add test func on python

process_trajectory.py

@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+'''
+@file               :process_trajectory.py
+@Description:       :
+@Date               :2023/12/11 11:10:24
+@Author             :lyzeng
+@Email              :pylyzeng@gmail.com
+@version            :1.0
+'''
+
+
+from runner import SimulationRunner
+import subprocess
+
+# 新增处理轨迹的方法
+def process_trajectory(temp_folder, output_folder, extract_interval):
+    # 根据提供的脚本逻辑读取和保存索引文件
+    ndx_dict = SimulationRunner.read_ndx_file(f'{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"]}
+        SimulationRunner.save_ndx_file(f"{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 {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
+        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'
+        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'
+    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"]}
+        SimulationRunner.save_ndx_file(f"{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 {tpr_file} -f {xtc_file} -n {temp_folder}/tarj_show.ndx -pbc mol -o {temp_folder}/temp.xtc'
+        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'
+        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'
+    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 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
+def save_ndx_file(filename, ndx_dict):
+    with open(filename, 'w') as file:
+        for section, content in ndx_dict.items():
+            file.write(f"[ {section} ]\n")
+            for i, num in enumerate(content, 1):
+                file.write(str(num))
+                if i % 15 == 0:
+                    file.write("\n")
+                else:
+                    file.write("\t")
+            file.write("\n")
+ndx_dict = read_ndx_file('index.ndx')
+new_ndx_dict = {key: value for key, value in ndx_dict.items() if key in ["Protein"]}
+temp_folder = 'traj_tmp'
+extract_interval = 100
+tpr_file = 'md.tpr'
+xtc_file = 'md.xtc'
+output_folder = 'extra_traj'
+save_ndx_file(f"{temp_folder}/tarj_show.ndx", new_ndx_dict)
+!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
+!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
+# - 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
+!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
+# - !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
+'''