| import json | |
| import urllib.request | |
| import numpy as np | |
| from Bio.Align import PairwiseAligner, substitution_matrices | |
| def alphafold_model(acc, directory): | |
| directory.mkdir(parents=True, exist_ok=True) | |
| f = directory / f"{acc}.pdb" | |
| if not f.exists(): | |
| meta = json.load(urllib.request.urlopen(f"https://alphafold.ebi.ac.uk/api/prediction/{acc}", timeout=60))[0] | |
| urllib.request.urlretrieve(meta["pdbUrl"], f) | |
| return f | |
| ALIGNER = PairwiseAligner(mode="global", open_gap_score=-11, extend_gap_score=-1) | |
| ALIGNER.substitution_matrix = substitution_matrices.load("BLOSUM62") | |
| def correspondence(s1, s2): | |
| aln = ALIGNER.align(s1, s2)[0] | |
| i1, i2 = [], [] | |
| for (a0, a1), (b0, b1) in zip(*aln.aligned): | |
| i1.extend(range(a0, a1)) | |
| i2.extend(range(b0, b1)) | |
| return np.array(i1), np.array(i2) | |
| def kabsch(P, Q): | |
| pc, qc = P.mean(0), Q.mean(0) | |
| U, _, Vt = np.linalg.svd((P - pc).T @ (Q - qc)) | |
| d = np.sign(np.linalg.det(U @ Vt)) | |
| R = U @ np.diag([1.0, 1.0, d]) @ Vt | |
| return R, pc, qc | |
| def tm_score(P, Q, L): | |
| n = len(P) | |
| d0 = max(1.24 * (max(L, 19) - 15) ** (1 / 3) - 1.8, 0.5) | |
| d0s = min(max(d0, 4.5), 8.0) | |
| best, best_rmsd = 0.0, np.nan | |
| sizes, f = [], n | |
| while f >= 4 and len(sizes) < 6: | |
| sizes.append(f) | |
| f //= 2 | |
| for size in sizes: | |
| step = max(1, size // 2) | |
| for start in range(0, n - size + 1, step): | |
| sel = np.arange(start, start + size) | |
| for _ in range(20): | |
| R, pc, qc = kabsch(P[sel], Q[sel]) | |
| d = np.linalg.norm((P - pc) @ R + qc - Q, axis=1) | |
| tm = np.sum(1 / (1 + (d / d0) ** 2)) / L | |
| if tm > best: | |
| best, best_rmsd = tm, float(np.sqrt(np.mean(d[d < 5] ** 2))) if np.any(d < 5) else np.nan | |
| cut = d0s | |
| new = np.where(d < cut)[0] | |
| while len(new) < 3: | |
| cut += 0.5 | |
| new = np.where(d < cut)[0] | |
| if len(new) == len(sel) and np.all(new == sel): | |
| break | |
| sel = new | |
| return best, best_rmsd | |