# 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"}