add sequencebaseclass

sequence_base.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+'''
+@file               :sequence_base.py
+@Description:       : 序列信息基类
+@Date               :2024/01/19 10:17:41
+@Author             :lyzeng
+@Email              :pylyzeng@gmail.com
+@version            :1.0
+'''
+from Bio.Data import IUPACData
+from pydantic import BaseModel, Field, FilePath, field_validator
+
+
+# 使用 BioPython 导入氨基酸缩写
+AMINO_ACIDS = set(IUPACData.protein_letters)
+
+class ProteinSequence(BaseModel):
+    label_asym_id: str
+    auth_asym_id: str
+    sequence: str
+    is_id_consistent: bool = Field(default=False)
+
+    @property
+    def is_id_consistent(self) -> bool:
+        return self.label_asym_id == self.auth_asym_id
+
+    def display_chain_id(self) -> str:
+        if not self.is_id_consistent:
+            return f"{self.label_asym_id} [auth {self.auth_asym_id}]"
+        return self.label_asym_id
+    
+class BaseProteinSequence(BaseModel):
+    sequence: str
+
+    @classmethod
+    def validate_amino_acids(cls, sequence: str) -> str:
+        if not set(sequence).issubset(AMINO_ACIDS):
+            raise ValueError('Sequence contains invalid amino acids, not conforming to IUPAC standards')
+        return sequence