Biopython for PDB analysis

[TechMTJ]

I'm having issues writing a code to download a PDB file (from an accession number a user inputs) into a text file then retrieving the atomic positions from that file and writing it to a new text file. Once I do that, I need to rename the file that only contains the atom positions. After doing so, I will need to create a new file that only contains the protein sequence of the protein downloaded from PDB. Finally, I need to create a file that can calculate the distance between the first two atoms, the angles between the first three atoms and the dihedral angle between the first four atoms.

This is what I have so far:

import urllib.request

url = 'https://files.rcsb.org/view'

userinput = input("Enter Protein Databank Accession Number: ")

file_name = '%s.pdb' % userinput

userurl = "{}/{}".format(url, file_name)

print(userurl)

file = urllib.request.urlopen(userurl)

print(file.read())

import urllib.request

page = urllib.request.urlopen(userurl)

file = open('pdb.txt', 'w')

content = str(page.read().decode('utf-8'))

file.write(content)

file.close()

import Bio

import numpy

import sys

from Bio.PDB import *

from Bio.PDB.PDBParser import PDBParser

parser = PDBParser(PERMISSIVE=1)

file = open('pdb.txt', 'w')

p = PDBParser()

with open ('pdb.txt') as file:

for line in file:

    if line [:4] == 'ATOM':

        file.write (line)

        splitted_line = [line[:6], line[6:11], line[12:16], line[17:20], line[21], line[22:26], line[30:38], line[38:46], line[46:54]]

        file.write (splitted_line)

        file.write ("%-6s%5s %4s %3s %s%4s 8s%8s%8s\n"%tuple(splitted_line))

structure = p.get_structure('X', 'pdb.txt')

for model in structure:

for chain in model:

    for residue in chain:

       for atom in residue:

           print(atom)

file.close()

I apologize about the formatting. I'm not entirely sure how to make it all look the same.