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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 | from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
from typing import Optional, Sequence
import numpy as np
from .graph_builders import build_protein_graph, protein_sequence_from_structure
from .schemas import ProteinEncoding
from .sequence_features import compute_sequence_features
from .structure_features import compute_structure_features
@dataclass
class ProteinEncoderConfig:
distance_threshold: float = 8.0
class ProteinEncoder:
"""Encode protein structures from PDB/mmCIF for scheduling/modeling."""
def __init__(self, config: Optional[ProteinEncoderConfig] = None):
self.config = config or ProteinEncoderConfig()
def encode_structure(
self,
target_id: str,
structure_path: str | Path,
pocket_residues: Sequence[str] | None = None,
) -> ProteinEncoding:
sequence = protein_sequence_from_structure(structure_path)
seq_features = compute_sequence_features(sequence)
struct_features = compute_structure_features(structure_path, pocket_residues=pocket_residues)
graph = build_protein_graph(
structure_path,
distance_threshold=self.config.distance_threshold,
pocket_residues=pocket_residues,
)
combined = {**seq_features, **struct_features}
vector = np.asarray(list(combined.values()), dtype=float)
return ProteinEncoding(
target_id=target_id,
sequence=sequence,
sequence_features=seq_features,
structure_features=struct_features,
graph=graph,
vector=vector,
)
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