from pathlib import Path from unittest import TestCase from shelxfile.refine.refine import ShelxlRefine from shelxfile.shelx.cards import RESI, ANIS, ABIN, SADI, DFIX, AFIX, PART from shelxfile.shelx.shelx import Shelxfile class TestCELL(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/p21c.res') def test_volume(self): self.assertEqual(4493.0474, round(self.shx.cell.volume, 4)) class TestRESI(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/p21c.res') def test_get_resi_1_tol(self): r = RESI(None, 'RESI 1 TOL'.split()) self.assertEqual(('TOL', 1, None, None), (r.residue_class, r.residue_number, r.chain_id, r.alias)) def test_tol_1(self): r = RESI(None, 'RESI TOL 1'.split()) self.assertEqual(('TOL', 1, None, None), (r.residue_class, r.residue_number, r.chain_id, r.alias)) def test_resi_chainid_tol(self): r = RESI(None, 'RESI A:100 TOL'.split()) self.assertEqual(('TOL', 100, 'A', None), (r.residue_class, r.residue_number, r.chain_id, r.alias)) def test_resi__negative_chain_tol(self): r = RESI(None, 'RESI -10 TOL'.split()) self.assertEqual(('TOL', -10, None, None), (r.residue_class, r.residue_number, r.chain_id, r.alias)) def test_resi_b_chain_tol(self): r = RESI(None, 'RESI b:-10 TOL'.split()) self.assertEqual(('TOL', -10, 'b', None), (r.residue_class, r.residue_number, r.chain_id, r.alias)) class TestFMAP(TestCase): def test_fmap_number(self): shx = Shelxfile() shx.read_file('tests/resources/p21c.res') self.assertEqual(2.0, shx.fmap.code) class TestACTA(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/p21c.res') self.ref = ShelxlRefine(self.shx, Path('./tests/resources/p21c.res')) def test_acta(self): self.assertEqual('ACTA 45', self.shx._reslist[12].__repr__()) self.assertEqual('ACTA 45', self.shx.acta.__repr__()) def test_remove_acta(self): self.ref.remove_acta_card(self.shx.acta) self.assertEqual('SIZE 0.12 0.23 0.33', self.shx._reslist[12].__repr__()) def test_restore_acta(self): self.ref.remove_acta_card(self.shx.acta) self.ref.restore_acta_card() self.assertEqual(8, self.shx.index_of(self.shx.acta)) self.assertEqual( ['UNIT 1 2 3 4 5 6', 'ACTA 45', 'LIST 4 ! automatically inserted. Change 6 to 4 for CHECKCIF!!'], [str(x) for x in self.shx._reslist[7:10]]) class TestPART(TestCase): def setUp(self) -> None: self.shx = None def test_part_n(self): """Test the result from PART.as_symbol""" self.assertEqual(PART(self.shx, ['PART', '1']).n, 1) self.assertEqual(PART(self.shx, ['PART', '-1']).n, -1) def test_part_resiclass(self): self.assertEqual(21.0, PART(self.shx, ['PART', '9', '21']).sof) self.assertEqual(9, PART(self.shx, ['PART', '9', '21']).n) self.assertEqual(-21.0, PART(self.shx, ['PART', '9', '-21']).sof) def test_part_sof(self): self.assertEqual(11.0, PART(self.shx, ['PART', '-2']).sof) class TestLSCycles(TestCase): def setUp(self) -> None: self.shx = Shelxfile(debug=True) self.shx.read_file('tests/resources/p21c.res') self.ref = ShelxlRefine(self.shx, Path('./resources/p21c.res')) def test_set_refine_cycles(self): self.shx.cycles.set_refine_cycles(44) self.assertEqual('L.S. 44', self.shx._reslist[self.shx.cycles.index].__repr__()) class TestSFACTable(TestCase): def setUp(self) -> None: self.shx = Shelxfile(debug=True) self.shx.read_file('tests/resources/p21c.res') def test_sfac_table(self): self.assertEqual('SFAC C H O F Al Ga', str(self.shx.sfac_table)) def test_unit_table(self): self.assertEqual('UNIT 1 2 3 4 5 6', str(self.shx.unit)) def test_sfac_add_element(self): self.shx.sfac_table.add_element('Au') self.assertEqual('SFAC C H O F Al Ga Au', str(self.shx.sfac_table)) def test_unit_add_element(self): self.shx.sfac_table.add_element('Au') self.assertEqual('UNIT 1 2 3 4 5 6 1', self.shx.unit.__repr__()) def test_unit_add_element_string_repr(self): self.shx.sfac_table.add_element('Au') self.assertEqual('UNIT 1 2 3 4 5 6 1', str(self.shx.unit)) class TestWGHT(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/p21c.res') def test_wght(self): self.assertEqual('WGHT 0.049 0.0', self.shx.wght.