155 lines
7.6 KiB
Python
155 lines
7.6 KiB
Python
#!/usr/bin/env python
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# -*- encoding: utf-8 -*-
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'''
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@file :runner.py
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@Description: :
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@Date :2023/12/04 14:34:36
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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 time
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import logging
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from dataclasses import dataclass, field
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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 os
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# 设置日志记录
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logging.basicConfig(level=logging.INFO, filename='simulation_log.log', filemode='a',
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format='%(asctime)s - %(levelname)s - %(message)s')
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logger = logging.getLogger()
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class SimulationRunner:
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pdb_file: Path
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nsteps: int
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dt: float
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base_folder: Path
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bash_script: Path = None # Bash脚本路径作为可选参数
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gmxrc_path: Path = None # GMXRC文件路径作为可选参数
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temp_folder: Path # 用于存储临时数据和结果数据的路径(轨迹数据处理中间数据等)
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runner_folder: Path = field(init=False)
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tpr_file: Path = field(init=False)
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xtc_file: Path = field(init=False)
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def __post_init__(self):
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# 初始化文件夹和文件路径
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self.runner_folder = self.base_folder / f"runner_{self.pdb_file.stem}"
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self.tpr_file = self.runner_folder / "md.tpr"
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self.xtc_file = self.runner_folder / "md.xtc"
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self.runner_folder.mkdir(exist_ok=True)
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self.temp_folder = self.runner_folder / "temp"
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self.temp_folder.mkdir(exist_ok=True)
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self.bash_script = self.bash_script.absolute() if self.bash_script else Path(__file__).resolve().parent / "md_gromacs.sh"
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# 设置 GMXRC_PATH 环境变量
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self.gmxrc_path = self.gmxrc_path or Path("/home/lingyuzeng/software/gmx2023.2/bin/GMXRC")
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def copy_pdb(self):
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shutil.copy(self.pdb_file, self.runner_folder / self.pdb_file.name)
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@staticmethod
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def read_ndx_file(filename):
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ndx_dict = {}
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current_section = None
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with open(filename, 'r') as file:
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for line in file:
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line = line.strip()
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if line.startswith('[') and line.endswith(']'):
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current_section = line[1:-1].strip()
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ndx_dict[current_section] = []
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else:
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if current_section is not None:
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ndx_dict[current_section].extend(map(int, line.split()))
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return ndx_dict
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@staticmethod
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echo "Protein" | gmx_mpi trjconv -dt {extract_interval} -s {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc
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# 新增处理轨迹的方法
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def process_trajectory(self, extract_interval):
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# 根据提供的脚本逻辑读取和保存索引文件
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ndx_dict = self.read_ndx_file(f'{self.runner_folder}/index.ndx')
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# 根据索引文件内容决定如何处理轨迹
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if any(key.startswith("LG") for key in ndx_dict):
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# 处理含有LG组的情况
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new_ndx_dict = {key: value for key, value in ndx_dict.items() if key.startswith("LG") or key in ["Protein", "Protein_LIG"]}
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self.save_ndx_file(f"{self.temp_folder}/tarj_show.ndx", new_ndx_dict)
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# 构建处理轨迹的命令
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command_1 = f'echo "Protein_LIG" | gmx trjconv -dt {extract_interval} -s {self.tpr_file} -f {self.xtc_file} -n {self.temp_folder}/tarj_show.ndx -pbc mol -o {self.temp_folder}/temp.xtc'
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command_2 = f'echo "Protein\nProtein\nProtein_LIG" | gmx trjconv -s {self.tpr_file} -f {self.temp_folder}/temp.xtc -n {self.temp_folder}/tarj_show.ndx -center -fit rot+trans -o {self.output_folder}/traj_show.xtc'
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command_3 = f'echo "Protein\nProtein\nProtein_LIG" | gmx trjconv -s {self.tpr_file} -f {self.temp_folder}/temp.xtc -n {self.temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {self.output_folder}/tarj_show.pdb'
