import pytest

from synth_pdb.generator import generate_pdb_content


class TestPTMs:
    """
    TDD Test Suite for Post-Translational Modifications (Phosphorylation).

    Biological Context:
    Phosphorylation replaces the hydroxyl group of Serine (SER), Threonine (THR),
    or Tyrosine (TYR) with a phosphate group (PO4), creating SEP, TPO, PTR.
    This creates a -2 charge and is a key regulatory mechanism.

    Code should:
    1. Accept a rate/probability for phosphorylation.
    2. Convert corresponding residues.
    3. Ensure OpenMM can minimize these non-standard residues.
    """

    def test_phosphorylation_injection(self):
        """Test that SER/THR/TYR are converted to SEP/TPO/PTR."""
        seq = "STY"  # Serine, Threonine, Tyrosine

        # NOTE: API not implemented yet
        try:
            pdb_content = generate_pdb_content(
                sequence_str=seq, phosphorylation_rate=1.0  # 100% conversion
            )
        except TypeError:
            pytest.fail("generate_pdb_content() does not accept 'phosphorylation_rate' kwarg.")

        assert "SEP" in pdb_content, "SER not converted to SEP"
        assert "TPO" in pdb_content, "THR not converted to TPO"
        assert "PTR" in pdb_content, "TYR not converted to PTR"

    def test_minimize_phosphorylated_residues(self):
        """Test that OpenMM physics engine accepts SEP/TPO/PTR."""
        # Use a simple phosphorylated peptide
        # This will fail unless underlying templates are correct
        # Not implementing yet, just stubbing the thought process
        pass

    def test_phosphorylation_rate_zero(self):
        """Test default behavior (no phosphorylation)."""
        seq = "STY"
        pdb_content = generate_pdb_content(sequence_str=seq, phosphorylation_rate=0.0)

        assert "SER" in pdb_content
        assert "THR" in pdb_content
        assert "TYR" in pdb_content
        assert "SEP" not in pdb_content
