Datasets:
SSP: protein secondary structure (TAPE training data + CASP12-16 test sets, rcsb/casp/tape versions)
1c12c1a verified | """CA RMSD between CASP12's target file and the PDB chain TAPE used, after optimal superposition.""" | |
| import sys, glob, os, json | |
| sys.path.insert(0, "scripts") | |
| import gemmi | |
| import ss_assign as A | |
| from Bio import Align | |
| from Bio.Align import substitution_matrices | |
| D = "data/original/casp12" | |
| seqs, cur = {}, None | |
| for line in open(f"{D}/casp12.seq.txt"): | |
| line = line.strip() | |
| if line.startswith(">"): cur = line[1:].split()[0]; seqs[cur] = "" | |
| elif cur: seqs[cur] += line | |
| files = {os.path.basename(p)[:-4]: p for p in glob.glob(f"{D}/x/**/*.pdb", recursive=True)} | |
| al = Align.PairwiseAligner(mode="local", substitution_matrix=substitution_matrices.load("BLOSUM62"), open_gap_score=-11, extend_gap_score=-1) | |
| def mapping(a, b): | |
| aln = al.align(a, b)[0] | |
| return {i: j for (i0, i1), (j0, j1) in zip(*aln.aligned) for i, j in zip(range(i0, i1), range(j0, j1))} | |
| pairs = {"5uvn-A": "T0918", "5sy1-A": "T0863", "5nv4-A": "T0892", "5uw2-A": "T0866", "5fhy-A": "T0886", "5aot-A": "T0900", | |
| "5j4a-B": "T0869", "5j4a-A": "T0868", "5a7d-L": "T0904", "5j5v-B": "T0862", "5jzr-A": "T0859", "5kkp-A": "T0943", | |
| "5mqp-A": "T0912", "5d9g-A": "T0864", "5lev-A": "T0945", "5j5v-C": "T0870"} | |
| for cid, t in pairs.items(): | |
| pdb, ch = cid.split("-") | |
| st = A.load(f"data/original/casp12_pdb/{pdb}.cif.gz") | |
| seqres, residues = A.chain_info(st, ch) | |
| m = mapping(seqres, seqs[t]) | |
| ca_pdb = {m[r.label_seq - 1]: r.find_atom("CA", "*").pos for r in residues if r.label_seq - 1 in m and r.find_atom("CA", "*")} | |
| cst = gemmi.read_structure(files[t]) | |
| ca_casp = {r.seqid.num - 1: r.find_atom("CA", "*").pos for r in cst[0][0] if r.find_atom("CA", "*")} | |
| common = sorted(set(ca_pdb) & set(ca_casp)) | |
| sup = gemmi.superpose_positions([ca_pdb[k] for k in common], [ca_casp[k] for k in common]) | |
| only_pdb = len(set(ca_pdb) - set(ca_casp)); only_casp = len(set(ca_casp) - set(ca_pdb)) | |
| print(f"{cid:8s} {t}: CA RMSD after superposition {sup.rmsd:6.2f} A over {len(common)} residues | residues only in PDB entry {only_pdb}, only in CASP file {only_casp}") | |