File size: 2,370 Bytes
23a728e | 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 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | # Copyright 2026 Emile de Bruyn
# SPDX-License-Identifier: Apache-2.0
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"}
|