pdbstat_deepclean.py

import sys
import subprocess
from os import listdir
import os
from paths import PDB_FILES

base_script = """
load coo pdb <infile>
set sscutoff 1.8
set omegac 40.0
check
dele bad
find close
dele bad close
dele bad bond
write coo pdb <outfile>
"""

if len(sys.argv) < 2:
    print("python3 pdbstat_deepclean.py <file_prefix>")
    raise

pdb_prefix = sys.argv[1]

input_pdb_files = [ f'{PDB_FILES}{f}' for f in listdir(f'{PDB_FILES}') if f.endswith('pdb') and f.find(pdb_prefix) != -1 and f.find('clean') == -1]
print(input_pdb_files)

output_file = '{PDB_FILES}'+pdb_prefix+'_clean.pdb'

base_script_file = './pdbstat_deepclean_script_base.txt'

s = ""
with open(base_script_file, 'r') as script:
    for line in script:
        if line.endswith('<infile>\n'):
            for file in input_pdb_files:
                s+= line.replace('<infile>', file)
                s += 'all\n'
        elif line.endswith('<outfile>\n'):
            s+= line.replace('<outfile>', output_file)
        else:
            s+= line
        s += '\n'
    print(s)

temp_script_file = './pdbstat_deepclean_script_'+pdb_prefix+'.txt'
with open(temp_script_file, 'w') as script:
    script.write(s)

command = ['pdbstat', '-s', '<', temp_script_file]

os.system('pdbstat -s < ' + temp_script_file)

os.system('rm ' + temp_script_file)