from unittest import TestCase from shelxfile.misc.misc import frac_to_cart from shelxfile.shelx.shelx import Shelxfile class TestAtoms(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/p21c.res') def test_u_eq_of_hydrogen_atom_in_single_afix(self): h = self.shx.atoms.get_atom_by_name('H34') self.assertEqual('C34', h.pivot.name) self.assertEqual(0.02959929, round(h.Uiso, 8)) self.assertEqual(h.pivot.Uiso * 1.2, h.Uiso) def test_u_eq_of_hydrogen_atom_in_afix_137(self): h1 = self.shx.atoms.get_atom_by_name('H36A') h2 = self.shx.atoms.get_atom_by_name('H36B') h3 = self.shx.atoms.get_atom_by_name('H36C') self.assertEqual('C36', h1.pivot.name) self.assertEqual('C36', h2.pivot.name) self.assertEqual('C36', h2.pivot.name) self.assertEqual(0.05123489, round(h1.Uiso, 8)) self.assertEqual(0.05123489, round(h2.Uiso, 8)) self.assertEqual(0.05123489, round(h3.Uiso, 8)) def test_uiso_of_pivot_of_H36x(self): c36 = self.shx.atoms.get_atom_by_name('C36') self.assertEqual(None, c36.pivot) self.assertEqual(0.03415659, round(c36.Uiso, 8)) self.assertEqual(0.03415659 * 1.5, 0.051234885) def test_number(self): self.assertEqual(148, self.shx.atoms.number) def test_has_atom_al1(self): self.assertEqual(True, self.shx.atoms.has_atom('Al1')) def test_has_atom_al1_0(self): self.assertEqual(True, self.shx.atoms.has_atom('Al1_0')) def test_has_atom_al2_0(self): self.assertEqual(False, self.shx.atoms.has_atom('Al2_0')) def test_get_atom_by_name(self): self.assertEqual("Atom ID: 73", self.shx.atoms.get_atom_by_name('Al1').__repr__()) def test_get_all_atomcoordinates(self): coordinate = {'O1_4': (0.074835, 0.238436, 0.402457), 'C1_4': (0.028576, 0.234542, 0.337234)} self.assertEqual(coordinate['O1_4'], self.shx.atoms.get_all_atomcoordinates()['O1_4']) self.assertEqual(coordinate['C1_4'], self.shx.atoms.get_all_atomcoordinates()['C1_4']) def test_residues(self): self.assertEqual([0, 1, 2, 3, 4], self.shx.atoms.residues) def test_q_peaks(self): self.assertEqual(['Atom ID: 328', 'Atom ID: 329', 'Atom ID: 330', 'Atom ID: 331', 'Atom ID: 332'], [x.__repr__() for x in self.shx.atoms.q_peaks[:5]]) def test_distance(self): self.assertEqual(2.154399, round(self.shx.atoms.distance('F1_2', 'F2_2'), 6)) def test_distance2(self): self.assertEqual(1.332854, round(self.shx.atoms.distance('C2_2', 'F1_2'), 6)) def test_angle(self): at1 = self.shx.atoms.get_atom_by_name('O1_4') at2 = self.shx.atoms.get_atom_by_name('C1_4') at3 = self.shx.atoms.get_atom_by_name('C2_4') # The angle between the three atoms is ... degree: self.assertEqual(109.688123, round(self.shx.atoms.angle(at1, at2, at3), 6)) def test_torsion_angle(self): at1 = self.shx.atoms.get_atom_by_name('O1') at2 = self.shx.atoms.get_atom_by_name('C1') at3 = self.shx.atoms.get_atom_by_name('C2') at4 = self.shx.atoms.get_atom_by_name('F1') # The torsion angle between the four atoms is ... degree: self.assertEqual(74.095731, round(self.shx.atoms.torsion_angle(at1, at2, at3, at4), 6)) # Thisis the other way round: at4 = self.shx.atoms.get_atom_by_name('F2') self.assertEqual(-44.467358, round(self.shx.atoms.torsion_angle(at1, at2, at3, at4), 