update last

manualfix/relax.py

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+from pathlib import Path
+import pyrosetta
+from multiprocessing import Pool
+from shutil import copyfile
+import logging
+
+# fix = ['6bga', '5ksb', '4z7v', '4p2o', '4ozi', '3qiu', '2ypl', '1zgl', '7z50', '6u3n']
+fix = ['1zgl']
+
+def fix_optimize(file: Path, out_file: Path):
+    # 设置日志
+    log_file = out_file.with_suffix('.log')
+    logger = logging.getLogger(log_file.name)
+    logger.setLevel(logging.INFO)
+    formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
+    file_handler = logging.FileHandler(log_file)
+    file_handler.setFormatter(formatter)
+    logger.addHandler(file_handler)
+
+    logger.info(f'Processing {file.name}')
+
+    pyrosetta.init()
+    pose = pyrosetta.pose_from_pdb(file.as_posix())
+    scorefxn = pyrosetta.create_score_function('ref2015')
+    relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn)
+    relax.apply(pose)
+    pose.dump_pdb(out_file.as_posix())
+
+    logger.info(f'Finished processing {file.name}')
+
+if __name__ == '__main__':
+    dir1 = Path('../pdb_test8')
+    dir2 = Path('../pdb_test7')
+    dirs = [dir1, dir2]
+    files = []
+    for dir in dirs:
+        files.extend(list(dir.rglob('*.modellerfix.pdb')))
+    for file in files:
+        if file.name.split('.')[0] in fix:
+            print(file)
+            target = Path('/mnt/mydrive/analysis_pdb-dev/manualfix') / file.name
+            copyfile(file.as_posix(), target.as_posix())
+    pyrosetta_fix = list(Path('/mnt/mydrive/analysis_pdb-dev/manualfix').rglob('*.modellerfix.pdb'))
+    with Pool(16) as p:
+        p.starmap(fix_optimize, [(file, file.with_stem(file.stem + '.fastrelax')) for file in pyrosetta_fix])
+    print('fastrelax done')