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Runtime error
Runtime error
File size: 1,267 Bytes
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import numpy as np
import os
import json
from tqdm import tqdm
pdbs = os.listdir('alphafold_pdb')
for pdb in tqdm(pdbs):
pdb_lines = open(f"alphafold_pdb/{pdb}").read().splitlines()
def add_noise_and_save(variance, file_name):
with open(file_name, "w") as file:
for line in pdb_lines:
if line.startswith("ATOM"):
parts = line.split()
try:
coords = np.array([float(parts[6]), float(parts[7]), float(parts[8])])
noise = np.random.normal(0, variance, coords.shape)
new_coords = coords + noise
new_line = f"{line[:30]}{new_coords[0]:8.3f}{new_coords[1]:8.3f}{new_coords[2]:8.3f}{line[54:]}"
file.write(new_line + "\n")
except:
file.write(line + "\n")
else:
file.write(line + "\n")
variances = [0.5]
for variance in variances:
file_name = f"alphafold_pdb_noise_{variance}/{pdb}"
try:
add_noise_and_save(variance, file_name)
except Exception as e:
print(e)
print(pdb)
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