6)) def test_atoms_in_class(self): atoms = ['O1', 'C1', 'C2', 'F1', 'F2', 'F3', 'C3', 'F4', 'F5', 'F6', 'C4', 'F7', 'F8', 'F9'] self.assertEqual(atoms, self.shx.atoms.atoms_in_class('CCF3')) def test_sfac_num(self): at = self.shx.atoms.get_atom_by_name('C1_4') self.assertEqual(1, at.sfac_num) def test_element_c(self): at = self.shx.atoms.get_atom_by_name('C1_4') self.assertEqual('C', at.element) def test_element_o(self): at = self.shx.atoms.get_atom_by_name('C1_4') at.element = 'O' self.assertEqual('O', at.element) self.assertEqual(3, at.sfac_num) def test_an(self): at = self.shx.atoms.get_atom_by_name('C1_4') self.assertEqual(6, at.an) def test_delete_show(self): # We have an atom with ID = 40 at = self.shx.atoms.get_atom_by_id(40) self.assertEqual('Atom ID: 40', at.__repr__()) def test_delete_show_list(self): # Before and after atom 40 are 38 and 42 self.assertEqual(['Atom ID: 38', 'Atom ID: 40', 'Atom ID: 42'], [x.__repr__() for x in self.shx.atoms.all_atoms[:3]]) def test_c1_4(self): # The name of atom 40 is C1_4 self.assertEqual('C1_4', self.shx.atoms.get_atom_by_id(40).fullname) def test_delete_atom40(self): # get atom 40 at = self.shx.atoms.get_atom_by_id(40) # Now delete atom 40 at.delete() # The resulting atoms list does not contain atom 40 new_atoms = ['Atom ID: 38', 'Atom ID: 41', 'Atom ID: 43'] self.assertEqual(new_atoms, [x.__repr__() for x in self.shx.atoms.all_atoms[:3]]) def test_delete2(self): self.shx.atoms.get_atom_by_id(40).delete() self.assertEqual(None, self.shx.atoms.get_atom_by_id(40)) def test_delete3(self): self.shx.atoms.get_atom_by_id(40).delete() self.assertEqual(None, self.shx.atoms.get_atom_by_name('C1_4')) def test_equal(self): self.assertEqual(True, self.shx.atoms.get_atom_by_id(40) == self.shx.atoms.get_atom_by_name('C1_4')) def test_find_atoms_around(self): at = self.shx.atoms.get_atom_by_name('C1_4') found = [x.__repr__() for x in at.find_atoms_around(dist=2, only_part=2)] shouldfind = ['Atom ID: 38', 'Atom ID: 42', 'Atom ID: 50', 'Atom ID: 58'] self.assertEqual(shouldfind, found) def test_get_coordinates(self): c = self.shx.atoms.get_atom_by_name('C1_4').cart_coords self.assertEqual([-0.19777464582151, 4.902748697, 6.89776640065678], [round(x, 14) for x in c]) def test_to_isotropic(self): # We have regular u values of atom 40 self.assertEqual([0.02311, 0.03617, 0.01096, -0.01, 0.00201, 0.00356], self.shx.atoms.get_atom_by_id(40).uvals) # We make them isotropic self.shx.atoms.get_atom_by_id(40).to_isotropic() # And the result is only one atomic u value: self.assertEqual([0.04, 0.0, 0.0, 0.0, 0.0, 0.0], self.shx.atoms.get_atom_by_id(40).uvals) def test_cart_coords(self): self.assertEqual([-0.19777464582151, 4.902748697, 6.89776640065678], [round(x, 14) for x in self.shx.atoms.get_atom_by_id(40).cart_coords]) def test_cartesian_from_method(self): self.assertEqual( [round(x, 13) for x in frac_to_cart(self.shx.atoms.get_atom_by_id(40).frac_coords, list(self.shx.cell))], [round(x, 13) for x in self.shx.atoms.get_atom_by_id(40).cart_coords]) def