| from __future__ import annotations |
|
|
| from pathlib import Path |
| from typing import Dict, Sequence |
|
|
| import numpy as np |
|
|
| from libs.utils.io_pdb import load_structure |
|
|
|
|
| def _residue_centroid(residue) -> np.ndarray | None: |
| coords = [atom.coord for atom in residue.get_atoms()] |
| if not coords: |
| return None |
| return np.mean(np.asarray(coords, dtype=float), axis=0) |
|
|
|
|
| def compute_structure_features(structure_path: str | Path, pocket_residues: Sequence[str] | None = None) -> Dict[str, float]: |
| """Compute structure-derived summary features from PDB/mmCIF.""" |
| structure = load_structure(structure_path) |
| residues = [r for r in structure.get_residues() if r.id[0] == " "] |
| atoms = list(structure.get_atoms()) |
|
|
| centroids = [] |
| for residue in residues: |
| c = _residue_centroid(residue) |
| if c is not None: |
| centroids.append(c) |
| if centroids: |
| xyz = np.vstack(centroids) |
| extent = xyz.max(axis=0) - xyz.min(axis=0) |
| mean_extent = float(np.mean(extent)) |
| else: |
| mean_extent = 0.0 |
|
|
| pocket_count = 0.0 |
| pocket_residue_set = set(pocket_residues or []) |
| if pocket_residue_set: |
| for residue in residues: |
| chain = residue.get_parent().id |
| idx = residue.id[1] |
| key = f"{chain}:{idx}" |
| if key in pocket_residue_set: |
| pocket_count += 1.0 |
|
|
| return { |
| "residue_count": float(len(residues)), |
| "atom_count": float(len(atoms)), |
| "mean_spatial_extent": mean_extent, |
| "pocket_residue_count": pocket_count, |
| } |
|
|
