From 4bf039ebd98fcb0583c60e83d2f39572a6356b96 Mon Sep 17 00:00:00 2001 From: root Date: Tue, 19 Dec 2023 12:50:56 +0800 Subject: [PATCH] update --- runner.py | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 60 insertions(+), 4 deletions(-) diff --git a/runner.py b/runner.py index cbd218b..747463d 100644 --- a/runner.py +++ b/runner.py @@ -22,7 +22,6 @@ logging.basicConfig(level=logging.INFO, filename='simulation_log.log', filemode= format='%(asctime)s - %(levelname)s - %(message)s') logger = logging.getLogger() -@dataclass class SimulationRunner: pdb_file: Path nsteps: int @@ -30,18 +29,73 @@ class SimulationRunner: 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 + 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) runner_folder: Path = field(init=False) + tpr_file: Path = field(init=False) + xtc_file: Path = field(init=False) def __post_init__(self): + # 初始化文件夹和文件路径 self.runner_folder = self.base_folder / f"runner_{self.pdb_file.stem}" + self.tpr_file = self.runner_folder / "md.tpr" + self.xtc_file = self.runner_folder / "md.xtc" self.runner_folder.mkdir(exist_ok=True) - self.bash_script = self.bash_script.absolute() or Path(__file__).resolve().parent / "md_gromacs.sh" + self.temp_folder = self.runner_folder / "temp" + self.temp_folder.mkdir(exist_ok=True) + self.bash_script = self.bash_script.absolute() if self.bash_script else Path(__file__).resolve().parent / "md_gromacs.sh" # 设置 GMXRC_PATH 环境变量 - self.gmxrc_path = self.gmxrc_path or Path("$HOME/software/gmx2023.2/bin/GMXRC") + 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) + @staticmethod + def read_ndx_file(filename): + ndx_dict = {} + current_section = None + + with open(filename, 'r') as file: + for line in file: + line = line.strip() + + if line.startswith('[') and line.endswith(']'): + current_section = line[1:-1].strip() + ndx_dict[current_section] = [] + else: + if current_section is not None: + ndx_dict[current_section].extend(map(int, line.split())) + + return ndx_dict + + @staticmethod +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 + + # 新增处理轨迹的方法 + def process_trajectory(self, extract_interval): + # 根据提供的脚本逻辑读取和保存索引文件 + ndx_dict = self.read_ndx_file(f'{self.runner_folder}/index.ndx') + + # 根据索引文件内容决定如何处理轨迹 + if any(key.startswith("LG") for key in ndx_dict): + # 处理含有LG组的情况 + new_ndx_dict = {key: value for key, value in ndx_dict.items() if key.startswith("LG") or key in ["Protein", "Protein_LIG"]} + self.save_ndx_file(f"{self.temp_folder}/tarj_show.ndx", new_ndx_dict) + # 构建处理轨迹的命令 + 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' + 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' + 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' + else: + # 处理只含有蛋白质组的情况 + new_ndx_dict = {key: value for key, value in ndx_dict.items() if key in ["Protein"]} + self.save_ndx_file(f"{self.temp_folder}/tarj_show.ndx", new_ndx_dict) + # 构建处理轨迹的命令 + 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' + 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' + 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' + subprocess.run(command_1, shell=True, check=True) + subprocess.run(command_2, shell=True, check=True) + subprocess.run(command_3, shell=True, check=True) + def run_simulation(self): start_time = time.time() result = None @@ -84,6 +138,8 @@ def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_p 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}.") + runner.process_trajectory(extract_interval=100) # 例如，每100ps抽取一次轨迹 + logger.info(f"Finished processing trajectory for {pdb_file.name}. per 100ps") if __name__ == "__main__": NSTEPS = 50000000 # Example: 50000000 steps @@ -92,7 +148,7 @@ if __name__ == "__main__": # 传入自定义的bash脚本路径 CUSTOM_BASH_SCRIPT_PATH = Path('md_gromacs.sh') # 传入 GMXRC 文件的路径 - GMXRC_PATH = Path('/home/zenglingyu/software/gmx2023.2/bin/GMXRC') + GMXRC_PATH = Path('/root/software/gmx2023.2/bin/GMXRC') main(NSTEPS, DT, PDB_FOLDER_PATH, CUSTOM_BASH_SCRIPT_PATH, GMXRC_PATH)