add python execute

runner.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+'''
+@file               :runner.py
+@Description:       :
+@Date               :2023/12/04 14:34:36
+@Author             :lyzeng
+@Email              :pylyzeng@gmail.com
+@version            :1.0
+'''
+
+import time
+import logging
+from dataclasses import dataclass, field
+from pathlib import Path
+import subprocess
+import shutil
+import os
+
+# 设置日志记录
+logging.basicConfig(level=logging.INFO, filename='simulation_log.log', filemode='a',
+                    format='%(asctime)s - %(levelname)s - %(message)s')
+logger = logging.getLogger()
+
+@dataclass
+class SimulationRunner:
+    pdb_file: Path
+    nsteps: int
+    dt: float
+    base_folder: Path
+    bash_script: Path = None  # Bash脚本路径作为可选参数
+    gmxrc_path: Path = None  # GMXRC文件路径作为可选参数
+    runner_folder: Path = field(init=False)
+
+    def __post_init__(self):
+        self.runner_folder = self.base_folder / f"runner_{self.pdb_file.stem}"
+        self.runner_folder.mkdir(exist_ok=True)
+        self.bash_script = self.bash_script.absolute() or Path(__file__).resolve().parent / "md_gromacs.sh"
+        # 设置 GMXRC_PATH 环境变量
+        self.gmxrc_path = self.gmxrc_path or Path("/home/lingyuzeng/software/gmx2023.2/bin/GMXRC")
+
+    def copy_pdb(self):
+        shutil.copy(self.pdb_file, self.runner_folder / self.pdb_file.name)
+
+    def run_simulation(self):
+        start_time = time.time()
+        result = None
+        try:
+            env_vars = {
+                "NAME": self.pdb_file.stem,  # 首先将 NAME 设置为文件的 stem
+                "NSTEPS": str(self.nsteps),
+                "DT": str(self.dt),
+                "GMXRC_PATH": str(self.gmxrc_path)
+            }
+            env_vars["HOME"] = os.environ["HOME"]
+            logger.info(f"pdb_file: {self.pdb_file.name}")
+            logger.info(f"Executing script at: {self.bash_script}")
+            result = subprocess.run(["bash", str(self.bash_script)], env=env_vars, cwd=self.runner_folder,
+                                    capture_output=True, text=True, check=True)
+        except subprocess.CalledProcessError as e:
+            logger.error(f"Error in simulation for {self.pdb_file.name}: {e}")
+            if e.stdout:
+                logger.error(f"Standard Output:\n{e.stdout}")
+            if e.stderr:
+                logger.error(f"Standard Error:\n{e.stderr}")
+
+        end_time = time.time()
+        duration = end_time - start_time
+
+        if result:
+            logger.info(f"Simulation for {self.pdb_file.name} completed successfully in {duration:.2f} seconds.")
+            if result.stdout:
+                logger.info(f"Shell Script Output:\n{result.stdout}")
+            if result.stderr:
+                logger.error(f"Shell Script Error Output:\n{result.stderr}")
+        else:
+            logger.error(f"Simulation for {self.pdb_file.name} failed in {duration:.2f} seconds.")
+
+def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_path):
+    pdb_folder = Path(pdb_folder_path).resolve()
+    for pdb_file in pdb_folder.glob("*.pdb"):
+        runner = SimulationRunner(pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path)
+        runner.copy_pdb()
+        logger.info(f"Running simulation for {pdb_file.name} in {runner.runner_folder}...")
+        runner.run_simulation()
+        logger.info(f"Finished simulation for {pdb_file.name}.")
+
+if __name__ == "__main__":
+    NSTEPS = 50000000  # Example: 50000000 steps
+    DT = 0.002  # Example: 2 fs time step
+    PDB_FOLDER_PATH = Path("./pdb_files")  # Assuming the PDB files are in a folder named 'pdb_files' in the current directory
+    # 传入自定义的bash脚本路径
+    CUSTOM_BASH_SCRIPT_PATH = Path('analysis_pdb/md_gromacs.sh')
+    # 传入 GMXRC 文件的路径
+    GMXRC_PATH = Path('/home/zenglingyu/software/gmx2023.2/bin/GMXRC')
+    main(NSTEPS, DT, PDB_FOLDER_PATH, CUSTOM_BASH_SCRIPT_PATH, GMXRC_PATH)
+
+