import biotite.structure as struc
import numpy as np
import pytest

# Try to import the module (will fail initially)
try:
    from synth_pdb import evolution
except ImportError:
    evolution = None


def create_mock_structure():
    """Creates a simple structure (Alpha Helix like)"""
    # We create a dummy atom array with coords.
    # 3 residues: ALA, ALA, ALA
    # For SASA, we need coords.
    # Let's just mock the atom array object structure
    atoms = struc.AtomArray(3)
    atoms.res_name = np.array(["ALA", "LEU", "GLY"])
    atoms.res_id = np.array([1, 2, 3])
    atoms.element = np.array(["C", "C", "C"])
    # Coords: 1 and 3 close, 2 far?
    # Actually, calculating SASA requires valid geometry.
    # We will mock the `calculate_sasa` function result in one test,
    # and test the `generate_msa` logic assuming SASA is known.
    return atoms


class TestMSAGenerator:

    def test_module_exists(self):
        if evolution is None:
            pytest.fail("synth_pdb.evolution module not found")

    def test_sasa_identification(self, mocker):
        """Test detection of buried vs exposed residues."""
        if evolution is None:
            pytest.skip("Module not implemented")

        atoms = create_mock_structure()

        # Mock biotite's SASA calc to return specific areas
        # Res 1: Exposed (High area), Res 2: Buried (Low area), Res 3: Exposed
        # sasa returns area per atom. We sum per residue.
        # Let's mock the module function `evolution.calculate_relative_sasa` directly
        # if we decouple it.

        # NOTE: Real SASA calculation is complex. We will implement a wrapper.
        # Test the wrapper logic if possible, or mock the biotite call.

        # Test Real Wrapper Logic using Mocked Biotite
        # We need an atom array
        atoms = create_mock_structure()

        # Mock biotite.structure.sasa
        # It takes atom array and radius, returns array of floats
        # 3 residues, 1 atom each in mock
        mock_areas = np.array([100.0, 10.0, 100.0])  # Res 1, 2, 3
        mocker.patch("biotite.structure.sasa", return_value=mock_areas)

        # Mock apply_residue_wise to just return the areas (since 1 atom per res)
        # Or let the real function run if it works on mocked array.
        # Real function: struc.apply_residue_wise(atom_array, sasa, np.sum)
        # If our atoms have res_id defined, this should work?
        # But biotite apply_residue_wise is complex. Let's mock it for simplicity/robustness.
        mocker.patch("biotite.structure.apply_residue_wise", return_value=mock_areas)

        # Mock get_residue_starts for normalization part
        mocker.patch("biotite.structure.get_residue_starts", return_value=[0, 1, 2])

        # Run function
        rel_sasa = evolution.calculate_relative_sasa(atoms)

        # Check normalization
        # Res 0 (ALA) -> 100 area. Max ALA ~ 121. Rel ~ 0.82
        # Res 1 (LEU) -> 10 area. Max LEU ~ 191. Rel ~ 0.05

        assert len(rel_sasa) == 3
        assert rel_sasa[0] > 0.5  # Exposed
        assert rel_sasa[1] < 0.2  # Buried

    def test_msa_generation_conservation(self, mocker):
        """Verify Core residues mutate less or conservatively."""
        if evolution is None:
            pytest.skip("Module not implemented")

        atoms = create_mock_structure()

        # Mock SASA: Middle residue (L) is BURIED (0% relative SASA)
        # 1 and 3 are EXPOSED (100%)
        # Relative SASA array for 3 residues
        mock_rel_sasa = np.array([1.0, 0.0, 1.0])

        mocker.patch("synth_pdb.evolution.calculate_relative_sasa", return_value=mock_rel_sasa)

        # Generate raw sequences
        msa_seqs = evolution.generate_msa_sequences(atoms, n_seqs=100, mutation_rate=0.5)

        # Analysis
        # Pos 0 (A -> Exposed) should vary
        # Pos 1 (L -> Buried) should be L or conserved hydrophobic (V, I, F)
        # Pos 2 (G -> Exposed) should vary

        # Check Pos 1 conservation
        pos1_variants = [s[1] for s in msa_seqs]
        # Should be mostly L, or at least Hydrophobic.
        # If our logic is strictly "Buried = Hydrophobic Conservation",
        # we check if it ever mutates to a charge (e.g. K, D).

        set("VILMFWA")
        charged = set("DEKR")

        # Count non-hydrophobic mutations in core
        # Note: If L mutates to K, that's a violation of our "Core" logic usually.
        violations = sum(1 for aa in pos1_variants if aa in charged)
        assert violations < 5, "Buried Core residue mutated to charged residue too often!"

        # Check Pos 0 variation
        pos0_variants = {s[0] for s in msa_seqs}
        assert len(pos0_variants) > 1, "Exposed residue did not mutate at all with high rate"

    def test_write_msa(self, tmp_path):
        """Test FASTA export."""
        if evolution is None:
            pytest.skip("Module not implemented")

        sequences = ["AAA", "AAB", "AAC"]
        outfile = tmp_path / "test.fasta"

        evolution.write_msa(sequences, str(outfile))

        content = outfile.read_text()
        assert ">seq_0" in content
        assert "AAA" in content
