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