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reduce_receptors.py
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reduce_receptors.py
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# you need reduce installed to use this: https://github.com/rlabduke/reduce
import os
import subprocess
import time
from tqdm import tqdm
start_time = time.time()
data_path = 'PDBBind'
overwrite = False
names = sorted(os.listdir(data_path))
for i, name in tqdm(enumerate(names)):
rec_path = os.path.join(data_path, name, f'{name}_protein_obabel.pdb')
return_code = subprocess.run(
f"reduce -Trim {rec_path} > {os.path.join(data_path, name, f'{name}_protein_obabel_reduce_tmp.pdb')}", shell=True)
print(return_code)
return_code2 = subprocess.run(
f"reduce -HIS {os.path.join(data_path, name, f'{name}_protein_obabel_reduce_tmp.pdb')} > {os.path.join(data_path, name, f'{name}_protein_obabel_reduce.pdb')}", shell=True)
print(return_code2)
return_code2 = subprocess.run(
f"rm {os.path.join(data_path, name, f'{name}_protein_obabel_reduce_tmp.pdb')}",
shell=True)
print(return_code2)
print("--- %s seconds ---" % (time.time() - start_time))