__repr__()) def test_wght_differene(self): self.assertEqual([0.0, 0.0], self.shx.wght.difference()) def test_wght_set(self): self.shx.wght.set('WGHT 0.1 99') self.assertEqual('WGHT 0.1 99.0', str(self.shx.wght)) self.assertEqual(0.1, self.shx.wght.a) self.assertEqual(99.0, self.shx.wght.b) class TestANIS(TestCase): def test_anis_n(self): a = ANIS(Shelxfile(), 'ANIS 12'.split()) self.assertEqual([], a.atoms) self.assertEqual(12, a.n) def test_anis_atoms(self): a = ANIS(Shelxfile(), 'ANIS C12 C23 Al3a'.split()) self.assertEqual(['C12', 'C23', 'Al3a'], a.atoms) self.assertEqual(False, hasattr(a, 'n')) class TestABIN(TestCase): def test_abin(self): a = ABIN(Shelxfile(), 'ABIN 1.234 4'.split()) self.assertEqual(1.234, a.n1) self.assertEqual(4, a.n2) class TestSADI(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/I-43d.res') def test_sadi_normal(self): a = SADI(self.shx, 'SADI C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(['C1', 'C2', 'C2', 'C3', 'C3', 'C4'], a.atoms) self.assertEqual('', a.residue_class) self.assertEqual([0], a.residue_number) def test_sadi_normal_with_resinum(self): a = SADI(self.shx, 'SADI_1 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(['C1', 'C2', 'C2', 'C3', 'C3', 'C4'], a.atoms) self.assertEqual('', a.residue_class) self.assertEqual([1], a.residue_number) def test_sadi_normal_with_resinum_on_atoms(self): a = SADI(self.shx, 'SADI C1_1 C2_1 C2_2 C3_2 C3_2 C4_2'.split()) self.assertEqual(['C1_1', 'C2_1', 'C2_2', 'C3_2', 'C3_2', 'C4_2'], a.atoms) self.assertEqual('', a.residue_class) self.assertEqual([0], a.residue_number) def test_sadi_normal_with_name(self): a = SADI(self.shx, 'SADI_CCF3 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(['C1', 'C2', 'C2', 'C3', 'C3', 'C4'], a.atoms) def test_sadi_with_name_2(self): a = SADI(self.shx, 'SADI_CCF3 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual('CCF3', a.residue_class) self.assertEqual([0], a.residue_number) def test_sadi_with_name_3(self): a = SADI(self.shx, 'SADI_CCF3 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(0.02, a.s) def test_sadi_with_name_4(self): a = SADI(self.shx, 'SADI_CCF3 0.001 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(0.001, a.s) class TestwithDEFS(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/p21c.res') def test_sadi_with_s(self): a = SADI(self.shx, 'SADI_CCF3 0.001 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(0.001, a.s) def test_sadi_without_s(self): a = SADI(self.shx, 'SADI C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(0.0234, a.s) def test_DFIX_without_s(self): a = DFIX(self.shx, 'DFIX 1.45 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(1.45, a.d) self.assertEqual(0.0234, a.s) self.assertEqual(0.0234, self.shx.defs.sd) def test_DFIX_with_s(self): a = DFIX(self.shx, 'DFIX 1.45 0.022 C1 C2 C2 C3 C3 C4'.split()) self.assertEqual(1.45, a.d) self.assertEqual(0.022, a.s) class TestPLAN(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/p21c.res') def test_plan__repr__(self): self.assertEqual('PLAN 20', self.shx.plan.__repr__()) def test_set_plan_value(self): self.shx.plan.set('PLAN 23') self.assertEqual('PLAN 23', self.shx.plan.__repr__()) def test_set_plan_all_values(self): self.shx.plan.set('PLAN 23 1.34 1.1') self.assertEqual('PLAN 23 1.34 1.1', self.shx.plan.__repr__()) class TestAFIX(TestCase): def test_afix_n(self): a = AFIX(Shelxfile(), 'AFIX 33'.split()) self.assertEqual(33, a.mn) self.assertEqual(None, a.d) self.assertEqual(10.08, a.U) self.assertEqual(11.0, a.sof) self.assertEqual(True, a.__bool__()) def test_afix_zero(self): a = AFIX(Shelxfile(), 'AFIX 0'.split()) self.assertEqual(0, a.mn) self.assertEqual(False, a.__bool__()) def test_afix_empty(self): a = AFIX(Shelxfile(), 'AFIX'.split()) self.assertEqual(None, a.mn) self.assertEqual(False, a.__bool__())