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else:
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# 处理只含有蛋白质组的情况
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new_ndx_dict = {key: value for key, value in ndx_dict.items() if key in ["Protein"]}
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self.save_ndx_file(f"{self.temp_folder}/tarj_show.ndx", new_ndx_dict)
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# 构建处理轨迹的命令
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command_1 = f'echo "Protein" | gmx trjconv -dt {extract_interval} -s {self.tpr_file} -f {self.xtc_file} -n {self.temp_folder}/tarj_show.ndx -pbc mol -o {self.temp_folder}/temp.xtc'
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command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {self.tpr_file} -f {self.temp_folder}/temp.xtc -n {self.temp_folder}/tarj_show.ndx -center -fit rot+trans -o {self.output_folder}/traj_show.xtc'
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command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {self.tpr_file} -f {self.temp_folder}/temp.xtc -n {self.temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {self.output_folder}/tarj_show.pdb'
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subprocess.run(command_1, shell=True, check=True)
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subprocess.run(command_2, shell=True, check=True)
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subprocess.run(command_3, shell=True, check=True)
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def run_simulation(self):
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start_time = time.time()
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result = None
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try:
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env_vars = {
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"NAME": self.pdb_file.stem, # 首先将 NAME 设置为文件的 stem
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"NSTEPS": str(self.nsteps),
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"DT": str(self.dt),
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"GMXRC_PATH": str(self.gmxrc_path)
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}
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env_vars["HOME"] = os.environ["HOME"]
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logger.info(f"pdb_file: {self.pdb_file.name}")
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logger.info(f"Executing script at: {self.bash_script}")
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result = subprocess.run(["bash", str(self.bash_script)], env=env_vars, cwd=self.runner_folder,
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capture_output=True, text=True, check=True)
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except subprocess.CalledProcessError as e:
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logger.error(f"Error in simulation for {self.pdb_file.name}: {e}")
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if e.stdout:
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logger.error(f"Standard Output:\n{e.stdout}")
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if e.stderr:
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logger.error(f"Standard Error:\n{e.stderr}")
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end_time = time.time()
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duration = end_time - start_time
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if result:
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logger.info(f"Simulation for {self.pdb_file.name} completed successfully in {duration:.2f} seconds.")
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if result.stdout:
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logger.info(f"Shell Script Output:\n{result.stdout}")
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if result.stderr:
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logger.error(f"Shell Script Error Output:\n{result.stderr}")
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else:
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logger.error(f"Simulation for {self.pdb_file.name} failed in {duration:.2f} seconds.")
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def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_path):
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pdb_folder = Path(pdb_folder_path).resolve()
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for pdb_file in pdb_folder.glob("*.pdb"):
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runner = SimulationRunner(pdb_file, simulation_steps, time_step, pdb_folder, bash_script_path, gmxrc_path)
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runner.copy_pdb()
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logger.info(f"Running simulation for {pdb_file.name} in {runner.runner_folder}...")
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runner.run_simulation()
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logger.info(f"Finished simulation for {pdb_file.name}.")
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runner.process_trajectory(extract_interval=100) # 例如，每100ps抽取一次轨迹
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logger.info(f"Finished processing trajectory for {pdb_file.name}. per 100ps")
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if __name__ == "__main__":
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NSTEPS = 50000000 # Example: 50000000 steps
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DT = 0.002 # Example: 2 fs time step
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PDB_FOLDER_PATH = Path("./pdb_files") # Assuming the PDB files are in a folder named 'pdb_files' in the current directory
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# 传入自定义的bash脚本路径
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CUSTOM_BASH_SCRIPT_PATH = Path('md_gromacs.sh')
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# 传入 GMXRC 文件的路径
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GMXRC_PATH = Path('/root/software/gmx2023.2/bin/GMXRC')
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main(NSTEPS, DT, PDB_FOLDER_PATH, CUSTOM_BASH_SCRIPT_PATH, GMXRC_PATH)
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