| |
| |
|
|
| from pathlib import Path |
|
|
| from Bio.PDB import PDBParser |
|
|
| from motifbench_prosite.normalisation import normalise_motif_pdb |
|
|
|
|
| def _write_tiny_pdb(path: Path, chain_id: str = "L", n_res: int = 5, resnum_start: int = 24, append: bool = False): |
| """Write a minimal PDB with n_res GLY residues for the given chain.""" |
| lines = [] |
| atom_serial = 1 |
| for i in range(n_res): |
| resnum = resnum_start + i |
| lines.append( |
| f"ATOM {atom_serial:5d} CA GLY {chain_id}{resnum:4d} " |
| f"{1.0 + i:8.3f}{0.0:8.3f}{0.0:8.3f} 1.00 20.00 C" |
| ) |
| atom_serial += 1 |
|
|
| new_block = "\n".join(lines) |
|
|
| if append and path.exists(): |
| existing = path.read_text() |
| existing = existing.rstrip() |
| if existing.endswith("END"): |
| existing = existing[: -len("END")].rstrip() |
| combined = existing + ("\n" if existing else "") + new_block + "\nEND\n" |
| path.write_text(combined) |
| else: |
| path.write_text(new_block + "\nEND\n") |
|
|
|
|
| def test_normalise_motif_pdb_simple(tmp_pdb_dir: Path): |
| pdb_path = tmp_pdb_dir / "test.pdb" |
| _write_tiny_pdb(pdb_path, chain_id="L", n_res=3) |
|
|
| segment_map, residue_map, chain_map_str = normalise_motif_pdb(pdb_path, "L24-26") |
|
|
| assert segment_map == {"L24-26": "A1-3"} |
| assert residue_map[("L", 24)] == ("A", 1) |
| assert residue_map[("L", 26)] == ("A", 3) |
|
|
| parser = PDBParser(QUIET=True) |
| structure = parser.get_structure("test", pdb_path.as_posix()) |
| model = next(structure.get_models()) |
| chain = model["A"] |
| res_ids = [res.id[1] for res in chain.get_residues()] |
| assert res_ids == [1, 2, 3] |
|
|
| text = pdb_path.read_text() |
| assert "NORMALISED MOTIFBENCH PDB" in text |
| assert "L24-26 -> A1-3" in text |
| assert "REMARK" in text |
|
|
|
|
| def test_normalise_motif_pdb_two_segments_two_chains(tmp_pdb_dir: Path): |
| pdb_path = tmp_pdb_dir / "test2.pdb" |
| _write_tiny_pdb(pdb_path, chain_id="L", n_res=3) |
| _write_tiny_pdb(pdb_path, chain_id="H", n_res=2, resnum_start=10, append=True) |
|
|
| seg_map, residue_map, chain_map_str = normalise_motif_pdb(pdb_path, "L24-26;H10-11") |
|
|
| assert seg_map["L24-26"].startswith("A") |
| assert seg_map["H10-11"].startswith("B") |
| assert set(ch for (ch, _) in residue_map.values()) == {"A", "B"} |
|
|
