89 lines
2.9 KiB
Python
89 lines
2.9 KiB
Python
#!/usr/bin/env python
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# -*- encoding: utf-8 -*-
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'''
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@file :mainfix.py
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@Description :批量调用modelbuilder.py进行结构修复
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@Date :2024/01/12 13:38:53
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@Author :lyzeng
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@Email :pylyzeng@gmail.com
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@version :1.0
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'''
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import argparse
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from pathlib import Path
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import subprocess
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import shutil
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import concurrent.futures
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import os
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import sys
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def process_pdb_file(pdb_file: Path, script_path: Path, working_dir: Path, python_interpreter: str, typestr="refine.very_fast", use_pymol_align_merge=False):
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pdb_id = pdb_file.stem
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runner_dir = working_dir / f"runner_{pdb_id}"
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runner_dir.mkdir(exist_ok=True)
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copied_pdb_file = runner_dir / pdb_file.name
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shutil.copy(pdb_file, copied_pdb_file)
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# 构建并运行modelbuilder.py脚本的命令
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command = [python_interpreter, script_path.absolute().as_posix(), copied_pdb_file.absolute().as_posix()]
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# 添加额外的参数
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command += ["--typestr", typestr]
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if use_pymol_align_merge:
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command += ["--use_pymol_align_merge"]
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# 运行modelbuilder.py脚本
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subprocess.run(command, cwd=runner_dir)
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def main():
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parser = argparse.ArgumentParser(description="Process multiple PDB files using modelbuilder.py")
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parser.add_argument("pdb_dir_path", help="Directory containing PDB files")
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parser.add_argument("script_path", help="Path to the modelbuilder.py script")
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parser.add_argument("--python_interpreter", default=sys.executable, help="Path to the Python interpreter")
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args = parser.parse_args()
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pdb_dir_path = args.pdb_dir_path
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script_path = args.script_path
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python_interpreter = args.python_interpreter
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pdb_dir = Path(pdb_dir_path)
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pdb_files = list(pdb_dir.glob("*.pdb"))
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script_path = Path(script_path).absolute() # 确保script_path是绝对路径
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max_workers = max(1, os.cpu_count() - 1) # 保留一个核心给系统
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with concurrent.futures.ProcessPoolExecutor(max_workers=max_workers) as executor:
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futures = [executor.submit(process_pdb_file, pdb_file, script_path, pdb_dir, python_interpreter) for pdb_file in pdb_files]
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for future in concurrent.futures.as_completed(futures):
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future.result()
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if __name__ == "__main__":
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main()
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# python mainfix.py pdb_test1 modelbuilder.py --python_interpreter /root/micromamba/envs/pyfastx/bin/python
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# 复制修复完成文件到指定文件夹
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# import os
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# import shutil
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# from pathlib import Path
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# # 设置源目录和目标目录
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# source_dir = Path('pdb_test1')
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# target_dir = Path('newfix')
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# # 确保目标目录存在
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# target_dir.mkdir(exist_ok=True)
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# # 遍历源目录
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# for subdir in source_dir.glob('runner_*'):
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# if subdir.is_dir():
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# # 查找所有匹配的文件
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# for file in subdir.glob('*.modellerfix.pdb'):
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# # 移动文件到目标目录
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# shutil.move(str(file), target_dir / file.name)
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# print("文件移动完成。")
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