how to calculate psi and phi angle for every residue of protein from pdb file

Is it possible to calculate using coordinate values?

Answer 1

[Om]

import math

import csv

import Bio.PDB

def degrees(rad_angle):

"""Converts any angle in radians to degrees.

If the input is None, it returns None.

For numerical input, the output is mapped to [-180,180].

"""

if rad_angle is None:

return None

angle = rad_angle * 180 / math.pi

while angle > 180:

angle -= 360

while angle < -180:

angle += 360

return angle

pdb_code = "3gou"

print("About to load Bio.PDB and the PDB file...")

structure = Bio.PDB.PDBParser().get_structure(pdb_code, f"{pdb_code}.pdb")

print("Done")

print("About to save angles to file...")

with open(f"{pdb_code}_biopython.csv", "w", newline="") as csvfile:

csvwriter = csv.writer(csvfile)

# Write the header row

csvwriter.writerow(["PDB Code", "Chain ID", "Residue", "Residue ID", "Phi (°)", "Psi (°)"])

# Iterate through the structure

for model in structure:

for chain in model:

print(f"Chain {str(chain.id)}")

polypeptides = Bio.PDB.CaPPBuilder().build_peptides(chain)

for poly_index, poly in enumerate(polypeptides):

phi_psi = poly.get_phi_psi_list()

for res_index, residue in enumerate(poly):

next_residue = poly[res_index + 1] if res_index + 1 < len(poly) else None

phi, psi = phi_psi[res_index]

if phi and psi:

# Write the data row

csvwriter.writerow([

pdb_code,

chain.id,

residue.resname,

residue.id[1],

degrees(phi),

degrees(psi),

])

print("Done")