3 dssp-to-pdb.py
#!/usr/bin/env python3 import os import os.path import pathlib import sys pdb_path = os.getcwd()+"/pdb_files" pdb_files = os.listdir(pdb_path) dssp_path = os.getcwd()+"/dssp_files" for pdb in pdb_files: dssp_filename = pdb.split('.') cmd = os.system("dssp -i "+" "+pdb_path+"/"+pdb+" "+"-o "+" "+dssp_path+"/"+dssp_filename+".dssp") print(cmd)
- Frishman, D., & Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins: Structure, Function, and Bioinformatics , 23 (4), 566-579.
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