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ef423c5 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | import subprocess
import re
from tqdm import tqdm
import os
RUNNER = '/datapool/data2/home/jiahan/Tool/TMalign-20180426/MMalign'
def align_pdb(pdb1,pdb2,pdb1_out):
subprocess.run([RUNNER,pdb1,pdb2,'-o',pdb1_out],stdout=subprocess.PIPE)
def get_tm_score(pdb1,pdb2):
cmd = subprocess.run(['TMscore',pdb1,pdb2],stdout=subprocess.PIPE)
out = cmd.stdout.decode()
tm_score = re.search(r"TM-score\s+=\s+(\d+\.\d+)", out)
rmsd = re.search(r"RMSD of the common residues=\s+(\d+\.\d+)", out)
return float(rmsd.group(1)),float(tm_score.group(1)) |