test_frac_coords(self): self.assertEqual((0.028576, 0.234542, 0.337234), self.shx.atoms.get_atom_by_id(40).frac_coords) def test_frac_x(self): self.assertEqual(0.028576, self.shx.atoms.get_atom_by_id(40).x) def test_cart_x(self): self.assertEqual(-0.1977746458, round(self.shx.atoms.get_atom_by_id(40).xc, 10)) def test_radius(self): self.assertEqual(0.77, self.shx.atoms.get_atom_by_id(40).radius) def test_resinum(self): self.assertEqual(4, self.shx.atoms.get_atom_by_id(40).resinum) def test_resiclass(self): self.assertEqual('CCF3', self.shx.atoms.get_atom_by_id(40).resiclass) def test_fullname(self): self.assertEqual('C1_4', self.shx.atoms.get_atom_by_id(40).fullname) def test_part(self): self.assertEqual('PART 2 -31', self.shx.atoms.get_atom_by_id(40).part.__repr__()) def test_part_number(self): self.assertEqual(2, self.shx.atoms.get_atom_by_id(40).part.n) def test_part_occupancy(self): self.assertEqual(0.44236, self.shx.atoms.get_atom_by_id(40).occupancy) def test_part_sof(self): self.assertEqual(-31.0, self.shx.atoms.get_atom_by_id(40).part.sof) def test_get_pivot_atom(self): self.assertEqual('C34', self.shx.atoms.all_atoms[45].pivot.name) def test_get_pivot_atom_of_fluorine(self): # This atom should not have a pivot atom, because it is heavy and not in an AFIX: self.assertEqual('F2', self.shx.atoms.all_atoms[4].name) self.assertEqual(None, self.shx.atoms.all_atoms[4].pivot) def test_hydrogen_atoms(self): self.assertEqual('[Atom ID: 134, Atom ID: 141, Atom ID: 148]', str(self.shx.atoms.hydrogen_atoms[:3])) def test_riding_atoms(self): self.assertEqual('[Atom ID: 134, Atom ID: 141, Atom ID: 148]', str(self.shx.atoms.riding_atoms[:3])) class TestRidingAtoms(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/sad-final.res') def test_hydrogen_atoms(self): # Returns the list of hydrogen atoms, regardless of their model self.assertEqual('[Atom ID: 71, Atom ID: 75, Atom ID: 76]', str(self.shx.atoms.hydrogen_atoms[3:6])) def test_riding_atoms(self): # Returns only riding atoms, therefore different IDs than above self.assertEqual('[Atom ID: 75, Atom ID: 76, Atom ID: 77]', str(self.shx.atoms.riding_atoms[3:6])) def test_number_of_anisotropic_atoms(self): self.assertEqual(79, self.shx.atoms.n_anisotropic_atoms) def test_number_of_isotropic_atoms(self): self.assertEqual(49, self.shx.atoms.n_isotropic_atoms) def test_number_of_hydrogen_atoms(self): self.assertEqual(49, self.shx.atoms.n_hydrogen_atoms) def test_number_of_anisotropic_hydrogen_atoms(self): self.assertEqual(0, self.shx.atoms.n_anisotropic_hydrogen_atoms) def test_number_of_hydrogen_adtoms_with_constrained_u_values(self): self.assertEqual(49, self.shx.atoms.n_hydrogen_atoms_with_constr_u_val) class TestUisoOfFreeRefine(TestCase): def setUp(self) -> None: self.shx = Shelxfile() self.shx.read_file('tests/resources/2240189.res') def test_free_refined_hydrogen(self): h1a = self.shx.atoms.get_atom_by_name('H1A') self.assertEqual(0.04654, h1a.Uiso) self.assertEqual([0.04654, 0.0, 0.0, 0.0, 0.0, 0.0], h1a.uvals) self.assertEqual("O3'", h1a.pivot.name)