first version

script/ppi.py

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+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+'''
+@file               :ppi.py
+@Description:       :
+@Date               :2023/09/01 16:56:22
+@Author             :lyzeng
+@Email              :pylyzeng@gmail.com
+@version            :1.0
+'''
+import sys
+from dataclasses import dataclass, field, InitVar
+from functools import partial
+from pymol import cmd
+from pymol.cmd import util
+from pathlib import Path
+from collections import defaultdict
+
+# local import 
+from .pymolbase import PyMOLBase
+
+@dataclass
+class PyMOLConcrete(PyMOLBase):
+    file: Path
+    ligand_positions: defaultdict = field(default_factory=lambda: defaultdict(list), init=False)
+    
+    def __post_init__(self, file):
+        self.load_file(file)
+        self.global_obj_name = self.cleanpdb(file.stem)
+
+    def load_file(self, file):
+        # 加载文件到PyMOL（这里是一个示例，您可能需要使用实际的PyMOL命令）
+        cmd.load(file)
+        pass
+
+    def collect_ligand_positions(self, model, chain, resn, resi):
+        position = f'/{model}//{chain}/{resi}'
+        self.ligand_positions[resn].append(position)
+
+    def gather_ligand_info(self):
+        cmd.iterate('organ', 'collect_ligand_positions(model, chain, resn, resi)', space={'collect_ligand_positions': partial(self.collect_ligand_positions)})
+
+
+    @staticmethod
+    def cleanpdb(before_string):
+        """
+        处理传入参数pdb 例如: pdb1b12.ent 1b12.pdb 转化成 1b12
+        """
+        # print(f'try to format {before_string}')
+        if '.ent' in before_string:
+            before_string = before_string[3:-4].lower() 
+        elif '.pdb' in before_string:
+            before_string = before_string[:4].lower()
+        elif len(before_string) == 4:
+            before_string = before_string.lower()
+        else:
+            if len(before_string) != 4:
+                raise ValueError(f'length out of 4 {before_string}')
+        return before_string
+
+@dataclass
+class PDBAnalyzer:
+    pdb: Path  # 使用Path对象代替字符串
+    ChA: str
+    ChB: str
+    dist: str
+    
+    
+    # 主运行函数
+    def run(self):
+        cmd.delete('all')
+        cmd.load(str(self.pdb))  # 将Path对象转为字符串以兼容PyMOL命令
+        pdb_name = self.pdb.stem  # 获取不包括扩展名的文件名
+        
+        # ...（省略了其他设置和选择）
+
+        # 调用封装好的函数
+        self.HBond()
+        self.Pi_Pi_interaction()
+        self.Cation_Pi_interaction()
+        self.Salt_bridge_positive()
+        self.Salt_bridge_negative()
+
+        # ...（省略了其他设置和保存）
+        
+        cmd.save(f'{pdb_name}_interaction.pse')
+
+class 
+
+# 主程序
+def main():
+    pdb_file = Path(sys.argv[1])  # 使用Path对象
+    CHA = sys.argv[2]
+    CHB = sys.argv[3]
+    dist = sys.argv[4]
+    cmd.set('bg_rgb', 'white')
+    
+    analyzer = PDBAnalyzer(pdb_file, CHA, CHB, dist)
+    analyzer.run()
+
+if __name__ == "__main__":
+    main()