import unittest
from andromeda import Peptide, Modification, Pscore

class TestAndromeda(unittest.TestCase):
    def test_calc_ptm_score(self):
        sequence = "PEPTIDE"
        fixed_modifications = []
        variable_modifications = [
            Modification(1, 80, ['E', 'D'], 'anywhere'),
            Modification(2, 42, ['P'], 'anywhere')
        ]
        mod_count = [1, 1]
        spec_masses = [100, 105, 110, 115, 120]
        spec_intensities = [10, 20, 30, 40, 50]
        ms2_tol = 0.1
        ms2_tol_unit = "Da"
        topx = 1
        mz = 500
        charge = 2

        score, best_pep, counts, delta, description, intensities, mass_diffs, mod_prob, mod_score_diffs = Pscore.calc_ptm_score(
            ms2_tol, ms2_tol_unit, topx, sequence, fixed_modifications, variable_modifications, mod_count, spec_masses, spec_intensities, mz, charge
        )

        self.assertIsNotNone(best_pep)
        self.assertGreater(score, 0)
        self.assertEqual(counts, 24)  # Number of possible modifications

if __name__ == "__main__":
    unittest.main()