File size: 2,008 Bytes
c289d87 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | from __future__ import annotations
from abc import ABC, abstractmethod
from dataclasses import dataclass, field
from pathlib import Path
from typing import Any, Dict, Sequence
@dataclass
class BackendCapability:
backend_name: str
available: bool
details: Dict[str, Any]
@dataclass
class DockingResult:
ligand_id: str
docking_score: float
pose_path: Path | None
backend_name: str
backend_mode: str
score_source: str
raw_output_file: str
parsed_from: str
fallback_used: bool
success: bool
message: str = ""
command: str = ""
extra: Dict[str, Any] = field(default_factory=dict)
class DockingError(RuntimeError):
"""Generic docking backend error."""
class BackendUnavailableError(DockingError):
"""Raised when requested backend capability is not available."""
class DockingBackend(ABC):
"""Common backend interface for all docking engines."""
@abstractmethod
def check_capability(self) -> BackendCapability:
pass
@abstractmethod
def prepare_target(self, target_path: str | Path, work_dir: str | Path) -> Dict[str, Any]:
pass
@abstractmethod
def prepare_ligand(self, ligand_id: str, smiles: str, work_dir: str | Path) -> Path:
pass
@abstractmethod
def build_site_or_constraints(
self,
target_context: Dict[str, Any],
reference_ligand: Path,
work_dir: str | Path,
) -> Path:
pass
@abstractmethod
def dock(
self,
target_context: Dict[str, Any],
ligand_files: Sequence[Path],
work_dir: str | Path,
allow_mock: bool = False,
require_real_backend: bool = False,
) -> list[DockingResult]:
pass
@abstractmethod
def parse_results(self, results: Sequence[DockingResult]) -> list[dict[str, Any]]:
pass
@abstractmethod
def extract_interface_features(self, parsed_results: Sequence[dict[str, Any]]) -> list[dict[str, float]]:
pass
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