83 lines
4.5 KiB
Python
Executable File
83 lines
4.5 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- encoding: utf-8 -*-
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'''
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@file :process_trajectory.py
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@Description: :
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@Date :2023/12/11 11:10:24
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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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from runner import SimulationRunner
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import subprocess
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# 新增处理轨迹的方法
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def process_trajectory(temp_folder, output_folder, 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 = SimulationRunner.read_ndx_file(f'{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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SimulationRunner.save_ndx_file(f"{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 {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
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command_2 = f'echo "Protein\nProtein\nProtein_LIG" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
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command_3 = f'echo "Protein\nProtein\nProtein_LIG" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {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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SimulationRunner.save_ndx_file(f"{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 {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
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command_2 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc'
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command_3 = f'echo "Protein\nProtein\nProtein" | gmx trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {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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'''
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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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def save_ndx_file(filename, ndx_dict):
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with open(filename, 'w') as file:
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for section, content in ndx_dict.items():
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file.write(f"[ {section} ]\n")
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for i, num in enumerate(content, 1):
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file.write(str(num))
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if i % 15 == 0:
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file.write("\n")
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else:
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file.write("\t")
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file.write("\n")
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ndx_dict = read_ndx_file('index.ndx')
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new_ndx_dict = {key: value for key, value in ndx_dict.items() if key in ["Protein"]}
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temp_folder = 'traj_tmp'
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extract_interval = 100
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tpr_file = 'md.tpr'
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xtc_file = 'md.xtc'
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output_folder = 'extra_traj'
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save_ndx_file(f"{temp_folder}/tarj_show.ndx", new_ndx_dict)
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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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!echo "Protein\nProtein\nProtein" | gmx_mpi trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc
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# - echo "Protein\nProtein\nProtein" | gmx_mpi trjconv -s {tpr_file} -f md.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -o {output_folder}/traj_show.xtc
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!echo "Protein\nProtein\nProtein" | gmx_mpi trjconv -s {tpr_file} -f {temp_folder}/temp.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb
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# - !echo "Protein\nProtein\nProtein" | gmx_mpi trjconv -s {tpr_file} -f md.xtc -n {temp_folder}/tarj_show.ndx -center -fit rot+trans -b 0 -e 0 -o {output_folder}/tarj_show.pdb
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''' |