import dataclasses import json from enum import Enum from typing import List, Dict, Tuple, Optional # Constants INTERFACE_MIN_ATOM_DIST = 8.0 SubunitName = str ChainedSubunitName = str ChainName = str PdbPath = str @dataclasses.dataclass class SubunitInfo: name: SubunitName chain_names: List[str] start_res: int # inclusive, should be greater than 0 sequence: str def get_unstructured_res_ids(self) -> List[int]: return [self.start_res + i for i, resname in enumerate(self.sequence) if resname == "X"] def get_end_res(self) -> int: return self.start_res + len(self.sequence) - 1 def get_active_res_ids(self) -> List[int]: return [i for i in range(self.start_res, self.get_end_res() + 1) if i not in self.get_unstructured_res_ids()] def get_relative_active_res_ids(self) -> List[int]: return [i - self.start_res for i in range(self.start_res, self.get_end_res() + 1) if i not in self.get_unstructured_res_ids()] def get_chained_names(self) -> List[str]: return [f"{self.name}_{chain_name}" for chain_name in self.chain_names] def to_dict(self): return dataclasses.asdict(self) @classmethod def from_dict(cls, d): return cls(**d) SubunitsInfo = Dict[SubunitName, SubunitInfo] def save_subunits_info(subunits_info: SubunitsInfo, output_path: str): json_data = {subunit_name: subunit_info.to_dict() for subunit_name, subunit_info in subunits_info.items()} json.dump(json_data, open(output_path, "w"), indent=2) def read_subunits_info(output_path: str) -> SubunitsInfo: json_data = json.load(open(output_path)) subunits_info = {subunit_name: SubunitInfo.from_dict({k: v for k, v in subunit_info.items() if k != "end_res"}) for subunit_name, subunit_info in json_data.items()} for subunit_name, subunit_info in subunits_info.items(): assert subunit_name == subunit_info.name, f"Key name and subunit info name must match, mismatch:" \ f" {subunit_name} and {subunit_info.name}" res_to_subunit_name = {} for subunit_name, subunit_info in subunits_info.items(): for chain_name in subunit_info.chain_names: for res_id in subunit_info.get_active_res_ids(): res_key = (chain_name, res_id) assert res_key not in res_to_subunit_name, \ f"Residue {res_id} in chain {chain_name} is present in multiple subunits - " \ f"{subunit_name} and {res_to_subunit_name[res_key]}. overlaps are not allowed in subunits." res_to_subunit_name[res_key] = subunit_name return subunits_info @dataclasses.dataclass class SubunitPdbInfo: chain_id: ChainName chain_residue_id: int pdb_residue_id: int length: int